Starting phenix.real_space_refine on Mon Oct 14 01:59:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/10_2024/8rkv_19284.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/10_2024/8rkv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/10_2024/8rkv_19284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/10_2024/8rkv_19284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/10_2024/8rkv_19284.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/10_2024/8rkv_19284.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/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: 9.86, per 1000 atoms: 0.60 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: 4.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 6.98 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: 7.37 Time building geometry restraints manager: 4.76 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 542 or resid 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.350 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.430 ------------------------------------------------------------------------------- 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= 0.373 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (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 TRP 0.027 0.003 TRP R 86 HIS 0.011 0.002 HIS S 258 PHE 0.029 0.003 PHE R 284 TYR 0.030 0.005 TYR R 233 ARG 0.035 0.004 ARG S 355 *********************** 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 fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 1.679 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 31 LYS cc_start: 0.6230 (tptt) cc_final: 0.5849 (mmtt) REVERT: R 112 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7751 (mt-10) REVERT: R 124 LYS cc_start: 0.6940 (pptt) cc_final: 0.6330 (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: 0.7188 (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: 0.5532 (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: 0.7611 (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: 0.6386 (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: 0.5158 (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: 0.6576 (m) outliers start: 27 outliers final: 7 residues processed: 303 average time/residue: 0.4367 time to fit residues: 181.9601 Evaluate side-chains 211 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 145 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 475 GLN R 531 GLN S 272 HIS S 295 ASN S 344 GLN S 363 GLN S 445 ASN T 206 HIS 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17128 Z= 0.248 Angle : 0.714 9.731 23906 Z= 0.393 Chirality : 0.043 0.201 2660 Planarity : 0.005 0.054 2487 Dihedral : 25.529 177.014 3777 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.51 % Allowed : 12.19 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1576 helix: -0.56 (0.20), residues: 594 sheet: -0.76 (0.33), residues: 214 loop : 0.03 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 86 HIS 0.008 0.001 HIS T 272 PHE 0.018 0.002 PHE S 306 TYR 0.025 0.002 TYR T 285 ARG 0.009 0.001 ARG R 322 *********************** 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 263 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7688 (mt-10) REVERT: R 172 SER cc_start: 0.6945 (t) cc_final: 0.6483 (p) REVERT: R 345 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7325 (mm-30) REVERT: R 411 MET cc_start: 0.7566 (mtp) cc_final: 0.7337 (mtp) REVERT: R 451 ARG cc_start: 0.8399 (mtm180) cc_final: 0.7956 (mtm-85) REVERT: R 478 GLU cc_start: 0.7472 (pm20) cc_final: 0.6633 (pt0) REVERT: R 491 SER cc_start: 0.8321 (m) cc_final: 0.7925 (t) REVERT: S 104 LYS cc_start: 0.7112 (mmtp) cc_final: 0.6740 (mmtt) REVERT: S 168 GLN cc_start: 0.8749 (tt0) cc_final: 0.8547 (pt0) REVERT: S 295 ASN cc_start: 0.8078 (m-40) cc_final: 0.7845 (m-40) REVERT: S 349 ASP cc_start: 0.6679 (m-30) cc_final: 0.6281 (t0) REVERT: S 503 ASN cc_start: 0.7239 (p0) cc_final: 0.6952 (p0) REVERT: T 261 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6693 (mm) REVERT: T 327 LEU cc_start: 0.5681 (mm) cc_final: 0.5200 (mm) REVERT: T 373 TYR cc_start: 0.5188 (OUTLIER) cc_final: 0.4193 (t80) REVERT: T 430 MET cc_start: 0.7470 (tpp) cc_final: 0.7168 (mmt) REVERT: U 245 ASP cc_start: 0.6735 (t0) cc_final: 0.6364 (t0) REVERT: U 309 HIS cc_start: 0.7006 (m-70) cc_final: 0.6742 (m-70) REVERT: U 473 HIS cc_start: 0.6097 (OUTLIER) cc_final: 0.5557 (m90) outliers start: 35 outliers final: 18 residues processed: 245 average time/residue: 0.4502 time to fit residues: 155.0388 Evaluate side-chains 208 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 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 272 HIS 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 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 86 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 344 GLN T 363 GLN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17128 Z= 0.240 Angle : 0.667 9.135 23906 Z= 0.365 Chirality : 0.042 0.260 2660 Planarity : 0.005 0.060 2487 Dihedral : 25.451 179.216 3759 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.94 % Allowed : 14.27 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1576 helix: -0.05 (0.21), residues: 592 sheet: -0.70 (0.33), residues: 222 loop : 0.06 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 86 HIS 0.014 0.001 HIS T 272 PHE 0.020 0.002 PHE S 306 TYR 0.021 0.002 TYR R 233 ARG 0.006 0.001 ARG R 235 *********************** 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 fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7711 (mt-10) REVERT: R 313 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6240 (mtm110) REVERT: R 345 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7299 (mm-30) REVERT: R 411 MET cc_start: 0.7518 (mtp) cc_final: 0.7317 (mtp) REVERT: R 451 ARG cc_start: 0.8476 (mtm180) cc_final: 0.8087 (mtm-85) REVERT: R 475 GLN cc_start: 0.7214 (mm110) cc_final: 0.6854 (mp10) REVERT: R 491 SER cc_start: 0.8319 (m) cc_final: 0.7951 (t) REVERT: S 104 LYS cc_start: 0.7155 (mmtp) cc_final: 0.6789 (mmtt) REVERT: S 295 ASN cc_start: 0.8106 (m-40) cc_final: 0.7890 (m-40) REVERT: S 349 ASP cc_start: 0.6818 (m-30) cc_final: 0.6274 (t0) REVERT: S 375 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: S 430 MET cc_start: 0.8047 (mpp) cc_final: 0.7286 (mpp) REVERT: S 471 ARG cc_start: 0.7407 (ppp80) cc_final: 0.7090 (tmm-80) REVERT: T 225 TRP cc_start: 0.6864 (m-90) cc_final: 0.6005 (m-10) REVERT: T 261 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6614 (mm) REVERT: T 327 LEU cc_start: 0.5620 (mm) cc_final: 0.5161 (mm) REVERT: T 373 TYR cc_start: 0.5259 (OUTLIER) cc_final: 0.4412 (t80) REVERT: U 241 ASN cc_start: 0.5493 (OUTLIER) cc_final: 0.5250 (m110) REVERT: U 245 ASP cc_start: 0.6661 (t0) cc_final: 0.6212 (t0) REVERT: U 372 ARG cc_start: 0.5757 (ttp80) cc_final: 0.4740 (ttp80) REVERT: U 473 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.5622 (m90) outliers start: 41 outliers final: 25 residues processed: 230 average time/residue: 0.4294 time to fit residues: 136.6191 Evaluate side-chains 218 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 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 277 THR 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 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 459 TYR Chi-restraints excluded: chain U residue 241 ASN 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 154 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 344 GLN ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 272 HIS ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 17128 Z= 0.421 Angle : 0.790 10.139 23906 Z= 0.426 Chirality : 0.047 0.226 2660 Planarity : 0.006 0.060 2487 Dihedral : 25.689 178.454 3759 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.59 % Allowed : 14.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1576 helix: -0.48 (0.20), residues: 590 sheet: -0.75 (0.33), residues: 220 loop : -0.31 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP S 86 HIS 0.010 0.001 HIS T 272 PHE 0.028 0.003 PHE S 306 TYR 0.035 0.003 TYR R 233 ARG 0.009 0.001 ARG U 223 *********************** 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 262 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 198 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7624 (mt-10) REVERT: R 124 LYS cc_start: 0.7134 (pptt) cc_final: 0.6765 (pptt) REVERT: R 171 LYS cc_start: 0.8491 (mptt) cc_final: 0.7857 (mmpt) REVERT: R 345 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7367 (mm-30) REVERT: R 431 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.5766 (m-80) REVERT: R 451 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8124 (mtm-85) REVERT: R 475 GLN cc_start: 0.7254 (mm110) cc_final: 0.6673 (mp10) REVERT: R 478 GLU cc_start: 0.7551 (pm20) cc_final: 0.6774 (pt0) REVERT: R 480 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6466 (pm20) REVERT: S 104 LYS cc_start: 0.7120 (mmtp) cc_final: 0.6813 (mmtt) REVERT: S 295 ASN cc_start: 0.8100 (m-40) cc_final: 0.7671 (m110) REVERT: S 349 ASP cc_start: 0.6900 (m-30) cc_final: 0.6302 (t0) REVERT: S 375 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8228 (mm-40) REVERT: T 225 TRP cc_start: 0.7109 (m-90) cc_final: 0.6102 (m-10) REVERT: T 235 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7314 (mmm-85) REVERT: T 261 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6501 (mm) REVERT: T 373 TYR cc_start: 0.5377 (OUTLIER) cc_final: 0.4633 (t80) REVERT: T 488 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6250 (mm-30) REVERT: U 225 TRP cc_start: 0.6726 (m100) cc_final: 0.6397 (m100) REVERT: U 245 ASP cc_start: 0.6868 (t0) cc_final: 0.6310 (t0) REVERT: U 300 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8282 (mp) REVERT: U 415 ARG cc_start: 0.6457 (mpp-170) cc_final: 0.6032 (mtm-85) REVERT: U 473 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.5795 (m90) outliers start: 64 outliers final: 40 residues processed: 242 average time/residue: 0.4191 time to fit residues: 139.8092 Evaluate side-chains 227 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 310 LEU Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 431 TYR Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 445 ASN Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain R residue 508 GLN 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 291 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 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 261 LEU Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 298 SER Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 384 GLN Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain T residue 488 GLU Chi-restraints excluded: chain 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 496 THR Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN T 272 HIS ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 465 GLN U 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3200 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= 0.220 Angle : 0.653 9.405 23906 Z= 0.355 Chirality : 0.040 0.204 2660 Planarity : 0.005 0.069 2487 Dihedral : 25.489 178.085 3759 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.09 % Allowed : 16.85 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1576 helix: 0.08 (0.21), residues: 594 sheet: -0.64 (0.34), residues: 202 loop : -0.25 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 275 HIS 0.014 0.001 HIS T 272 PHE 0.019 0.002 PHE S 306 TYR 0.019 0.002 TYR R 233 ARG 0.007 0.000 ARG R 235 *********************** 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 fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 1.648 Fit side-chains REVERT: R 112 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7739 (mt-10) REVERT: R 137 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7829 (tpp80) REVERT: R 165 GLU cc_start: 0.8650 (tp30) cc_final: 0.8188 (mm-30) REVERT: R 313 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6510 (mtm110) REVERT: R 316 GLU cc_start: 0.7706 (mp0) cc_final: 0.7435 (mp0) REVERT: R 345 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7304 (mm-30) REVERT: R 381 MET cc_start: 0.8556 (mmm) cc_final: 0.8281 (mmm) REVERT: R 451 ARG cc_start: 0.8589 (mtm180) cc_final: 0.8167 (mtm-85) REVERT: R 475 GLN cc_start: 0.7224 (mm110) cc_final: 0.6938 (mp10) REVERT: S 104 LYS cc_start: 0.7184 (mmtp) cc_final: 0.6838 (mmtt) REVERT: S 157 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7159 (mt) REVERT: S 295 ASN cc_start: 0.8091 (m-40) cc_final: 0.7698 (m-40) REVERT: S 349 ASP cc_start: 0.6820 (m-30) cc_final: 0.6280 (t0) REVERT: S 360 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5307 (mt-10) REVERT: S 428 ASN cc_start: 0.6628 (OUTLIER) cc_final: 0.5989 (t160) REVERT: S 471 ARG cc_start: 0.7344 (ppp80) cc_final: 0.7034 (tmm-80) REVERT: T 199 ASN cc_start: 0.4496 (OUTLIER) cc_final: 0.4283 (t0) REVERT: T 225 TRP cc_start: 0.6952 (m-90) cc_final: 0.6023 (m-10) REVERT: T 235 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7193 (mmm-85) REVERT: T 261 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6524 (mm) REVERT: T 373 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.4969 (t80) REVERT: U 245 ASP cc_start: 0.6794 (t0) cc_final: 0.6182 (t0) REVERT: U 300 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8071 (mt) REVERT: U 404 ARG cc_start: 0.5148 (OUTLIER) cc_final: 0.3867 (mmp-170) REVERT: U 473 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.5602 (m90) outliers start: 57 outliers final: 30 residues processed: 232 average time/residue: 0.4057 time to fit residues: 131.6348 Evaluate side-chains 221 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 234 SER Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 360 GLU 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 428 ASN 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 220 ILE Chi-restraints excluded: chain T residue 261 LEU 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 55 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS R 295 ASN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 363 GLN ** T 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 445 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17128 Z= 0.231 Angle : 0.661 10.378 23906 Z= 0.356 Chirality : 0.041 0.244 2660 Planarity : 0.005 0.060 2487 Dihedral : 25.430 177.220 3757 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.01 % Allowed : 17.92 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1576 helix: 0.17 (0.21), residues: 600 sheet: -0.56 (0.35), residues: 199 loop : -0.27 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 225 HIS 0.009 0.001 HIS T 272 PHE 0.018 0.002 PHE S 306 TYR 0.020 0.001 TYR R 233 ARG 0.007 0.000 ARG R 447 *********************** 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 fitting. rotamer outliers: 56 poor density : 193 time to evaluate : 1.852 Fit side-chains REVERT: R 112 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7826 (mt-10) REVERT: R 137 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7837 (tpp80) REVERT: R 165 GLU cc_start: 0.8602 (tp30) cc_final: 0.8139 (mm-30) REVERT: R 282 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: R 313 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6489 (mtm110) REVERT: R 316 GLU cc_start: 0.7717 (mp0) cc_final: 0.7405 (mp0) REVERT: R 381 MET cc_start: 0.8557 (mmm) cc_final: 0.8349 (mmm) REVERT: R 451 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8182 (mtm-85) REVERT: R 475 GLN cc_start: 0.7207 (mm110) cc_final: 0.6924 (mp10) REVERT: R 480 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6625 (pm20) REVERT: S 104 LYS cc_start: 0.7156 (mmtp) cc_final: 0.6816 (mmtt) REVERT: S 157 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7210 (mt) REVERT: S 349 ASP cc_start: 0.6924 (m-30) cc_final: 0.6415 (t0) REVERT: S 360 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5387 (mt-10) REVERT: S 471 ARG cc_start: 0.7357 (ppp80) cc_final: 0.7076 (tmm-80) REVERT: T 235 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.7208 (mmm-85) REVERT: T 261 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6520 (mm) REVERT: T 275 TRP cc_start: 0.5896 (OUTLIER) cc_final: 0.5164 (t60) REVERT: T 373 TYR cc_start: 0.5553 (OUTLIER) cc_final: 0.5037 (t80) REVERT: T 461 GLN cc_start: 0.7587 (tp40) cc_final: 0.7252 (tp-100) REVERT: U 233 TYR cc_start: 0.6251 (t80) cc_final: 0.6014 (t80) REVERT: U 245 ASP cc_start: 0.6818 (t0) cc_final: 0.6418 (t70) REVERT: U 300 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (mp) REVERT: U 404 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.3965 (mmp-170) REVERT: U 415 ARG cc_start: 0.6360 (mpp-170) cc_final: 0.6049 (mtm-85) REVERT: U 473 HIS cc_start: 0.6189 (OUTLIER) cc_final: 0.5637 (m90) outliers start: 56 outliers final: 34 residues processed: 232 average time/residue: 0.4169 time to fit residues: 134.5028 Evaluate side-chains 229 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 282 GLU Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 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 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 234 SER Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 360 GLU 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 240 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 298 SER Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2988 > 50: distance: 138 - 142: 10.301 distance: 142 - 143: 8.553 distance: 142 - 148: 7.764 distance: 143 - 144: 8.895 distance: 143 - 146: 10.287 distance: 144 - 145: 14.961 distance: 144 - 149: 7.488 distance: 146 - 147: 10.865 distance: 147 - 148: 15.146 distance: 149 - 150: 5.976 distance: 149 - 155: 6.039 distance: 150 - 151: 5.012 distance: 150 - 153: 7.095 distance: 151 - 152: 12.500 distance: 151 - 156: 16.882 distance: 153 - 154: 14.709 distance: 154 - 155: 13.111 distance: 157 - 158: 3.252 distance: 158 - 159: 6.480 distance: 158 - 164: 5.201 distance: 159 - 192: 10.159 distance: 160 - 161: 13.430 distance: 161 - 162: 11.247 distance: 161 - 163: 15.672 distance: 164 - 165: 4.419 distance: 165 - 166: 4.387 distance: 165 - 168: 8.554 distance: 166 - 167: 9.976 distance: 166 - 176: 6.731 distance: 167 - 199: 11.341 distance: 168 - 169: 5.607 distance: 169 - 170: 4.420 distance: 169 - 171: 5.178 distance: 170 - 172: 5.965 distance: 171 - 173: 6.642 distance: 172 - 174: 7.907 distance: 173 - 174: 6.899 distance: 174 - 175: 8.210 distance: 176 - 177: 3.663 distance: 177 - 180: 5.973 distance: 178 - 179: 7.291 distance: 178 - 185: 5.148 distance: 179 - 207: 6.516 distance: 180 - 181: 7.858 distance: 181 - 182: 9.255 distance: 182 - 183: 7.134 distance: 183 - 184: 8.241 distance: 185 - 186: 7.209 distance: 186 - 189: 6.735 distance: 187 - 188: 17.076 distance: 187 - 192: 4.912 distance: 188 - 218: 13.623 distance: 189 - 190: 10.650 distance: 189 - 191: 12.748 distance: 193 - 196: 6.971 distance: 194 - 195: 5.291 distance: 194 - 199: 9.429 distance: 195 - 225: 10.442 distance: 196 - 197: 7.873 distance: 196 - 198: 4.943 distance: 199 - 200: 5.150 distance: 200 - 203: 6.981 distance: 201 - 202: 4.516 distance: 201 - 207: 3.530 distance: 202 - 233: 6.734 distance: 203 - 204: 5.460 distance: 204 - 205: 7.833 distance: 204 - 206: 8.971 distance: 208 - 209: 11.961 distance: 208 - 211: 10.292 distance: 209 - 210: 30.965 distance: 209 - 218: 20.356 distance: 211 - 212: 6.489 distance: 212 - 213: 9.577 distance: 213 - 214: 7.816 distance: 214 - 215: 3.438 distance: 215 - 216: 3.050 distance: 218 - 219: 17.096 distance: 219 - 220: 13.512 distance: 219 - 222: 8.861 distance: 220 - 221: 6.273 distance: 220 - 225: 4.214 distance: 222 - 223: 10.788 distance: 222 - 224: 13.494