Starting phenix.real_space_refine on Fri Jun 28 21:28:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/06_2024/8rkv_19284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/06_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_19284/06_2024/8rkv_19284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/06_2024/8rkv_19284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/06_2024/8rkv_19284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkv_19284/06_2024/8rkv_19284.pdb" } 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 Residue "R TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 9.36, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 7.64 Conformation dependent library (CDL) restraints added in 2.4 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: 6.10 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: 6.05 Time building geometry restraints manager: 8.21 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: 95.99 - 103.59: 470 103.59 - 111.19: 7274 111.19 - 118.80: 6823 118.80 - 126.40: 8641 126.40 - 134.00: 698 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 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.590 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.220 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.950 ------------------------------------------------------------------------------- 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 : 1.616 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: 0.3679 time to fit residues: 152.9181 Evaluate side-chains 211 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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: 30.0000 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 427 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 428 ASN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 481 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17128 Z= 0.281 Angle : 0.722 9.911 23906 Z= 0.397 Chirality : 0.043 0.225 2660 Planarity : 0.005 0.055 2487 Dihedral : 25.541 175.786 3777 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.72 % Allowed : 12.90 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.21), residues: 1576 helix: -0.67 (0.20), residues: 595 sheet: -0.72 (0.34), residues: 214 loop : -0.08 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 86 HIS 0.007 0.001 HIS T 272 PHE 0.021 0.003 PHE S 284 TYR 0.026 0.002 TYR R 233 ARG 0.007 0.001 ARG U 389 *********************** 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 259 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7749 (mt-10) REVERT: R 165 GLU cc_start: 0.8358 (tp30) cc_final: 0.8156 (tp30) REVERT: R 172 SER cc_start: 0.7004 (t) cc_final: 0.6503 (p) REVERT: R 188 ARG cc_start: 0.7238 (ttm170) cc_final: 0.6846 (ttm170) REVERT: R 411 MET cc_start: 0.7645 (mtp) cc_final: 0.7388 (mtp) REVERT: R 451 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7972 (mtm-85) REVERT: R 478 GLU cc_start: 0.7526 (pm20) cc_final: 0.6708 (pt0) REVERT: S 104 LYS cc_start: 0.7029 (mmtp) cc_final: 0.6671 (mmtt) REVERT: S 168 GLN cc_start: 0.8739 (tt0) cc_final: 0.8532 (pt0) REVERT: S 327 LEU cc_start: 0.6179 (tp) cc_final: 0.5937 (tp) REVERT: S 349 ASP cc_start: 0.6658 (m-30) cc_final: 0.6228 (t0) REVERT: S 384 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6711 (tm-30) REVERT: S 503 ASN cc_start: 0.7266 (p0) cc_final: 0.6964 (p0) REVERT: T 225 TRP cc_start: 0.6911 (m-90) cc_final: 0.5975 (m-10) REVERT: T 233 TYR cc_start: 0.5927 (m-80) cc_final: 0.5712 (m-10) REVERT: T 261 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6685 (mm) REVERT: T 327 LEU cc_start: 0.5668 (mm) cc_final: 0.5137 (mm) REVERT: T 373 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.3976 (t80) REVERT: T 384 GLN cc_start: 0.6028 (mt0) cc_final: 0.5811 (mt0) REVERT: U 245 ASP cc_start: 0.6747 (t0) cc_final: 0.6347 (t0) REVERT: U 309 HIS cc_start: 0.7008 (m-70) cc_final: 0.6737 (m-70) REVERT: U 404 ARG cc_start: 0.5488 (OUTLIER) cc_final: 0.4394 (mmp-170) REVERT: U 415 ARG cc_start: 0.5985 (mpp-170) cc_final: 0.5746 (mtm-85) REVERT: U 473 HIS cc_start: 0.6099 (OUTLIER) cc_final: 0.5546 (m90) outliers start: 38 outliers final: 22 residues processed: 241 average time/residue: 0.3728 time to fit residues: 125.4651 Evaluate side-chains 218 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 457 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 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 485 ASP 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: 5.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 445 ASN S 272 HIS S 344 GLN S 508 GLN T 363 GLN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17128 Z= 0.242 Angle : 0.660 8.961 23906 Z= 0.362 Chirality : 0.041 0.214 2660 Planarity : 0.005 0.059 2487 Dihedral : 25.464 179.252 3761 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.94 % Allowed : 14.98 % Favored : 82.08 % 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: -0.37 (0.21), residues: 1576 helix: -0.12 (0.21), residues: 595 sheet: -0.69 (0.33), residues: 226 loop : -0.01 (0.24), residues: 755 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 0.022 0.002 TYR R 233 ARG 0.010 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 253 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 212 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7748 (mt-10) REVERT: R 188 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6885 (ttm170) REVERT: R 451 ARG cc_start: 0.8458 (mtm180) cc_final: 0.8102 (mtm-85) REVERT: R 475 GLN cc_start: 0.7145 (mm110) cc_final: 0.6827 (mp10) REVERT: S 104 LYS cc_start: 0.7027 (mmtp) cc_final: 0.6693 (mmtt) REVERT: S 349 ASP cc_start: 0.6706 (m-30) cc_final: 0.6222 (t0) REVERT: S 384 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6897 (tm-30) REVERT: S 430 MET cc_start: 0.8051 (mpp) cc_final: 0.7165 (mpp) REVERT: S 431 TYR cc_start: 0.6245 (m-80) cc_final: 0.5716 (m-80) REVERT: T 225 TRP cc_start: 0.6896 (m-90) cc_final: 0.5976 (m-10) REVERT: T 261 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6694 (mm) REVERT: T 327 LEU cc_start: 0.5699 (mm) cc_final: 0.5175 (mm) REVERT: T 373 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4313 (t80) REVERT: U 245 ASP cc_start: 0.6768 (t0) cc_final: 0.6286 (t0) REVERT: U 372 ARG cc_start: 0.5791 (ttp80) cc_final: 0.4730 (ttp80) REVERT: U 404 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4302 (mmp-170) REVERT: U 473 HIS cc_start: 0.6163 (OUTLIER) cc_final: 0.5611 (m90) outliers start: 41 outliers final: 26 residues processed: 237 average time/residue: 0.3663 time to fit residues: 120.0075 Evaluate side-chains 216 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 415 ARG Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 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 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 417 THR Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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: 1.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN R 295 ASN R 445 ASN S 272 HIS S 344 GLN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 ASN U 475 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17128 Z= 0.168 Angle : 0.601 9.883 23906 Z= 0.329 Chirality : 0.038 0.169 2660 Planarity : 0.004 0.060 2487 Dihedral : 25.350 178.544 3761 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.58 % Allowed : 17.13 % Favored : 80.29 % 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: 0.04 (0.22), residues: 1576 helix: 0.37 (0.22), residues: 604 sheet: -0.62 (0.33), residues: 220 loop : 0.13 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 86 HIS 0.008 0.001 HIS T 272 PHE 0.014 0.001 PHE T 284 TYR 0.019 0.001 TYR T 338 ARG 0.007 0.000 ARG R 235 *********************** 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 246 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7806 (mt-10) REVERT: R 133 GLN cc_start: 0.7079 (mp10) cc_final: 0.6777 (mp10) REVERT: R 137 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7831 (tpp80) REVERT: R 165 GLU cc_start: 0.8600 (tp30) cc_final: 0.8065 (mm-30) REVERT: R 188 ARG cc_start: 0.7288 (ttm170) cc_final: 0.7073 (ttm170) REVERT: R 451 ARG cc_start: 0.8468 (mtm180) cc_final: 0.8030 (mtm-85) REVERT: R 475 GLN cc_start: 0.7179 (mm110) cc_final: 0.6932 (mp10) REVERT: R 491 SER cc_start: 0.8151 (m) cc_final: 0.7798 (t) REVERT: S 104 LYS cc_start: 0.7054 (mmtp) cc_final: 0.6724 (mmtt) REVERT: S 157 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7201 (mt) REVERT: S 268 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: S 295 ASN cc_start: 0.7911 (m-40) cc_final: 0.7574 (m-40) REVERT: S 344 GLN cc_start: 0.7272 (tp40) cc_final: 0.6710 (tp-100) REVERT: S 349 ASP cc_start: 0.6683 (m-30) cc_final: 0.6168 (t0) REVERT: S 430 MET cc_start: 0.8079 (mpp) cc_final: 0.7708 (mmt) REVERT: S 431 TYR cc_start: 0.6299 (m-80) cc_final: 0.5753 (m-80) REVERT: S 471 ARG cc_start: 0.7319 (ppp80) cc_final: 0.6984 (tmm-80) REVERT: T 225 TRP cc_start: 0.6738 (m-90) cc_final: 0.5934 (m-10) REVERT: T 261 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6691 (mm) REVERT: U 225 TRP cc_start: 0.6777 (m100) cc_final: 0.6282 (m100) REVERT: U 245 ASP cc_start: 0.6632 (t0) cc_final: 0.6361 (t70) REVERT: U 300 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8031 (mt) REVERT: U 372 ARG cc_start: 0.5821 (ttp80) cc_final: 0.5604 (tmm-80) REVERT: U 375 GLN cc_start: 0.6755 (mm110) cc_final: 0.6495 (mm110) REVERT: U 404 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.4349 (mmp-170) REVERT: U 473 HIS cc_start: 0.6039 (OUTLIER) cc_final: 0.5491 (m90) outliers start: 36 outliers final: 21 residues processed: 236 average time/residue: 0.3599 time to fit residues: 119.6221 Evaluate side-chains 212 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU 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 94 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 358 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 261 LEU 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 417 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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: 10.0000 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 428 ASN T 272 HIS ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17128 Z= 0.342 Angle : 0.711 10.479 23906 Z= 0.383 Chirality : 0.043 0.203 2660 Planarity : 0.005 0.060 2487 Dihedral : 25.474 177.839 3759 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.52 % Allowed : 17.06 % Favored : 78.42 % 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: -0.27 (0.22), residues: 1576 helix: 0.09 (0.21), residues: 592 sheet: -0.56 (0.35), residues: 210 loop : -0.12 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 86 HIS 0.004 0.001 HIS R 283 PHE 0.024 0.002 PHE S 306 TYR 0.031 0.002 TYR R 233 ARG 0.006 0.001 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 253 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7713 (mt-10) REVERT: R 124 LYS cc_start: 0.7003 (pptt) cc_final: 0.6674 (pptt) REVERT: R 137 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7885 (tpp80) REVERT: R 235 ARG cc_start: 0.6689 (mmm160) cc_final: 0.5655 (mmt-90) REVERT: R 416 ARG cc_start: 0.5623 (mmt180) cc_final: 0.5396 (mmt180) REVERT: R 451 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8164 (mtm-85) REVERT: R 475 GLN cc_start: 0.7256 (mm110) cc_final: 0.7015 (mp10) REVERT: S 104 LYS cc_start: 0.7084 (mmtp) cc_final: 0.6803 (mmtt) REVERT: S 268 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: S 349 ASP cc_start: 0.6750 (m-30) cc_final: 0.6193 (t0) REVERT: S 360 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5557 (mp0) REVERT: S 375 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8027 (mm-40) REVERT: S 384 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: S 428 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6240 (t160) REVERT: S 430 MET cc_start: 0.8003 (mpp) cc_final: 0.7599 (mpp) REVERT: S 431 TYR cc_start: 0.6422 (m-80) cc_final: 0.5804 (m-80) REVERT: S 471 ARG cc_start: 0.7374 (ppp80) cc_final: 0.7128 (tmm-80) REVERT: T 199 ASN cc_start: 0.4344 (OUTLIER) cc_final: 0.4057 (t0) REVERT: T 225 TRP cc_start: 0.7070 (m-90) cc_final: 0.6137 (m-10) REVERT: T 261 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6701 (mm) REVERT: T 275 TRP cc_start: 0.5976 (OUTLIER) cc_final: 0.5012 (t60) REVERT: T 325 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7682 (pmmt) REVERT: T 424 LEU cc_start: 0.8131 (mp) cc_final: 0.7930 (mp) REVERT: T 488 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6214 (mm-30) REVERT: U 245 ASP cc_start: 0.6754 (t0) cc_final: 0.6417 (t70) REVERT: U 300 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8067 (mt) REVERT: U 375 GLN cc_start: 0.6686 (mm110) cc_final: 0.6485 (mm110) REVERT: U 404 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.4311 (mmp-170) REVERT: U 415 ARG cc_start: 0.6321 (mpp-170) cc_final: 0.5842 (mtm-85) REVERT: U 473 HIS cc_start: 0.6314 (OUTLIER) cc_final: 0.5733 (m90) outliers start: 63 outliers final: 32 residues processed: 234 average time/residue: 0.3344 time to fit residues: 110.4320 Evaluate side-chains 228 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 228 THR Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 508 GLN 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 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 360 GLU Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 428 ASN Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 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 384 GLN 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 356 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 485 ASP 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: 9.9990 chunk 149 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 272 HIS ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 463 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17128 Z= 0.201 Angle : 0.637 9.646 23906 Z= 0.343 Chirality : 0.040 0.228 2660 Planarity : 0.005 0.061 2487 Dihedral : 25.372 176.591 3759 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.30 % Allowed : 18.06 % Favored : 78.64 % 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: -0.10 (0.22), residues: 1576 helix: 0.36 (0.22), residues: 601 sheet: -0.52 (0.35), residues: 207 loop : -0.13 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 225 HIS 0.006 0.001 HIS T 272 PHE 0.017 0.002 PHE S 306 TYR 0.018 0.001 TYR R 233 ARG 0.006 0.000 ARG R 235 *********************** 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 236 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7818 (mt-10) REVERT: R 137 ARG cc_start: 0.8228 (tpp80) cc_final: 0.7853 (tpp80) REVERT: R 165 GLU cc_start: 0.8629 (tp30) cc_final: 0.8142 (mm-30) REVERT: R 188 ARG cc_start: 0.7269 (ttm170) cc_final: 0.6811 (ttm170) REVERT: R 451 ARG cc_start: 0.8548 (mtm180) cc_final: 0.8151 (mtm-85) REVERT: S 104 LYS cc_start: 0.7042 (mmtp) cc_final: 0.6717 (mmtt) REVERT: S 157 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7185 (mt) REVERT: S 268 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7230 (pp20) REVERT: S 349 ASP cc_start: 0.6740 (m-30) cc_final: 0.6202 (t0) REVERT: S 384 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: S 430 MET cc_start: 0.8099 (mpp) cc_final: 0.7825 (mpp) REVERT: S 431 TYR cc_start: 0.6543 (m-80) cc_final: 0.5847 (m-80) REVERT: S 471 ARG cc_start: 0.7411 (ppp80) cc_final: 0.7166 (tmm-80) REVERT: T 199 ASN cc_start: 0.4389 (OUTLIER) cc_final: 0.4170 (t0) REVERT: T 225 TRP cc_start: 0.6928 (m-90) cc_final: 0.6090 (m-10) REVERT: T 261 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6752 (mm) REVERT: T 275 TRP cc_start: 0.5922 (OUTLIER) cc_final: 0.4781 (t60) REVERT: T 373 TYR cc_start: 0.5281 (OUTLIER) cc_final: 0.4832 (t80) REVERT: U 203 GLN cc_start: 0.5392 (tp40) cc_final: 0.5015 (tp-100) REVERT: U 245 ASP cc_start: 0.6742 (t0) cc_final: 0.6391 (t70) REVERT: U 300 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8025 (mt) REVERT: U 404 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.4282 (mmp-170) REVERT: U 415 ARG cc_start: 0.6090 (mpp-170) cc_final: 0.5633 (mtm-85) REVERT: U 473 HIS cc_start: 0.6161 (OUTLIER) cc_final: 0.5615 (m90) outliers start: 46 outliers final: 26 residues processed: 220 average time/residue: 0.3542 time to fit residues: 110.9922 Evaluate side-chains 222 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU 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 436 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 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 384 GLN 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 485 ASP 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 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 76 optimal weight: 0.0040 chunk 102 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 344 GLN T 363 GLN T 445 ASN U 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17128 Z= 0.159 Angle : 0.597 9.508 23906 Z= 0.322 Chirality : 0.038 0.183 2660 Planarity : 0.004 0.061 2487 Dihedral : 25.169 176.962 3759 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.72 % Allowed : 19.78 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.22), residues: 1576 helix: 0.72 (0.22), residues: 605 sheet: -0.55 (0.33), residues: 211 loop : -0.05 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 86 HIS 0.004 0.001 HIS R 283 PHE 0.012 0.001 PHE T 284 TYR 0.014 0.001 TYR T 459 ARG 0.007 0.000 ARG U 208 *********************** 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 247 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 133 GLN cc_start: 0.7063 (mp10) cc_final: 0.6676 (mp10) REVERT: R 137 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7852 (tpp80) REVERT: R 165 GLU cc_start: 0.8586 (tp30) cc_final: 0.8134 (mm-30) REVERT: R 188 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6978 (ttm170) REVERT: R 316 GLU cc_start: 0.7672 (mp0) cc_final: 0.7425 (mp0) REVERT: R 451 ARG cc_start: 0.8580 (mtm180) cc_final: 0.8172 (mtm-85) REVERT: S 104 LYS cc_start: 0.7076 (mmtp) cc_final: 0.6731 (mmtt) REVERT: S 143 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7298 (mtp-110) REVERT: S 157 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7169 (mt) REVERT: S 268 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: S 295 ASN cc_start: 0.7764 (m110) cc_final: 0.7429 (m-40) REVERT: S 344 GLN cc_start: 0.7232 (tp40) cc_final: 0.6729 (tp-100) REVERT: S 349 ASP cc_start: 0.6757 (m-30) cc_final: 0.6255 (t0) REVERT: S 384 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: S 430 MET cc_start: 0.8092 (mpp) cc_final: 0.7806 (mmt) REVERT: S 431 TYR cc_start: 0.6643 (m-80) cc_final: 0.6026 (m-80) REVERT: S 471 ARG cc_start: 0.7440 (ppp80) cc_final: 0.7230 (tmm-80) REVERT: T 225 TRP cc_start: 0.6801 (m-90) cc_final: 0.5998 (m-10) REVERT: T 238 MET cc_start: 0.5585 (mpp) cc_final: 0.5331 (mpp) REVERT: T 261 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6601 (mm) REVERT: T 275 TRP cc_start: 0.5777 (OUTLIER) cc_final: 0.4384 (t60) REVERT: T 373 TYR cc_start: 0.5285 (OUTLIER) cc_final: 0.4945 (t80) REVERT: U 238 MET cc_start: 0.2626 (OUTLIER) cc_final: 0.2062 (pmm) REVERT: U 300 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.7962 (mt) REVERT: U 368 TYR cc_start: 0.6060 (m-80) cc_final: 0.5822 (m-80) REVERT: U 473 HIS cc_start: 0.6106 (OUTLIER) cc_final: 0.5573 (m90) outliers start: 38 outliers final: 22 residues processed: 234 average time/residue: 0.3456 time to fit residues: 113.8885 Evaluate side-chains 215 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 508 GLN Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 458 VAL 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 U residue 238 MET Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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 99 optimal weight: 9.9990 chunk 49 optimal weight: 0.0060 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17128 Z= 0.176 Angle : 0.613 12.367 23906 Z= 0.328 Chirality : 0.038 0.171 2660 Planarity : 0.004 0.055 2487 Dihedral : 25.110 178.696 3759 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.30 % Allowed : 19.50 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.22), residues: 1576 helix: 0.74 (0.22), residues: 604 sheet: -0.55 (0.33), residues: 211 loop : -0.05 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP U 225 HIS 0.003 0.001 HIS R 283 PHE 0.014 0.001 PHE S 306 TYR 0.014 0.001 TYR R 233 ARG 0.008 0.000 ARG S 137 *********************** 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 fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 LYS cc_start: 0.7624 (mttt) cc_final: 0.6811 (ttmm) REVERT: R 133 GLN cc_start: 0.7101 (mp10) cc_final: 0.6804 (mp10) REVERT: R 137 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7876 (tpp80) REVERT: R 165 GLU cc_start: 0.8580 (tp30) cc_final: 0.8140 (mm-30) REVERT: R 451 ARG cc_start: 0.8587 (mtm180) cc_final: 0.8168 (mtm-85) REVERT: R 475 GLN cc_start: 0.6980 (mp10) cc_final: 0.6726 (mp-120) REVERT: S 104 LYS cc_start: 0.7075 (mmtp) cc_final: 0.6733 (mmtt) REVERT: S 157 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7208 (mt) REVERT: S 188 ARG cc_start: 0.6571 (ptp90) cc_final: 0.6195 (ptp-110) REVERT: S 268 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7269 (pp20) REVERT: S 344 GLN cc_start: 0.7239 (tp40) cc_final: 0.6687 (tp40) REVERT: S 349 ASP cc_start: 0.6792 (m-30) cc_final: 0.6281 (t0) REVERT: S 384 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: S 430 MET cc_start: 0.8064 (mpp) cc_final: 0.7762 (mmt) REVERT: S 431 TYR cc_start: 0.6620 (m-80) cc_final: 0.6008 (m-80) REVERT: S 471 ARG cc_start: 0.7464 (ppp80) cc_final: 0.7257 (ttp80) REVERT: T 225 TRP cc_start: 0.6832 (m-90) cc_final: 0.6037 (m-10) REVERT: T 261 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6744 (mm) REVERT: T 275 TRP cc_start: 0.5798 (OUTLIER) cc_final: 0.4431 (t60) REVERT: T 373 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.5322 (t80) REVERT: U 238 MET cc_start: 0.2580 (OUTLIER) cc_final: 0.2022 (pmm) REVERT: U 300 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7927 (mt) REVERT: U 368 TYR cc_start: 0.6092 (m-80) cc_final: 0.5850 (m-80) REVERT: U 473 HIS cc_start: 0.6213 (OUTLIER) cc_final: 0.5664 (m90) outliers start: 46 outliers final: 29 residues processed: 226 average time/residue: 0.3466 time to fit residues: 109.9226 Evaluate side-chains 222 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL 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 94 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 252 VAL 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 459 TYR Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 238 MET 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 407 ASP Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 0.1980 chunk 163 optimal weight: 0.3980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 272 HIS ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 363 GLN T 384 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17128 Z= 0.203 Angle : 0.623 11.348 23906 Z= 0.334 Chirality : 0.039 0.174 2660 Planarity : 0.005 0.055 2487 Dihedral : 25.152 179.801 3759 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.23 % Allowed : 20.14 % Favored : 76.63 % 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: 0.04 (0.22), residues: 1576 helix: 0.60 (0.22), residues: 604 sheet: -0.46 (0.34), residues: 202 loop : -0.17 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 86 HIS 0.005 0.001 HIS T 283 PHE 0.016 0.001 PHE S 306 TYR 0.017 0.001 TYR R 233 ARG 0.008 0.000 ARG U 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: R 124 LYS cc_start: 0.6851 (pptt) cc_final: 0.6547 (pptt) REVERT: R 137 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7857 (tpp80) REVERT: R 165 GLU cc_start: 0.8585 (tp30) cc_final: 0.8130 (mm-30) REVERT: R 451 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8049 (mtm-85) REVERT: R 475 GLN cc_start: 0.7120 (mp10) cc_final: 0.6893 (mp-120) REVERT: S 104 LYS cc_start: 0.7057 (mmtp) cc_final: 0.6707 (mmtt) REVERT: S 157 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7210 (mt) REVERT: S 188 ARG cc_start: 0.6399 (ptp90) cc_final: 0.6031 (ptp-110) REVERT: S 268 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7325 (pp20) REVERT: S 349 ASP cc_start: 0.6844 (m-30) cc_final: 0.6362 (t0) REVERT: S 384 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: S 430 MET cc_start: 0.8125 (mpp) cc_final: 0.7797 (mmt) REVERT: S 431 TYR cc_start: 0.6550 (m-80) cc_final: 0.5861 (m-80) REVERT: S 471 ARG cc_start: 0.7485 (ppp80) cc_final: 0.7234 (ttp80) REVERT: T 225 TRP cc_start: 0.6924 (m-90) cc_final: 0.6137 (m-10) REVERT: T 235 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7513 (mmm-85) REVERT: T 261 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6769 (mm) REVERT: T 275 TRP cc_start: 0.5758 (OUTLIER) cc_final: 0.4403 (t60) REVERT: T 373 TYR cc_start: 0.5618 (OUTLIER) cc_final: 0.5327 (t80) REVERT: U 223 ARG cc_start: 0.6463 (ptm-80) cc_final: 0.6242 (ptp-170) REVERT: U 238 MET cc_start: 0.2778 (OUTLIER) cc_final: 0.2087 (pmm) REVERT: U 300 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8115 (mp) REVERT: U 404 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.4653 (mmp-170) REVERT: U 473 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5706 (m90) outliers start: 45 outliers final: 30 residues processed: 209 average time/residue: 0.3739 time to fit residues: 110.8276 Evaluate side-chains 216 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 193 LEU 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 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 252 VAL 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 384 GLN Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 238 MET Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 272 HIS ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 344 GLN ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 428 ASN U 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17128 Z= 0.294 Angle : 0.684 10.939 23906 Z= 0.367 Chirality : 0.042 0.167 2660 Planarity : 0.005 0.057 2487 Dihedral : 25.360 179.075 3759 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.23 % Allowed : 20.50 % Favored : 76.27 % 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: -0.23 (0.21), residues: 1576 helix: 0.23 (0.21), residues: 603 sheet: -0.36 (0.35), residues: 201 loop : -0.27 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 225 HIS 0.005 0.001 HIS R 283 PHE 0.023 0.002 PHE S 306 TYR 0.028 0.002 TYR R 233 ARG 0.010 0.001 ARG S 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 124 LYS cc_start: 0.6947 (pptt) cc_final: 0.6629 (pptt) REVERT: R 137 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7914 (tpp80) REVERT: R 165 GLU cc_start: 0.8605 (tp30) cc_final: 0.8099 (mm-30) REVERT: R 235 ARG cc_start: 0.6718 (mmm160) cc_final: 0.6417 (mmm160) REVERT: R 451 ARG cc_start: 0.8641 (mtm180) cc_final: 0.8186 (mtm-85) REVERT: R 475 GLN cc_start: 0.7163 (mp10) cc_final: 0.6928 (mp-120) REVERT: S 104 LYS cc_start: 0.7012 (mmtp) cc_final: 0.6743 (mmtt) REVERT: S 157 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7297 (mt) REVERT: S 188 ARG cc_start: 0.6361 (ptp90) cc_final: 0.5994 (ptp-110) REVERT: S 268 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: S 349 ASP cc_start: 0.6851 (m-30) cc_final: 0.6345 (t0) REVERT: S 384 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: S 430 MET cc_start: 0.8067 (mpp) cc_final: 0.7710 (mmm) REVERT: T 225 TRP cc_start: 0.7046 (m-90) cc_final: 0.6245 (m-10) REVERT: T 235 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7523 (mmm-85) REVERT: T 261 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6804 (mm) REVERT: T 275 TRP cc_start: 0.5865 (OUTLIER) cc_final: 0.4619 (t60) REVERT: T 373 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.5310 (t80) REVERT: U 238 MET cc_start: 0.2906 (OUTLIER) cc_final: 0.2133 (pmm) REVERT: U 295 ASN cc_start: 0.6719 (p0) cc_final: 0.6495 (p0) REVERT: U 300 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8171 (mp) REVERT: U 404 ARG cc_start: 0.5580 (OUTLIER) cc_final: 0.4483 (mmp-170) REVERT: U 473 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.5776 (m90) outliers start: 45 outliers final: 31 residues processed: 205 average time/residue: 0.3350 time to fit residues: 97.2341 Evaluate side-chains 211 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL 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 157 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 252 VAL 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 459 TYR Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 238 MET 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 485 ASP Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0670 chunk 125 optimal weight: 0.0870 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 344 GLN ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 363 GLN U 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.210002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.173615 restraints weight = 23668.828| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.58 r_work: 0.3974 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17128 Z= 0.181 Angle : 0.617 11.682 23906 Z= 0.330 Chirality : 0.038 0.156 2660 Planarity : 0.005 0.066 2487 Dihedral : 25.217 179.708 3759 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.65 % Allowed : 21.58 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.00 (0.22), residues: 1576 helix: 0.54 (0.22), residues: 604 sheet: -0.33 (0.35), residues: 196 loop : -0.21 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 86 HIS 0.004 0.001 HIS S 473 PHE 0.016 0.001 PHE S 306 TYR 0.014 0.001 TYR R 233 ARG 0.009 0.001 ARG S 137 =============================================================================== Job complete usr+sys time: 3933.53 seconds wall clock time: 70 minutes 20.53 seconds (4220.53 seconds total)