Starting phenix.real_space_refine on Tue Nov 19 09:56:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/11_2024/6bob_7123.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/11_2024/6bob_7123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/11_2024/6bob_7123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/11_2024/6bob_7123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/11_2024/6bob_7123.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/11_2024/6bob_7123.cif" } resolution = 3.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 12524 2.51 5 N 3244 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19340 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 10.51, per 1000 atoms: 0.54 Number of scatterers: 19340 At special positions: 0 Unit cell: (132.3, 132.3, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3436 8.00 N 3244 7.00 C 12524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.4 seconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 59.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.831A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.574A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.902A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.530A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.730A pdb=" N GLY A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.688A pdb=" N VAL A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE A 306 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 3.599A pdb=" N TYR A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.675A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG A 469 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.592A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 502 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.554A pdb=" N LEU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.831A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.573A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.683A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.729A pdb=" N GLY B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.688A pdb=" N VAL B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.598A pdb=" N ILE B 306 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.593A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 484 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.830A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.573A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.730A pdb=" N GLY C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.689A pdb=" N VAL C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE C 306 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 435 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 3.573A pdb=" N VAL C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG C 469 " --> pdb=" O TYR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 486 removed outlier: 3.592A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP C 494 " --> pdb=" O MET C 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 502 " --> pdb=" O VAL C 498 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 524 through 537 removed outlier: 3.546A pdb=" N ALA C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 563 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 570 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.830A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.574A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.729A pdb=" N GLY D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.689A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 336 " --> pdb=" O GLY D 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 408 through 410 No H-bonds generated for 'chain 'D' and resid 408 through 410' Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL D 458 " --> pdb=" O SER D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.524A pdb=" N ARG D 469 " --> pdb=" O TYR D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 486 removed outlier: 3.593A pdb=" N THR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 480 " --> pdb=" O PRO D 476 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP D 494 " --> pdb=" O MET D 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY D 502 " --> pdb=" O VAL D 498 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 579 removed outlier: 3.602A pdb=" N SER D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 570 " --> pdb=" O THR D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE A 265 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 276 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE B 265 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU B 276 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE C 265 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU C 276 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE D 265 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 276 " --> pdb=" O ILE D 265 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6065 1.34 - 1.46: 3828 1.46 - 1.57: 9667 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 19788 Sorted by residual: bond pdb=" C ASP C 515 " pdb=" N PRO C 516 " ideal model delta sigma weight residual 1.337 1.309 0.027 1.06e-02 8.90e+03 6.68e+00 bond pdb=" C ASP D 515 " pdb=" N PRO D 516 " ideal model delta sigma weight residual 1.337 1.309 0.027 1.06e-02 8.90e+03 6.53e+00 bond pdb=" C ASP A 515 " pdb=" N PRO A 516 " ideal model delta sigma weight residual 1.337 1.310 0.027 1.06e-02 8.90e+03 6.43e+00 bond pdb=" C ASP B 515 " pdb=" N PRO B 516 " ideal model delta sigma weight residual 1.337 1.310 0.026 1.06e-02 8.90e+03 6.13e+00 bond pdb=" N ASN D 357 " pdb=" CA ASN D 357 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.70e+00 ... (remaining 19783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 26441 3.79 - 7.57: 343 7.57 - 11.36: 76 11.36 - 15.15: 4 15.15 - 18.93: 4 Bond angle restraints: 26868 Sorted by residual: angle pdb=" N CYS B 610 " pdb=" CA CYS B 610 " pdb=" C CYS B 610 " ideal model delta sigma weight residual 114.56 106.24 8.32 1.27e+00 6.20e-01 4.29e+01 angle pdb=" N CYS C 610 " pdb=" CA CYS C 610 " pdb=" C CYS C 610 " ideal model delta sigma weight residual 114.56 106.27 8.29 1.27e+00 6.20e-01 4.26e+01 angle pdb=" N CYS D 610 " pdb=" CA CYS D 610 " pdb=" C CYS D 610 " ideal model delta sigma weight residual 114.56 106.28 8.28 1.27e+00 6.20e-01 4.25e+01 angle pdb=" N CYS A 610 " pdb=" CA CYS A 610 " pdb=" C CYS A 610 " ideal model delta sigma weight residual 114.56 106.29 8.27 1.27e+00 6.20e-01 4.24e+01 angle pdb=" CA LEU C 228 " pdb=" CB LEU C 228 " pdb=" CG LEU C 228 " ideal model delta sigma weight residual 116.30 135.23 -18.93 3.50e+00 8.16e-02 2.93e+01 ... (remaining 26863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 10894 15.61 - 31.21: 672 31.21 - 46.82: 182 46.82 - 62.42: 20 62.42 - 78.03: 12 Dihedral angle restraints: 11780 sinusoidal: 4732 harmonic: 7048 Sorted by residual: dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N ILE B 355 " pdb=" CA ILE B 355 " ideal model delta harmonic sigma weight residual 180.00 -132.20 -47.80 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ARG C 354 " pdb=" C ARG C 354 " pdb=" N ILE C 355 " pdb=" CA ILE C 355 " ideal model delta harmonic sigma weight residual -180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA ARG D 354 " pdb=" C ARG D 354 " pdb=" N ILE D 355 " pdb=" CA ILE D 355 " ideal model delta harmonic sigma weight residual -180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 ... (remaining 11777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2089 0.054 - 0.107: 739 0.107 - 0.161: 182 0.161 - 0.215: 30 0.215 - 0.268: 16 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA THR D 310 " pdb=" N THR D 310 " pdb=" C THR D 310 " pdb=" CB THR D 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR A 310 " pdb=" N THR A 310 " pdb=" C THR A 310 " pdb=" CB THR A 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA THR C 310 " pdb=" N THR C 310 " pdb=" C THR C 310 " pdb=" CB THR C 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3053 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 354 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ARG D 354 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG D 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE D 355 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 354 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ARG C 354 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG C 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE C 355 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 354 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ARG B 354 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG B 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE B 355 " 0.021 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5012 2.79 - 3.32: 18582 3.32 - 3.84: 32030 3.84 - 4.37: 37973 4.37 - 4.90: 61282 Nonbonded interactions: 154879 Sorted by model distance: nonbonded pdb=" OH TYR C 323 " pdb=" O PRO C 613 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR D 323 " pdb=" O PRO D 613 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR A 323 " pdb=" O PRO A 613 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 323 " pdb=" O PRO B 613 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR C 338 " pdb=" O SER C 391 " model vdw 2.274 3.040 ... (remaining 154874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.700 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 19788 Z= 0.431 Angle : 1.198 18.931 26868 Z= 0.634 Chirality : 0.060 0.268 3056 Planarity : 0.007 0.067 3396 Dihedral : 11.836 78.026 7236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.14 % Favored : 88.52 % Rotamer: Outliers : 0.76 % Allowed : 8.03 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.96 (0.13), residues: 2396 helix: -3.23 (0.09), residues: 1292 sheet: -0.70 (0.59), residues: 76 loop : -3.48 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 29 HIS 0.006 0.002 HIS D 425 PHE 0.019 0.003 PHE D 530 TYR 0.022 0.003 TYR D 62 ARG 0.009 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 714 time to evaluate : 2.096 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: A 29 TRP cc_start: 0.7146 (t60) cc_final: 0.6603 (t60) REVERT: A 40 GLN cc_start: 0.8477 (tt0) cc_final: 0.8216 (mt0) REVERT: A 51 LEU cc_start: 0.7720 (tt) cc_final: 0.7314 (mt) REVERT: A 96 GLN cc_start: 0.8134 (tt0) cc_final: 0.7899 (mt0) REVERT: A 195 LEU cc_start: 0.7870 (mm) cc_final: 0.7137 (mt) REVERT: A 218 LEU cc_start: 0.8566 (tp) cc_final: 0.8133 (tt) REVERT: A 222 TYR cc_start: 0.7850 (m-80) cc_final: 0.6990 (m-80) REVERT: A 252 ILE cc_start: 0.7742 (mt) cc_final: 0.7426 (tp) REVERT: A 267 TRP cc_start: 0.7013 (p-90) cc_final: 0.6810 (p-90) REVERT: A 305 GLN cc_start: 0.8018 (mt0) cc_final: 0.7605 (tm-30) REVERT: A 480 MET cc_start: 0.7175 (mtm) cc_final: 0.6659 (mmt) REVERT: B 29 TRP cc_start: 0.7059 (t60) cc_final: 0.6565 (t60) REVERT: B 51 LEU cc_start: 0.7672 (tt) cc_final: 0.7176 (mt) REVERT: B 61 LEU cc_start: 0.8174 (mt) cc_final: 0.7972 (mt) REVERT: B 80 GLU cc_start: 0.6115 (pm20) cc_final: 0.5914 (pm20) REVERT: B 218 LEU cc_start: 0.8592 (tp) cc_final: 0.8053 (mt) REVERT: B 222 TYR cc_start: 0.8106 (m-80) cc_final: 0.7396 (m-80) REVERT: B 252 ILE cc_start: 0.7616 (mt) cc_final: 0.7193 (tp) REVERT: B 276 LEU cc_start: 0.7362 (tp) cc_final: 0.7027 (tp) REVERT: B 305 GLN cc_start: 0.7946 (mt0) cc_final: 0.7462 (tm-30) REVERT: B 329 CYS cc_start: 0.7409 (m) cc_final: 0.7034 (t) REVERT: B 458 VAL cc_start: 0.7589 (m) cc_final: 0.7354 (p) REVERT: B 490 MET cc_start: 0.7147 (tpt) cc_final: 0.6168 (mtt) REVERT: B 515 ASP cc_start: 0.7686 (t0) cc_final: 0.7087 (t0) REVERT: B 595 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7673 (mt0) REVERT: C 29 TRP cc_start: 0.6997 (t60) cc_final: 0.6315 (t60) REVERT: C 40 GLN cc_start: 0.8414 (tt0) cc_final: 0.8203 (mt0) REVERT: C 51 LEU cc_start: 0.7712 (tt) cc_final: 0.7316 (mt) REVERT: C 74 GLN cc_start: 0.7087 (tp-100) cc_final: 0.6875 (mp10) REVERT: C 96 GLN cc_start: 0.8300 (tt0) cc_final: 0.8078 (mt0) REVERT: C 116 GLU cc_start: 0.6612 (tt0) cc_final: 0.6285 (tt0) REVERT: C 218 LEU cc_start: 0.8584 (tp) cc_final: 0.8003 (mt) REVERT: C 222 TYR cc_start: 0.8232 (m-80) cc_final: 0.7593 (m-80) REVERT: C 449 GLU cc_start: 0.7248 (pp20) cc_final: 0.6878 (pt0) REVERT: C 490 MET cc_start: 0.6945 (tpt) cc_final: 0.5915 (mtt) REVERT: C 595 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7762 (mt0) REVERT: D 40 GLN cc_start: 0.8540 (tt0) cc_final: 0.8315 (mt0) REVERT: D 51 LEU cc_start: 0.7831 (tt) cc_final: 0.7407 (mt) REVERT: D 195 LEU cc_start: 0.7997 (mm) cc_final: 0.7600 (tp) REVERT: D 218 LEU cc_start: 0.8555 (tp) cc_final: 0.8253 (mt) REVERT: D 273 THR cc_start: 0.7036 (p) cc_final: 0.6509 (p) REVERT: D 305 GLN cc_start: 0.7896 (mt0) cc_final: 0.7357 (tm-30) REVERT: D 449 GLU cc_start: 0.7190 (pp20) cc_final: 0.6907 (pt0) REVERT: D 454 SER cc_start: 0.7867 (t) cc_final: 0.7626 (t) REVERT: D 462 CYS cc_start: 0.8268 (m) cc_final: 0.8068 (m) REVERT: D 480 MET cc_start: 0.7051 (mtm) cc_final: 0.6748 (mmt) REVERT: D 490 MET cc_start: 0.6758 (tpt) cc_final: 0.6069 (mtt) REVERT: D 508 TYR cc_start: 0.6994 (t80) cc_final: 0.6397 (t80) outliers start: 16 outliers final: 7 residues processed: 724 average time/residue: 0.3376 time to fit residues: 363.3023 Evaluate side-chains 432 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 425 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 217 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 HIS A 206 GLN A 208 ASN A 217 ASN A 227 HIS A 251 ASN A 257 HIS A 357 ASN A 360 ASN A 463 ASN B 40 GLN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 206 GLN B 208 ASN B 217 ASN B 227 HIS B 251 ASN B 257 HIS B 357 ASN B 360 ASN B 445 ASN B 463 ASN B 571 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 153 HIS C 206 GLN C 208 ASN C 217 ASN C 227 HIS C 251 ASN C 257 HIS C 357 ASN C 360 ASN C 463 ASN D 96 GLN D 118 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS D 208 ASN D 217 ASN D 227 HIS D 251 ASN D 257 HIS D 309 GLN D 357 ASN D 360 ASN D 463 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19788 Z= 0.238 Angle : 0.756 11.982 26868 Z= 0.378 Chirality : 0.045 0.169 3056 Planarity : 0.005 0.039 3396 Dihedral : 6.025 46.375 2649 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.40 % Allowed : 14.96 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.91 (0.15), residues: 2396 helix: -1.09 (0.12), residues: 1384 sheet: -0.21 (0.59), residues: 84 loop : -3.41 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 612 HIS 0.011 0.001 HIS C 257 PHE 0.025 0.002 PHE A 342 TYR 0.026 0.002 TYR B 62 ARG 0.006 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 477 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8350 (tt0) cc_final: 0.8118 (tt0) REVERT: A 80 GLU cc_start: 0.6836 (pm20) cc_final: 0.6617 (pm20) REVERT: A 144 SER cc_start: 0.8961 (p) cc_final: 0.8529 (t) REVERT: A 161 TYR cc_start: 0.8625 (t80) cc_final: 0.8238 (t80) REVERT: A 214 GLN cc_start: 0.7962 (tt0) cc_final: 0.7495 (tm-30) REVERT: A 215 MET cc_start: 0.7316 (ttm) cc_final: 0.6943 (mtt) REVERT: A 259 MET cc_start: 0.8758 (tpp) cc_final: 0.8504 (mpp) REVERT: A 329 CYS cc_start: 0.7993 (m) cc_final: 0.7666 (t) REVERT: A 480 MET cc_start: 0.7346 (mtm) cc_final: 0.6785 (mmt) REVERT: A 527 MET cc_start: 0.7971 (tpt) cc_final: 0.7702 (tpp) REVERT: A 595 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7349 (mm-40) REVERT: B 29 TRP cc_start: 0.6919 (t60) cc_final: 0.6638 (t60) REVERT: B 99 MET cc_start: 0.8650 (mmp) cc_final: 0.8225 (tmm) REVERT: B 100 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7226 (pp20) REVERT: B 144 SER cc_start: 0.9007 (p) cc_final: 0.8537 (t) REVERT: B 214 GLN cc_start: 0.7886 (tt0) cc_final: 0.7421 (tm-30) REVERT: B 215 MET cc_start: 0.6973 (ttm) cc_final: 0.6732 (mtp) REVERT: B 222 TYR cc_start: 0.7799 (m-80) cc_final: 0.7208 (m-80) REVERT: B 305 GLN cc_start: 0.7998 (mt0) cc_final: 0.7601 (tm-30) REVERT: B 490 MET cc_start: 0.7099 (tpt) cc_final: 0.6176 (mtt) REVERT: B 515 ASP cc_start: 0.7801 (t0) cc_final: 0.7490 (t0) REVERT: B 521 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6640 (t-90) REVERT: B 523 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6746 (p90) REVERT: B 553 MET cc_start: 0.8365 (mmm) cc_final: 0.8105 (mmm) REVERT: C 40 GLN cc_start: 0.8369 (tt0) cc_final: 0.8096 (tt0) REVERT: C 74 GLN cc_start: 0.6977 (tp-100) cc_final: 0.6771 (mp10) REVERT: C 100 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7468 (pp20) REVERT: C 144 SER cc_start: 0.9106 (p) cc_final: 0.8725 (t) REVERT: C 180 ARG cc_start: 0.8573 (mmt90) cc_final: 0.8190 (mmm-85) REVERT: C 214 GLN cc_start: 0.7768 (tt0) cc_final: 0.7318 (tm-30) REVERT: C 222 TYR cc_start: 0.8023 (m-80) cc_final: 0.7585 (m-10) REVERT: C 490 MET cc_start: 0.6626 (tpt) cc_final: 0.5806 (mtt) REVERT: C 521 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.5812 (t-90) REVERT: C 527 MET cc_start: 0.8332 (tpp) cc_final: 0.7855 (tpp) REVERT: D 116 GLU cc_start: 0.7576 (tt0) cc_final: 0.7028 (tm-30) REVERT: D 214 GLN cc_start: 0.7822 (tt0) cc_final: 0.7316 (tm-30) REVERT: D 305 GLN cc_start: 0.8046 (mt0) cc_final: 0.7779 (tm-30) REVERT: D 480 MET cc_start: 0.7449 (mtm) cc_final: 0.6998 (mmt) REVERT: D 496 MET cc_start: 0.6636 (ttp) cc_final: 0.6408 (tpp) REVERT: D 521 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6387 (t-90) REVERT: D 553 MET cc_start: 0.8367 (mmm) cc_final: 0.8114 (tpt) REVERT: D 593 ARG cc_start: 0.8030 (mpt-90) cc_final: 0.7765 (tpp80) outliers start: 92 outliers final: 39 residues processed: 539 average time/residue: 0.3104 time to fit residues: 260.9230 Evaluate side-chains 425 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 382 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 218 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 463 ASN B 40 GLN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS B 463 ASN B 571 ASN C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 425 HIS C 463 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19788 Z= 0.177 Angle : 0.690 11.625 26868 Z= 0.340 Chirality : 0.042 0.211 3056 Planarity : 0.004 0.059 3396 Dihedral : 5.465 46.267 2639 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.78 % Allowed : 18.55 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.09 (0.16), residues: 2396 helix: -0.29 (0.14), residues: 1388 sheet: -0.30 (0.55), residues: 84 loop : -3.27 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 612 HIS 0.005 0.001 HIS A 227 PHE 0.036 0.001 PHE B 492 TYR 0.015 0.001 TYR C 62 ARG 0.004 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 425 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8236 (tt0) cc_final: 0.7953 (tt0) REVERT: A 80 GLU cc_start: 0.7021 (pm20) cc_final: 0.6664 (pm20) REVERT: A 144 SER cc_start: 0.9043 (p) cc_final: 0.8624 (t) REVERT: A 214 GLN cc_start: 0.7928 (tt0) cc_final: 0.7492 (tm-30) REVERT: A 222 TYR cc_start: 0.7780 (m-10) cc_final: 0.7036 (m-80) REVERT: A 329 CYS cc_start: 0.8025 (m) cc_final: 0.7679 (t) REVERT: A 358 ARG cc_start: 0.6737 (mpt180) cc_final: 0.6288 (ptp-110) REVERT: A 433 PHE cc_start: 0.7369 (m-10) cc_final: 0.7168 (m-10) REVERT: A 480 MET cc_start: 0.7481 (mtm) cc_final: 0.6947 (mmt) REVERT: A 492 PHE cc_start: 0.7024 (t80) cc_final: 0.6635 (t80) REVERT: A 496 MET cc_start: 0.6785 (ttp) cc_final: 0.6411 (tpp) REVERT: A 527 MET cc_start: 0.8064 (tpt) cc_final: 0.7812 (tpp) REVERT: A 577 MET cc_start: 0.6797 (mmt) cc_final: 0.6527 (mmt) REVERT: A 595 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7511 (mm-40) REVERT: B 29 TRP cc_start: 0.6922 (t60) cc_final: 0.6676 (t60) REVERT: B 99 MET cc_start: 0.8541 (mmp) cc_final: 0.8075 (tmm) REVERT: B 116 GLU cc_start: 0.6939 (tp30) cc_final: 0.6697 (tt0) REVERT: B 144 SER cc_start: 0.9102 (p) cc_final: 0.8666 (t) REVERT: B 214 GLN cc_start: 0.7865 (tt0) cc_final: 0.7423 (tm-30) REVERT: B 215 MET cc_start: 0.7019 (ttm) cc_final: 0.6797 (mtt) REVERT: B 259 MET cc_start: 0.8969 (tpp) cc_final: 0.8544 (mpp) REVERT: B 305 GLN cc_start: 0.7944 (mt0) cc_final: 0.7593 (tm-30) REVERT: B 308 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: B 490 MET cc_start: 0.7122 (tpt) cc_final: 0.6234 (mtt) REVERT: B 515 ASP cc_start: 0.8126 (t0) cc_final: 0.7884 (t0) REVERT: B 521 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6133 (t-90) REVERT: C 40 GLN cc_start: 0.8255 (tt0) cc_final: 0.7950 (tt0) REVERT: C 144 SER cc_start: 0.9118 (p) cc_final: 0.8735 (t) REVERT: C 214 GLN cc_start: 0.7942 (tt0) cc_final: 0.7466 (tm-30) REVERT: C 219 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8470 (mm) REVERT: C 465 MET cc_start: 0.8514 (mmm) cc_final: 0.8248 (mmm) REVERT: C 490 MET cc_start: 0.6384 (tpt) cc_final: 0.5474 (mtt) REVERT: C 521 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.5771 (t-90) REVERT: C 577 MET cc_start: 0.7357 (mmt) cc_final: 0.7077 (mmt) REVERT: C 581 HIS cc_start: 0.5572 (t70) cc_final: 0.5325 (t70) REVERT: D 144 SER cc_start: 0.9227 (p) cc_final: 0.8755 (t) REVERT: D 214 GLN cc_start: 0.7751 (tt0) cc_final: 0.7321 (tm-30) REVERT: D 219 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8407 (mm) REVERT: D 305 GLN cc_start: 0.7947 (mt0) cc_final: 0.7727 (tm-30) REVERT: D 308 ASP cc_start: 0.7976 (t70) cc_final: 0.7581 (t70) REVERT: D 480 MET cc_start: 0.7460 (mtm) cc_final: 0.7013 (mmt) REVERT: D 521 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.5882 (t-90) REVERT: D 553 MET cc_start: 0.8115 (mmm) cc_final: 0.7235 (tpt) REVERT: D 593 ARG cc_start: 0.8044 (mpt-90) cc_final: 0.7795 (tpp80) REVERT: D 595 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7422 (mm-40) REVERT: D 633 GLU cc_start: 0.8069 (pt0) cc_final: 0.7800 (mt-10) outliers start: 79 outliers final: 39 residues processed: 480 average time/residue: 0.2972 time to fit residues: 222.3015 Evaluate side-chains 422 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 377 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 521 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.5980 chunk 164 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 463 ASN B 96 GLN B 122 HIS B 463 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 571 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19788 Z= 0.182 Angle : 0.688 11.840 26868 Z= 0.334 Chirality : 0.043 0.188 3056 Planarity : 0.004 0.048 3396 Dihedral : 5.099 46.214 2639 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.11 % Allowed : 20.12 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.77 (0.17), residues: 2396 helix: 0.02 (0.14), residues: 1392 sheet: -0.71 (0.51), residues: 84 loop : -3.17 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 612 HIS 0.003 0.001 HIS D 157 PHE 0.028 0.001 PHE A 255 TYR 0.030 0.001 TYR C 508 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 420 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8291 (tt0) cc_final: 0.8058 (tt0) REVERT: A 80 GLU cc_start: 0.7022 (pm20) cc_final: 0.6819 (pm20) REVERT: A 144 SER cc_start: 0.9112 (p) cc_final: 0.8709 (t) REVERT: A 214 GLN cc_start: 0.8048 (tt0) cc_final: 0.7722 (tm-30) REVERT: A 259 MET cc_start: 0.8810 (tpp) cc_final: 0.8558 (mpp) REVERT: A 268 THR cc_start: 0.7575 (p) cc_final: 0.7367 (m) REVERT: A 305 GLN cc_start: 0.7944 (tt0) cc_final: 0.7456 (tm-30) REVERT: A 329 CYS cc_start: 0.7935 (m) cc_final: 0.7723 (t) REVERT: A 358 ARG cc_start: 0.6710 (mpt180) cc_final: 0.6329 (ptp-110) REVERT: A 465 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: A 480 MET cc_start: 0.7558 (mtm) cc_final: 0.7088 (mmt) REVERT: A 492 PHE cc_start: 0.6939 (t80) cc_final: 0.6699 (t80) REVERT: A 496 MET cc_start: 0.6748 (ttp) cc_final: 0.6325 (tpp) REVERT: A 527 MET cc_start: 0.8107 (tpt) cc_final: 0.7898 (tpp) REVERT: A 595 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7436 (mm-40) REVERT: B 29 TRP cc_start: 0.6938 (t60) cc_final: 0.6579 (t60) REVERT: B 99 MET cc_start: 0.8517 (mmp) cc_final: 0.8057 (tmm) REVERT: B 116 GLU cc_start: 0.7052 (tp30) cc_final: 0.6801 (tt0) REVERT: B 144 SER cc_start: 0.9160 (p) cc_final: 0.8727 (t) REVERT: B 214 GLN cc_start: 0.7984 (tt0) cc_final: 0.7542 (tm-30) REVERT: B 219 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (mm) REVERT: B 305 GLN cc_start: 0.7918 (mt0) cc_final: 0.7627 (tm-30) REVERT: B 490 MET cc_start: 0.7123 (tpt) cc_final: 0.6236 (mtt) REVERT: B 515 ASP cc_start: 0.8246 (t0) cc_final: 0.7938 (t0) REVERT: B 521 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6260 (t-90) REVERT: C 40 GLN cc_start: 0.8309 (tt0) cc_final: 0.7974 (tt0) REVERT: C 144 SER cc_start: 0.9158 (p) cc_final: 0.8783 (t) REVERT: C 161 TYR cc_start: 0.8343 (t80) cc_final: 0.7937 (t80) REVERT: C 176 GLU cc_start: 0.8655 (pt0) cc_final: 0.8426 (pm20) REVERT: C 177 GLU cc_start: 0.8729 (mp0) cc_final: 0.8302 (mp0) REVERT: C 214 GLN cc_start: 0.8012 (tt0) cc_final: 0.7588 (tm-30) REVERT: C 219 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8379 (mm) REVERT: C 305 GLN cc_start: 0.7945 (tp40) cc_final: 0.7072 (tm-30) REVERT: C 490 MET cc_start: 0.6374 (tpt) cc_final: 0.5488 (mtt) REVERT: C 521 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.5572 (t-90) REVERT: C 553 MET cc_start: 0.8163 (mmm) cc_final: 0.7718 (tpp) REVERT: C 633 GLU cc_start: 0.8141 (pt0) cc_final: 0.7785 (mt-10) REVERT: D 116 GLU cc_start: 0.7688 (tt0) cc_final: 0.7217 (tm-30) REVERT: D 144 SER cc_start: 0.9209 (p) cc_final: 0.8718 (t) REVERT: D 214 GLN cc_start: 0.7876 (tt0) cc_final: 0.7429 (tm-30) REVERT: D 219 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8364 (mm) REVERT: D 305 GLN cc_start: 0.7947 (mt0) cc_final: 0.7713 (tm-30) REVERT: D 308 ASP cc_start: 0.8105 (t70) cc_final: 0.7799 (m-30) REVERT: D 465 MET cc_start: 0.8484 (mmm) cc_final: 0.8239 (mmm) REVERT: D 480 MET cc_start: 0.7557 (mtm) cc_final: 0.7096 (mmt) REVERT: D 496 MET cc_start: 0.6458 (ttp) cc_final: 0.6129 (tpp) REVERT: D 521 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.6020 (t-90) REVERT: D 530 PHE cc_start: 0.7921 (t80) cc_final: 0.7706 (t80) REVERT: D 553 MET cc_start: 0.8192 (mmm) cc_final: 0.7771 (tpp) REVERT: D 593 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.7832 (tpp80) REVERT: D 595 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7401 (mm-40) REVERT: D 633 GLU cc_start: 0.8148 (pt0) cc_final: 0.7894 (mt-10) outliers start: 86 outliers final: 49 residues processed: 473 average time/residue: 0.2939 time to fit residues: 218.9364 Evaluate side-chains 432 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 40.0000 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 0.0370 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 521 HIS B 425 HIS B 463 ASN B 571 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN C 463 ASN C 521 HIS C 581 HIS ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19788 Z= 0.220 Angle : 0.707 14.590 26868 Z= 0.342 Chirality : 0.043 0.205 3056 Planarity : 0.004 0.041 3396 Dihedral : 5.017 45.873 2639 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.06 % Allowed : 21.32 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.61 (0.17), residues: 2396 helix: 0.17 (0.14), residues: 1388 sheet: -1.02 (0.51), residues: 84 loop : -3.09 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 612 HIS 0.003 0.001 HIS A 157 PHE 0.044 0.002 PHE B 492 TYR 0.012 0.001 TYR A 554 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 420 time to evaluate : 2.267 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8276 (tt0) cc_final: 0.8034 (tt0) REVERT: A 80 GLU cc_start: 0.7163 (pm20) cc_final: 0.6915 (pm20) REVERT: A 108 GLU cc_start: 0.7784 (pt0) cc_final: 0.7423 (pm20) REVERT: A 144 SER cc_start: 0.9120 (p) cc_final: 0.8714 (t) REVERT: A 161 TYR cc_start: 0.8483 (t80) cc_final: 0.8060 (t80) REVERT: A 214 GLN cc_start: 0.8086 (tt0) cc_final: 0.7745 (tm-30) REVERT: A 305 GLN cc_start: 0.7989 (tt0) cc_final: 0.7476 (tm-30) REVERT: A 329 CYS cc_start: 0.7899 (m) cc_final: 0.7572 (m) REVERT: A 465 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: A 480 MET cc_start: 0.7526 (mtm) cc_final: 0.7039 (mmt) REVERT: A 492 PHE cc_start: 0.7013 (t80) cc_final: 0.6681 (t80) REVERT: A 522 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.5395 (p90) REVERT: A 595 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7497 (mm-40) REVERT: B 99 MET cc_start: 0.8283 (mmp) cc_final: 0.8002 (tmm) REVERT: B 116 GLU cc_start: 0.7032 (tp30) cc_final: 0.6774 (tm-30) REVERT: B 144 SER cc_start: 0.9212 (p) cc_final: 0.8817 (t) REVERT: B 214 GLN cc_start: 0.8020 (tt0) cc_final: 0.7606 (tm-30) REVERT: B 259 MET cc_start: 0.8944 (mmp) cc_final: 0.8557 (mmp) REVERT: B 305 GLN cc_start: 0.7908 (mt0) cc_final: 0.7586 (tm-30) REVERT: B 308 ASP cc_start: 0.8174 (m-30) cc_final: 0.7705 (m-30) REVERT: B 465 MET cc_start: 0.8763 (mmm) cc_final: 0.8457 (mmm) REVERT: B 480 MET cc_start: 0.6924 (mmt) cc_final: 0.6685 (mtp) REVERT: B 490 MET cc_start: 0.7127 (tpt) cc_final: 0.6342 (mtt) REVERT: B 553 MET cc_start: 0.8306 (mmm) cc_final: 0.8084 (tpt) REVERT: B 581 HIS cc_start: 0.4978 (t70) cc_final: 0.4716 (t70) REVERT: B 593 ARG cc_start: 0.7941 (mpt-90) cc_final: 0.7652 (tpp80) REVERT: C 40 GLN cc_start: 0.8284 (tt0) cc_final: 0.7983 (tt0) REVERT: C 144 SER cc_start: 0.9126 (p) cc_final: 0.8705 (t) REVERT: C 161 TYR cc_start: 0.8443 (t80) cc_final: 0.8064 (t80) REVERT: C 177 GLU cc_start: 0.8824 (mp0) cc_final: 0.8342 (mp0) REVERT: C 214 GLN cc_start: 0.7987 (tt0) cc_final: 0.7589 (tm-30) REVERT: C 305 GLN cc_start: 0.8090 (tp40) cc_final: 0.7209 (tm-30) REVERT: C 465 MET cc_start: 0.8785 (mmm) cc_final: 0.8535 (mmm) REVERT: C 490 MET cc_start: 0.6459 (tpt) cc_final: 0.5696 (mtt) REVERT: C 553 MET cc_start: 0.8142 (mmm) cc_final: 0.7788 (tpp) REVERT: C 571 ASN cc_start: 0.6725 (m110) cc_final: 0.6506 (m-40) REVERT: C 593 ARG cc_start: 0.8000 (mpt-90) cc_final: 0.7761 (tpp80) REVERT: C 595 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7514 (mm-40) REVERT: D 144 SER cc_start: 0.9237 (p) cc_final: 0.8731 (t) REVERT: D 176 GLU cc_start: 0.8729 (pt0) cc_final: 0.8333 (pm20) REVERT: D 214 GLN cc_start: 0.8028 (tt0) cc_final: 0.7568 (tm-30) REVERT: D 305 GLN cc_start: 0.8013 (mt0) cc_final: 0.7710 (tm-30) REVERT: D 308 ASP cc_start: 0.8426 (t70) cc_final: 0.8074 (m-30) REVERT: D 480 MET cc_start: 0.7590 (mtm) cc_final: 0.7187 (mmt) REVERT: D 496 MET cc_start: 0.6559 (ttp) cc_final: 0.6347 (tpp) REVERT: D 553 MET cc_start: 0.8184 (mmm) cc_final: 0.7808 (tpp) REVERT: D 593 ARG cc_start: 0.8049 (mpt-90) cc_final: 0.7825 (tpp80) REVERT: D 633 GLU cc_start: 0.8189 (pt0) cc_final: 0.7924 (mt-10) outliers start: 85 outliers final: 46 residues processed: 475 average time/residue: 0.2978 time to fit residues: 221.6625 Evaluate side-chains 417 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 369 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 40 GLN B 463 ASN C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN D 122 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19788 Z= 0.168 Angle : 0.696 12.995 26868 Z= 0.330 Chirality : 0.043 0.221 3056 Planarity : 0.003 0.039 3396 Dihedral : 4.776 46.360 2639 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.30 % Allowed : 23.33 % Favored : 73.37 % 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: -1.44 (0.17), residues: 2396 helix: 0.34 (0.14), residues: 1392 sheet: -1.20 (0.49), residues: 84 loop : -3.07 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 29 HIS 0.005 0.001 HIS B 157 PHE 0.020 0.001 PHE D 492 TYR 0.014 0.001 TYR A 554 ARG 0.003 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 401 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8302 (tt0) cc_final: 0.7935 (tt0) REVERT: A 80 GLU cc_start: 0.7246 (pm20) cc_final: 0.6792 (pm20) REVERT: A 127 ASN cc_start: 0.8881 (m110) cc_final: 0.8551 (m110) REVERT: A 144 SER cc_start: 0.9129 (p) cc_final: 0.8726 (t) REVERT: A 189 ILE cc_start: 0.8385 (mm) cc_final: 0.8176 (mm) REVERT: A 214 GLN cc_start: 0.8110 (tt0) cc_final: 0.7761 (tm-30) REVERT: A 305 GLN cc_start: 0.7990 (tt0) cc_final: 0.7462 (tm-30) REVERT: A 465 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8324 (mmm) REVERT: A 480 MET cc_start: 0.7563 (mtm) cc_final: 0.7153 (mmt) REVERT: A 492 PHE cc_start: 0.6981 (t80) cc_final: 0.6555 (t80) REVERT: A 496 MET cc_start: 0.6602 (ttp) cc_final: 0.6299 (tpp) REVERT: A 521 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.6651 (t-90) REVERT: A 522 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.5086 (p90) REVERT: A 595 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7474 (mm-40) REVERT: B 99 MET cc_start: 0.8296 (mmp) cc_final: 0.7981 (tmm) REVERT: B 144 SER cc_start: 0.9202 (p) cc_final: 0.8790 (t) REVERT: B 189 ILE cc_start: 0.8510 (mm) cc_final: 0.8212 (mm) REVERT: B 214 GLN cc_start: 0.7990 (tt0) cc_final: 0.7598 (tm-30) REVERT: B 259 MET cc_start: 0.8957 (mmp) cc_final: 0.8610 (mmp) REVERT: B 281 GLU cc_start: 0.7643 (tp30) cc_final: 0.7433 (mm-30) REVERT: B 305 GLN cc_start: 0.7955 (mt0) cc_final: 0.7709 (tm-30) REVERT: B 446 SER cc_start: 0.7118 (t) cc_final: 0.6695 (p) REVERT: B 465 MET cc_start: 0.8784 (mmm) cc_final: 0.8469 (mmm) REVERT: B 480 MET cc_start: 0.6926 (mmt) cc_final: 0.6623 (mtp) REVERT: B 490 MET cc_start: 0.7131 (tpt) cc_final: 0.6170 (mtt) REVERT: B 492 PHE cc_start: 0.6836 (t80) cc_final: 0.6439 (t80) REVERT: B 496 MET cc_start: 0.6536 (ttp) cc_final: 0.6257 (tpp) REVERT: B 521 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6161 (t-90) REVERT: B 553 MET cc_start: 0.8315 (mmm) cc_final: 0.8085 (tpt) REVERT: B 581 HIS cc_start: 0.5164 (t70) cc_final: 0.4904 (t70) REVERT: B 593 ARG cc_start: 0.7969 (mpt-90) cc_final: 0.7541 (ttm-80) REVERT: C 40 GLN cc_start: 0.8280 (tt0) cc_final: 0.7942 (tt0) REVERT: C 144 SER cc_start: 0.9110 (p) cc_final: 0.8695 (t) REVERT: C 189 ILE cc_start: 0.8454 (mm) cc_final: 0.8248 (mm) REVERT: C 214 GLN cc_start: 0.8028 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 305 GLN cc_start: 0.8048 (tp40) cc_final: 0.7179 (tm-30) REVERT: C 465 MET cc_start: 0.8704 (mmm) cc_final: 0.8430 (mmm) REVERT: C 490 MET cc_start: 0.6473 (tpt) cc_final: 0.5696 (mtt) REVERT: C 521 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.6094 (t-90) REVERT: C 553 MET cc_start: 0.7936 (mmm) cc_final: 0.7615 (tpp) REVERT: C 593 ARG cc_start: 0.8000 (mpt-90) cc_final: 0.7731 (tpp80) REVERT: C 633 GLU cc_start: 0.8245 (pt0) cc_final: 0.7914 (mt-10) REVERT: D 144 SER cc_start: 0.9221 (p) cc_final: 0.8783 (t) REVERT: D 214 GLN cc_start: 0.8133 (tt0) cc_final: 0.7662 (tm-30) REVERT: D 215 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6827 (mtt) REVERT: D 305 GLN cc_start: 0.7983 (mt0) cc_final: 0.7754 (tm-30) REVERT: D 308 ASP cc_start: 0.8413 (t70) cc_final: 0.8203 (t0) REVERT: D 446 SER cc_start: 0.7294 (t) cc_final: 0.6945 (p) REVERT: D 480 MET cc_start: 0.7618 (mtm) cc_final: 0.7130 (mmt) REVERT: D 496 MET cc_start: 0.6501 (ttp) cc_final: 0.6258 (tpp) REVERT: D 553 MET cc_start: 0.8011 (mmm) cc_final: 0.7675 (tpp) REVERT: D 593 ARG cc_start: 0.8038 (mpt-90) cc_final: 0.7829 (tpp80) REVERT: D 602 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8096 (ttt) outliers start: 69 outliers final: 39 residues processed: 450 average time/residue: 0.3032 time to fit residues: 214.6415 Evaluate side-chains 421 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 375 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 602 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 0.3980 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 40 GLN B 463 ASN C 96 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19788 Z= 0.172 Angle : 0.706 13.189 26868 Z= 0.332 Chirality : 0.044 0.326 3056 Planarity : 0.003 0.036 3396 Dihedral : 4.664 46.123 2639 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.11 % Allowed : 23.52 % Favored : 73.37 % 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: -1.36 (0.17), residues: 2396 helix: 0.38 (0.14), residues: 1408 sheet: -1.35 (0.48), residues: 84 loop : -3.00 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 29 HIS 0.003 0.001 HIS B 157 PHE 0.023 0.001 PHE D 492 TYR 0.019 0.001 TYR B 62 ARG 0.006 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 393 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8298 (tt0) cc_final: 0.7955 (tt0) REVERT: A 80 GLU cc_start: 0.7267 (pm20) cc_final: 0.6805 (pm20) REVERT: A 127 ASN cc_start: 0.8791 (m110) cc_final: 0.8469 (m110) REVERT: A 144 SER cc_start: 0.9149 (p) cc_final: 0.8755 (t) REVERT: A 189 ILE cc_start: 0.8277 (mm) cc_final: 0.8047 (mm) REVERT: A 214 GLN cc_start: 0.8098 (tt0) cc_final: 0.7739 (tm-30) REVERT: A 215 MET cc_start: 0.7891 (tpp) cc_final: 0.7404 (tpp) REVERT: A 305 GLN cc_start: 0.7996 (tt0) cc_final: 0.7455 (tm-30) REVERT: A 465 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (mmm) REVERT: A 480 MET cc_start: 0.7484 (mtm) cc_final: 0.7082 (mmt) REVERT: A 492 PHE cc_start: 0.7049 (t80) cc_final: 0.6564 (t80) REVERT: A 496 MET cc_start: 0.6736 (ttp) cc_final: 0.6423 (tpp) REVERT: A 521 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.6612 (t-90) REVERT: A 522 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.5242 (p90) REVERT: A 595 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7403 (mm-40) REVERT: B 99 MET cc_start: 0.8269 (mmp) cc_final: 0.7954 (tmm) REVERT: B 144 SER cc_start: 0.9211 (p) cc_final: 0.8810 (t) REVERT: B 175 SER cc_start: 0.7834 (t) cc_final: 0.7462 (t) REVERT: B 189 ILE cc_start: 0.8515 (mm) cc_final: 0.8191 (mm) REVERT: B 214 GLN cc_start: 0.7918 (tt0) cc_final: 0.7549 (tm-30) REVERT: B 259 MET cc_start: 0.8925 (mmp) cc_final: 0.8638 (mmp) REVERT: B 281 GLU cc_start: 0.7701 (tp30) cc_final: 0.7488 (mm-30) REVERT: B 305 GLN cc_start: 0.7938 (mt0) cc_final: 0.7724 (tm-30) REVERT: B 383 LEU cc_start: 0.8267 (tt) cc_final: 0.8038 (tp) REVERT: B 446 SER cc_start: 0.7204 (t) cc_final: 0.6677 (p) REVERT: B 490 MET cc_start: 0.7121 (tpt) cc_final: 0.6178 (mtt) REVERT: B 496 MET cc_start: 0.6645 (ttp) cc_final: 0.6342 (tpp) REVERT: B 553 MET cc_start: 0.8255 (mmm) cc_final: 0.8033 (tpt) REVERT: B 593 ARG cc_start: 0.7982 (mpt-90) cc_final: 0.7566 (ttm-80) REVERT: C 40 GLN cc_start: 0.8302 (tt0) cc_final: 0.7954 (tt0) REVERT: C 144 SER cc_start: 0.9140 (p) cc_final: 0.8731 (t) REVERT: C 164 GLU cc_start: 0.7199 (mp0) cc_final: 0.6918 (pm20) REVERT: C 214 GLN cc_start: 0.8053 (tt0) cc_final: 0.7633 (tm-30) REVERT: C 305 GLN cc_start: 0.8058 (tp40) cc_final: 0.7207 (tm-30) REVERT: C 446 SER cc_start: 0.6811 (t) cc_final: 0.6337 (p) REVERT: C 465 MET cc_start: 0.8674 (mmm) cc_final: 0.8399 (mmm) REVERT: C 490 MET cc_start: 0.6528 (tpt) cc_final: 0.5726 (mtt) REVERT: C 553 MET cc_start: 0.7894 (mmm) cc_final: 0.7640 (tpp) REVERT: C 593 ARG cc_start: 0.8036 (mpt-90) cc_final: 0.7689 (ttm-80) REVERT: C 595 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7510 (mm-40) REVERT: C 633 GLU cc_start: 0.8333 (pt0) cc_final: 0.8008 (mt-10) REVERT: D 144 SER cc_start: 0.9229 (p) cc_final: 0.8879 (t) REVERT: D 214 GLN cc_start: 0.8185 (tt0) cc_final: 0.7686 (tm-30) REVERT: D 215 MET cc_start: 0.7295 (ttm) cc_final: 0.6948 (mtt) REVERT: D 305 GLN cc_start: 0.7967 (mt0) cc_final: 0.7746 (tm-30) REVERT: D 308 ASP cc_start: 0.8430 (t70) cc_final: 0.8216 (t0) REVERT: D 446 SER cc_start: 0.7351 (t) cc_final: 0.6921 (p) REVERT: D 480 MET cc_start: 0.7582 (mtm) cc_final: 0.7164 (mmt) REVERT: D 553 MET cc_start: 0.7905 (mmm) cc_final: 0.7553 (tpp) REVERT: D 593 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7839 (tpp80) outliers start: 65 outliers final: 45 residues processed: 441 average time/residue: 0.2967 time to fit residues: 203.9858 Evaluate side-chains 421 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0980 chunk 92 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 463 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19788 Z= 0.167 Angle : 0.712 13.480 26868 Z= 0.332 Chirality : 0.044 0.294 3056 Planarity : 0.003 0.036 3396 Dihedral : 4.557 46.379 2639 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.44 % Allowed : 23.95 % Favored : 72.61 % 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: -1.26 (0.17), residues: 2396 helix: 0.43 (0.14), residues: 1412 sheet: -1.39 (0.47), residues: 84 loop : -2.93 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 29 HIS 0.003 0.001 HIS B 157 PHE 0.037 0.001 PHE D 492 TYR 0.018 0.001 TYR A 216 ARG 0.005 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 397 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7130 (mmt) cc_final: 0.5949 (mpp) REVERT: A 80 GLU cc_start: 0.7291 (pm20) cc_final: 0.7009 (pm20) REVERT: A 127 ASN cc_start: 0.8756 (m110) cc_final: 0.8425 (m110) REVERT: A 144 SER cc_start: 0.9192 (p) cc_final: 0.8819 (t) REVERT: A 164 GLU cc_start: 0.7569 (mp0) cc_final: 0.7243 (pm20) REVERT: A 214 GLN cc_start: 0.8121 (tt0) cc_final: 0.7769 (tm-30) REVERT: A 305 GLN cc_start: 0.7971 (tt0) cc_final: 0.7412 (tm-30) REVERT: A 465 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: A 480 MET cc_start: 0.7429 (mtm) cc_final: 0.7033 (mmt) REVERT: A 492 PHE cc_start: 0.7055 (t80) cc_final: 0.6601 (t80) REVERT: A 496 MET cc_start: 0.6679 (ttp) cc_final: 0.6347 (tpp) REVERT: A 521 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.6534 (t-90) REVERT: A 522 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.5165 (p90) REVERT: A 595 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7341 (mm-40) REVERT: A 602 MET cc_start: 0.8551 (ttp) cc_final: 0.8261 (ttp) REVERT: B 78 MET cc_start: 0.7208 (mmt) cc_final: 0.6564 (mpp) REVERT: B 99 MET cc_start: 0.8285 (mmp) cc_final: 0.7945 (tmm) REVERT: B 144 SER cc_start: 0.9173 (p) cc_final: 0.8761 (t) REVERT: B 189 ILE cc_start: 0.8435 (mm) cc_final: 0.8225 (mm) REVERT: B 214 GLN cc_start: 0.7930 (tt0) cc_final: 0.7570 (tm-30) REVERT: B 259 MET cc_start: 0.8912 (mmp) cc_final: 0.8650 (mmp) REVERT: B 281 GLU cc_start: 0.7717 (tp30) cc_final: 0.7498 (mm-30) REVERT: B 305 GLN cc_start: 0.7958 (mt0) cc_final: 0.7747 (tm-30) REVERT: B 362 ARG cc_start: 0.8883 (ppt170) cc_final: 0.8478 (ptt-90) REVERT: B 446 SER cc_start: 0.7219 (t) cc_final: 0.6626 (p) REVERT: B 490 MET cc_start: 0.7109 (tpt) cc_final: 0.6182 (mtt) REVERT: B 496 MET cc_start: 0.6648 (ttp) cc_final: 0.6388 (tpp) REVERT: B 521 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.6180 (t-90) REVERT: B 553 MET cc_start: 0.8200 (mmm) cc_final: 0.7965 (tpt) REVERT: B 595 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8196 (mt0) REVERT: C 78 MET cc_start: 0.7035 (mmt) cc_final: 0.5828 (mpp) REVERT: C 144 SER cc_start: 0.9167 (p) cc_final: 0.8768 (t) REVERT: C 164 GLU cc_start: 0.7144 (mp0) cc_final: 0.6675 (pm20) REVERT: C 214 GLN cc_start: 0.8142 (tt0) cc_final: 0.7667 (tm-30) REVERT: C 305 GLN cc_start: 0.8075 (tp40) cc_final: 0.7218 (tm-30) REVERT: C 354 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.2913 (ptt180) REVERT: C 446 SER cc_start: 0.6837 (t) cc_final: 0.6430 (p) REVERT: C 465 MET cc_start: 0.8637 (mmm) cc_final: 0.8304 (mmm) REVERT: C 490 MET cc_start: 0.6340 (tpt) cc_final: 0.5599 (mtt) REVERT: C 521 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.6123 (t-90) REVERT: C 553 MET cc_start: 0.7898 (mmm) cc_final: 0.7666 (tpp) REVERT: C 593 ARG cc_start: 0.8107 (mpt-90) cc_final: 0.7746 (ttm-80) REVERT: C 633 GLU cc_start: 0.8328 (pt0) cc_final: 0.8048 (mt-10) REVERT: D 144 SER cc_start: 0.9237 (p) cc_final: 0.8906 (t) REVERT: D 214 GLN cc_start: 0.8254 (tt0) cc_final: 0.7736 (tm-30) REVERT: D 215 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6948 (mtt) REVERT: D 305 GLN cc_start: 0.8002 (mt0) cc_final: 0.7782 (tm-30) REVERT: D 480 MET cc_start: 0.7576 (mtm) cc_final: 0.7203 (mmt) REVERT: D 492 PHE cc_start: 0.6660 (t80) cc_final: 0.6263 (t80) REVERT: D 496 MET cc_start: 0.6364 (ttp) cc_final: 0.6147 (tpp) REVERT: D 521 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.6242 (t-90) REVERT: D 553 MET cc_start: 0.7879 (mmm) cc_final: 0.7611 (tpp) REVERT: D 569 MET cc_start: 0.7558 (tpp) cc_final: 0.7304 (mmm) REVERT: D 593 ARG cc_start: 0.8080 (mpt-90) cc_final: 0.7866 (tpp80) outliers start: 72 outliers final: 41 residues processed: 451 average time/residue: 0.2924 time to fit residues: 208.4757 Evaluate side-chains 414 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 169 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 41 GLN B 463 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS C 425 HIS ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19788 Z= 0.174 Angle : 0.732 13.840 26868 Z= 0.340 Chirality : 0.044 0.387 3056 Planarity : 0.003 0.036 3396 Dihedral : 4.536 45.943 2639 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.77 % Allowed : 25.05 % Favored : 72.18 % 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: -1.19 (0.17), residues: 2396 helix: 0.45 (0.14), residues: 1416 sheet: -1.42 (0.48), residues: 84 loop : -2.82 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 29 HIS 0.003 0.001 HIS C 157 PHE 0.037 0.001 PHE D 492 TYR 0.016 0.001 TYR B 62 ARG 0.006 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 382 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7960 (tt0) REVERT: A 80 GLU cc_start: 0.7298 (pm20) cc_final: 0.6990 (pm20) REVERT: A 144 SER cc_start: 0.9195 (p) cc_final: 0.8821 (t) REVERT: A 164 GLU cc_start: 0.7670 (mp0) cc_final: 0.7304 (pm20) REVERT: A 175 SER cc_start: 0.8021 (t) cc_final: 0.7748 (t) REVERT: A 189 ILE cc_start: 0.8087 (mm) cc_final: 0.7846 (mm) REVERT: A 214 GLN cc_start: 0.8162 (tt0) cc_final: 0.7808 (tm-30) REVERT: A 215 MET cc_start: 0.7988 (tpp) cc_final: 0.7554 (tpp) REVERT: A 305 GLN cc_start: 0.7987 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 465 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8126 (mmm) REVERT: A 480 MET cc_start: 0.7484 (mtm) cc_final: 0.7149 (mmt) REVERT: A 492 PHE cc_start: 0.6989 (t80) cc_final: 0.6530 (t80) REVERT: A 496 MET cc_start: 0.6682 (ttp) cc_final: 0.6347 (tpp) REVERT: A 521 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.6565 (t-90) REVERT: A 522 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.5353 (p90) REVERT: A 595 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7347 (mm-40) REVERT: A 602 MET cc_start: 0.8536 (ttp) cc_final: 0.8246 (ttp) REVERT: B 78 MET cc_start: 0.6730 (mmt) cc_final: 0.6289 (mpp) REVERT: B 99 MET cc_start: 0.8295 (mmp) cc_final: 0.7930 (tmm) REVERT: B 144 SER cc_start: 0.9197 (p) cc_final: 0.8804 (t) REVERT: B 189 ILE cc_start: 0.8388 (mm) cc_final: 0.8152 (mm) REVERT: B 214 GLN cc_start: 0.7936 (tt0) cc_final: 0.7573 (tm-30) REVERT: B 259 MET cc_start: 0.8926 (mmp) cc_final: 0.8668 (mmp) REVERT: B 281 GLU cc_start: 0.7727 (tp30) cc_final: 0.7497 (mm-30) REVERT: B 305 GLN cc_start: 0.7960 (mt0) cc_final: 0.7750 (tm-30) REVERT: B 362 ARG cc_start: 0.8908 (ppt170) cc_final: 0.8493 (ptt-90) REVERT: B 446 SER cc_start: 0.6903 (t) cc_final: 0.6367 (p) REVERT: B 490 MET cc_start: 0.7073 (tpt) cc_final: 0.6171 (mtt) REVERT: B 496 MET cc_start: 0.6652 (ttp) cc_final: 0.6356 (tpp) REVERT: B 522 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.5204 (p90) REVERT: B 553 MET cc_start: 0.8209 (mmm) cc_final: 0.7977 (tpt) REVERT: B 593 ARG cc_start: 0.8039 (mpt-90) cc_final: 0.7624 (ttm-80) REVERT: B 595 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8173 (mt0) REVERT: C 40 GLN cc_start: 0.8743 (tm-30) cc_final: 0.7954 (tt0) REVERT: C 144 SER cc_start: 0.9188 (p) cc_final: 0.8800 (t) REVERT: C 164 GLU cc_start: 0.7324 (mp0) cc_final: 0.6758 (pm20) REVERT: C 214 GLN cc_start: 0.8189 (tt0) cc_final: 0.7699 (tm-30) REVERT: C 305 GLN cc_start: 0.8086 (tp40) cc_final: 0.7219 (tm-30) REVERT: C 354 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.2830 (ptt180) REVERT: C 446 SER cc_start: 0.6822 (t) cc_final: 0.6435 (p) REVERT: C 465 MET cc_start: 0.8617 (mmm) cc_final: 0.8266 (mmm) REVERT: C 490 MET cc_start: 0.6325 (tpt) cc_final: 0.5593 (mtt) REVERT: C 553 MET cc_start: 0.7865 (mmm) cc_final: 0.7362 (tpt) REVERT: C 593 ARG cc_start: 0.8117 (mpt-90) cc_final: 0.7740 (ttm-80) REVERT: C 595 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8000 (mm-40) REVERT: C 633 GLU cc_start: 0.8328 (pt0) cc_final: 0.8046 (mt-10) REVERT: D 144 SER cc_start: 0.9299 (p) cc_final: 0.8945 (t) REVERT: D 214 GLN cc_start: 0.8189 (tt0) cc_final: 0.7698 (tm-30) REVERT: D 215 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7027 (mtp) REVERT: D 305 GLN cc_start: 0.7999 (mt0) cc_final: 0.7757 (tm-30) REVERT: D 480 MET cc_start: 0.7620 (mtm) cc_final: 0.7132 (mmt) REVERT: D 496 MET cc_start: 0.6485 (ttp) cc_final: 0.6262 (tpp) REVERT: D 521 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.6237 (t-90) REVERT: D 553 MET cc_start: 0.7862 (mmm) cc_final: 0.7603 (tpp) REVERT: D 569 MET cc_start: 0.7522 (tpp) cc_final: 0.7231 (mmm) REVERT: D 593 ARG cc_start: 0.8154 (mpt-90) cc_final: 0.7924 (tpp80) outliers start: 58 outliers final: 41 residues processed: 422 average time/residue: 0.2917 time to fit residues: 192.8290 Evaluate side-chains 414 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 366 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 139 optimal weight: 0.0980 chunk 108 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 0.0980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 463 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19788 Z= 0.187 Angle : 0.745 13.344 26868 Z= 0.345 Chirality : 0.044 0.381 3056 Planarity : 0.003 0.035 3396 Dihedral : 4.495 45.847 2637 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.68 % Allowed : 25.29 % Favored : 72.04 % 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: -1.13 (0.17), residues: 2396 helix: 0.43 (0.14), residues: 1416 sheet: -0.12 (0.48), residues: 64 loop : -2.77 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 29 HIS 0.007 0.001 HIS C 227 PHE 0.044 0.001 PHE D 492 TYR 0.015 0.001 TYR B 62 ARG 0.006 0.000 ARG C 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8035 (tt0) REVERT: A 80 GLU cc_start: 0.7360 (pm20) cc_final: 0.7047 (pm20) REVERT: A 108 GLU cc_start: 0.7764 (pt0) cc_final: 0.7460 (pm20) REVERT: A 144 SER cc_start: 0.9205 (p) cc_final: 0.8836 (t) REVERT: A 164 GLU cc_start: 0.7736 (mp0) cc_final: 0.7468 (pm20) REVERT: A 175 SER cc_start: 0.8077 (t) cc_final: 0.7812 (t) REVERT: A 189 ILE cc_start: 0.8068 (mm) cc_final: 0.7835 (mm) REVERT: A 214 GLN cc_start: 0.8197 (tt0) cc_final: 0.7840 (tm-30) REVERT: A 305 GLN cc_start: 0.8019 (tt0) cc_final: 0.7460 (tm-30) REVERT: A 465 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: A 480 MET cc_start: 0.7423 (mtm) cc_final: 0.7117 (mmt) REVERT: A 492 PHE cc_start: 0.6953 (t80) cc_final: 0.6533 (t80) REVERT: A 496 MET cc_start: 0.6677 (ttp) cc_final: 0.6340 (tpp) REVERT: A 521 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.6563 (t-90) REVERT: A 522 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.5401 (p90) REVERT: A 595 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7345 (mm-40) REVERT: A 602 MET cc_start: 0.8565 (ttp) cc_final: 0.8264 (ttp) REVERT: B 78 MET cc_start: 0.6825 (mmt) cc_final: 0.6389 (mpp) REVERT: B 99 MET cc_start: 0.8285 (mmp) cc_final: 0.7926 (tmm) REVERT: B 144 SER cc_start: 0.9197 (p) cc_final: 0.8804 (t) REVERT: B 177 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8433 (mp0) REVERT: B 189 ILE cc_start: 0.8381 (mm) cc_final: 0.8143 (mm) REVERT: B 214 GLN cc_start: 0.8055 (tt0) cc_final: 0.7708 (tm-30) REVERT: B 281 GLU cc_start: 0.7758 (tp30) cc_final: 0.7548 (mm-30) REVERT: B 362 ARG cc_start: 0.8915 (ppt170) cc_final: 0.8530 (ptt-90) REVERT: B 446 SER cc_start: 0.6899 (t) cc_final: 0.6364 (p) REVERT: B 490 MET cc_start: 0.7065 (tpt) cc_final: 0.6170 (mtt) REVERT: B 496 MET cc_start: 0.6571 (ttp) cc_final: 0.6329 (tpp) REVERT: B 553 MET cc_start: 0.8092 (mmm) cc_final: 0.7675 (tpt) REVERT: B 593 ARG cc_start: 0.8035 (mpt-90) cc_final: 0.7601 (ttm-80) REVERT: B 595 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8178 (mt0) REVERT: C 40 GLN cc_start: 0.8754 (tm-30) cc_final: 0.7974 (tt0) REVERT: C 144 SER cc_start: 0.9189 (p) cc_final: 0.8800 (t) REVERT: C 164 GLU cc_start: 0.7379 (mp0) cc_final: 0.6629 (pm20) REVERT: C 175 SER cc_start: 0.8093 (t) cc_final: 0.7838 (t) REVERT: C 214 GLN cc_start: 0.8180 (tt0) cc_final: 0.7820 (tm-30) REVERT: C 305 GLN cc_start: 0.8104 (tp40) cc_final: 0.7223 (tm-30) REVERT: C 354 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.2780 (ptt180) REVERT: C 383 LEU cc_start: 0.8195 (tt) cc_final: 0.7969 (tp) REVERT: C 446 SER cc_start: 0.6834 (t) cc_final: 0.6442 (p) REVERT: C 465 MET cc_start: 0.8605 (mmm) cc_final: 0.8256 (mmm) REVERT: C 490 MET cc_start: 0.6361 (tpt) cc_final: 0.5607 (mtt) REVERT: C 553 MET cc_start: 0.7860 (mmm) cc_final: 0.7367 (tpt) REVERT: C 571 ASN cc_start: 0.6649 (m-40) cc_final: 0.6426 (m-40) REVERT: C 593 ARG cc_start: 0.8109 (mpt-90) cc_final: 0.7733 (ttm-80) REVERT: C 595 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7515 (mm-40) REVERT: C 633 GLU cc_start: 0.8330 (pt0) cc_final: 0.8043 (mt-10) REVERT: D 144 SER cc_start: 0.9307 (p) cc_final: 0.8948 (t) REVERT: D 214 GLN cc_start: 0.8219 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 215 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6977 (mtp) REVERT: D 305 GLN cc_start: 0.7962 (mt0) cc_final: 0.7715 (tm-30) REVERT: D 480 MET cc_start: 0.7544 (mtm) cc_final: 0.7169 (mmt) REVERT: D 492 PHE cc_start: 0.6598 (t80) cc_final: 0.6235 (t80) REVERT: D 496 MET cc_start: 0.6454 (ttp) cc_final: 0.6230 (tpp) REVERT: D 521 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.6282 (t-90) REVERT: D 553 MET cc_start: 0.7828 (mmm) cc_final: 0.7581 (tpp) REVERT: D 569 MET cc_start: 0.7550 (tpp) cc_final: 0.7251 (mmm) REVERT: D 593 ARG cc_start: 0.8162 (mpt-90) cc_final: 0.7936 (tpp80) outliers start: 56 outliers final: 44 residues processed: 416 average time/residue: 0.2016 time to fit residues: 132.9106 Evaluate side-chains 418 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 368 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 28 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 74 GLN B 463 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124375 restraints weight = 32021.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126515 restraints weight = 22501.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127998 restraints weight = 17922.666| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6713 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: