Starting phenix.real_space_refine on Wed Nov 19 01:00:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bob_7123/11_2025/6bob_7123.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bob_7123/11_2025/6bob_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 { model { file = "/net/cci-nas-00/data/ceres_data/6bob_7123/11_2025/6bob_7123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bob_7123/11_2025/6bob_7123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bob_7123/11_2025/6bob_7123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bob_7123/11_2025/6bob_7123.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: B, C, D Time building chain proxies: 4.60, per 1000 atoms: 0.24 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: 1.88 Conformation dependent library (CDL) restraints added in 891.5 milliseconds 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: 0.64 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: 3.18 Time building geometry restraints manager: 2.47 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: 0.06 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.540 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- 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= 0.328 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG B 262 TYR 0.022 0.003 TYR D 62 PHE 0.019 0.003 PHE D 530 TRP 0.023 0.003 TRP A 29 HIS 0.006 0.002 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00682 (19788) covalent geometry : angle 1.19823 (26868) hydrogen bonds : bond 0.30101 ( 844) hydrogen bonds : angle 9.58323 ( 2436) *********************** 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 : 0.724 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: 0.1530 time to fit residues: 165.6699 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 : 0.797 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 153 HIS A 206 GLN A 208 ASN A 217 ASN A 227 HIS A 257 HIS A 309 GLN A 357 ASN A 360 ASN A 463 ASN B 40 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 257 HIS B 309 GLN B 357 ASN B 360 ASN B 445 ASN B 463 ASN B 571 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 357 ASN D 360 ASN D 463 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130645 restraints weight = 32184.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131956 restraints weight = 23907.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132629 restraints weight = 18776.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132720 restraints weight = 17727.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132806 restraints weight = 17934.972| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19788 Z= 0.147 Angle : 0.745 12.110 26868 Z= 0.372 Chirality : 0.044 0.166 3056 Planarity : 0.005 0.038 3396 Dihedral : 6.006 46.713 2649 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.11 % Allowed : 15.01 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.15), residues: 2396 helix: -1.10 (0.12), residues: 1388 sheet: -0.38 (0.58), residues: 84 loop : -3.37 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 322 TYR 0.026 0.002 TYR B 62 PHE 0.025 0.001 PHE A 342 TRP 0.015 0.001 TRP B 612 HIS 0.010 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00321 (19788) covalent geometry : angle 0.74462 (26868) hydrogen bonds : bond 0.04737 ( 844) hydrogen bonds : angle 5.36244 ( 2436) *********************** 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 565 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 479 time to evaluate : 0.781 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: A 144 SER cc_start: 0.8753 (p) cc_final: 0.8173 (t) REVERT: A 366 LEU cc_start: 0.6720 (mp) cc_final: 0.6149 (tp) REVERT: A 433 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7452 (m-10) REVERT: A 595 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7953 (mm-40) REVERT: B 29 TRP cc_start: 0.6356 (t60) cc_final: 0.6144 (t60) REVERT: B 100 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6525 (pp20) REVERT: B 144 SER cc_start: 0.8832 (p) cc_final: 0.8221 (t) REVERT: B 180 ARG cc_start: 0.8393 (mmt90) cc_final: 0.8105 (mmt90) REVERT: B 329 CYS cc_start: 0.7105 (m) cc_final: 0.6587 (t) REVERT: B 463 ASN cc_start: 0.8740 (t160) cc_final: 0.8489 (t0) REVERT: B 521 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7224 (t-90) REVERT: B 576 MET cc_start: 0.8202 (mmt) cc_final: 0.7966 (mmt) REVERT: C 100 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6868 (pp20) REVERT: C 110 MET cc_start: 0.7667 (mtt) cc_final: 0.7453 (mtt) REVERT: C 144 SER cc_start: 0.8923 (p) cc_final: 0.8434 (t) REVERT: C 180 ARG cc_start: 0.8301 (mmt90) cc_final: 0.7983 (mmm-85) REVERT: C 463 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7867 (t0) REVERT: D 521 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7543 (t-90) REVERT: D 553 MET cc_start: 0.8335 (mmm) cc_final: 0.7850 (tpt) REVERT: D 593 ARG cc_start: 0.7977 (mpt-90) cc_final: 0.7754 (tpp80) outliers start: 86 outliers final: 35 residues processed: 538 average time/residue: 0.1343 time to fit residues: 113.6821 Evaluate side-chains 426 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 387 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 339 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 409 LEU 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 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 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 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 463 ASN Chi-restraints excluded: chain C residue 537 LEU 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 329 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 568 LEU 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 146 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 130 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 HIS A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 309 GLN A 445 ASN A 463 ASN A 521 HIS B 40 GLN B 84 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 309 GLN B 425 HIS B 521 HIS ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 96 GLN C 118 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 521 HIS D 40 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 425 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 521 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116044 restraints weight = 32754.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118120 restraints weight = 22972.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119513 restraints weight = 18296.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120260 restraints weight = 15808.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120979 restraints weight = 14469.420| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19788 Z= 0.224 Angle : 0.781 13.269 26868 Z= 0.393 Chirality : 0.047 0.178 3056 Planarity : 0.005 0.058 3396 Dihedral : 5.799 45.144 2641 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.78 % Allowed : 18.26 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.16), residues: 2396 helix: -0.45 (0.14), residues: 1384 sheet: -0.47 (0.54), residues: 84 loop : -3.21 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 322 TYR 0.018 0.002 TYR A 327 PHE 0.044 0.002 PHE B 492 TRP 0.016 0.002 TRP B 612 HIS 0.004 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00522 (19788) covalent geometry : angle 0.78061 (26868) hydrogen bonds : bond 0.04645 ( 844) hydrogen bonds : angle 5.22734 ( 2436) *********************** 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 533 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 433 time to evaluate : 0.674 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 144 SER cc_start: 0.8923 (p) cc_final: 0.8366 (t) REVERT: A 329 CYS cc_start: 0.7840 (m) cc_final: 0.7474 (m) REVERT: A 492 PHE cc_start: 0.8465 (t80) cc_final: 0.8105 (t80) REVERT: A 522 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.7366 (p90) REVERT: A 577 MET cc_start: 0.8009 (mmt) cc_final: 0.7782 (mmt) REVERT: A 602 MET cc_start: 0.8290 (ttp) cc_final: 0.8087 (ttp) REVERT: B 40 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7550 (mm110) REVERT: B 80 GLU cc_start: 0.7332 (pm20) cc_final: 0.6555 (pm20) REVERT: B 144 SER cc_start: 0.9012 (p) cc_final: 0.8454 (t) REVERT: B 222 TYR cc_start: 0.7806 (m-80) cc_final: 0.7414 (m-80) REVERT: B 463 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8767 (t0) REVERT: B 593 ARG cc_start: 0.7848 (mpt-90) cc_final: 0.7584 (ttm-80) REVERT: B 595 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8366 (mm-40) REVERT: C 144 SER cc_start: 0.8881 (p) cc_final: 0.8292 (t) REVERT: C 160 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7670 (pp) REVERT: C 161 TYR cc_start: 0.8870 (t80) cc_final: 0.8528 (t80) REVERT: C 490 MET cc_start: 0.7324 (mtt) cc_final: 0.6725 (tpt) REVERT: C 494 TRP cc_start: 0.8203 (m100) cc_final: 0.7898 (m100) REVERT: C 540 ILE cc_start: 0.9246 (pt) cc_final: 0.8590 (mt) REVERT: C 553 MET cc_start: 0.8117 (mmm) cc_final: 0.7601 (tpt) REVERT: C 593 ARG cc_start: 0.8025 (mpt-90) cc_final: 0.7799 (tpp80) REVERT: C 606 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7812 (mtmt) REVERT: D 144 SER cc_start: 0.8990 (p) cc_final: 0.8377 (t) REVERT: D 473 MET cc_start: 0.6163 (ptp) cc_final: 0.5854 (ptp) REVERT: D 492 PHE cc_start: 0.8399 (t80) cc_final: 0.7913 (t80) REVERT: D 553 MET cc_start: 0.8239 (mmm) cc_final: 0.7557 (tpt) REVERT: D 593 ARG cc_start: 0.8185 (mpt-90) cc_final: 0.7916 (tpp80) REVERT: D 595 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8252 (mm-40) outliers start: 100 outliers final: 54 residues processed: 499 average time/residue: 0.1421 time to fit residues: 109.9976 Evaluate side-chains 417 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 359 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 390 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 451 VAL 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 A residue 591 LEU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 40 GLN 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 313 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 495 LEU 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 160 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU 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 334 ILE Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 626 ASP 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 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 626 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 521 HIS B 571 ASN C 40 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 571 ASN D 96 GLN D 118 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119375 restraints weight = 32549.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121703 restraints weight = 21920.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123237 restraints weight = 17050.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124095 restraints weight = 14510.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124192 restraints weight = 13150.101| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19788 Z= 0.135 Angle : 0.709 11.755 26868 Z= 0.347 Chirality : 0.043 0.188 3056 Planarity : 0.004 0.048 3396 Dihedral : 5.281 46.125 2639 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.16 % Allowed : 20.60 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.17), residues: 2396 helix: -0.06 (0.14), residues: 1388 sheet: -0.75 (0.52), residues: 84 loop : -3.10 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.015 0.001 TYR C 622 PHE 0.046 0.001 PHE B 492 TRP 0.015 0.001 TRP B 29 HIS 0.006 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00305 (19788) covalent geometry : angle 0.70906 (26868) hydrogen bonds : bond 0.03758 ( 844) hydrogen bonds : angle 4.71330 ( 2436) *********************** 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 484 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 397 time to evaluate : 0.767 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: A 144 SER cc_start: 0.8875 (p) cc_final: 0.8316 (t) REVERT: A 329 CYS cc_start: 0.7605 (m) cc_final: 0.7251 (m) REVERT: A 492 PHE cc_start: 0.8335 (t80) cc_final: 0.8044 (t80) REVERT: A 521 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.7352 (t-90) REVERT: A 522 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.6932 (p90) REVERT: A 595 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8106 (mm-40) REVERT: B 144 SER cc_start: 0.8951 (p) cc_final: 0.8368 (t) REVERT: B 329 CYS cc_start: 0.7533 (m) cc_final: 0.7248 (m) REVERT: B 338 TYR cc_start: 0.9153 (t80) cc_final: 0.8913 (t80) REVERT: B 490 MET cc_start: 0.7685 (mtt) cc_final: 0.7449 (mtt) REVERT: B 521 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.7793 (t70) REVERT: B 553 MET cc_start: 0.8446 (mmm) cc_final: 0.8032 (tpt) REVERT: B 593 ARG cc_start: 0.7897 (mpt-90) cc_final: 0.7593 (ttm-80) REVERT: C 144 SER cc_start: 0.8930 (p) cc_final: 0.8372 (t) REVERT: C 161 TYR cc_start: 0.8792 (t80) cc_final: 0.8450 (t80) REVERT: C 540 ILE cc_start: 0.9186 (pt) cc_final: 0.8522 (mt) REVERT: C 553 MET cc_start: 0.8067 (mmm) cc_final: 0.7552 (tpp) REVERT: D 144 SER cc_start: 0.8929 (p) cc_final: 0.8305 (t) REVERT: D 177 GLU cc_start: 0.8202 (mp0) cc_final: 0.7700 (mp0) REVERT: D 492 PHE cc_start: 0.8368 (t80) cc_final: 0.7862 (t80) REVERT: D 553 MET cc_start: 0.8104 (mmm) cc_final: 0.7711 (tpp) REVERT: D 593 ARG cc_start: 0.8114 (mpt-90) cc_final: 0.7912 (tpp80) outliers start: 87 outliers final: 40 residues processed: 455 average time/residue: 0.1400 time to fit residues: 99.9183 Evaluate side-chains 407 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 364 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 465 MET Chi-restraints excluded: chain A residue 495 LEU 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 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 389 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 294 LEU Chi-restraints excluded: chain C residue 329 CYS 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 521 HIS Chi-restraints excluded: chain C residue 602 MET 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 389 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 572 LEU 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 79 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 463 ASN B 521 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 521 HIS D 84 HIS ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 521 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116838 restraints weight = 32604.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118908 restraints weight = 22254.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120445 restraints weight = 17545.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121430 restraints weight = 15003.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121875 restraints weight = 13545.944| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19788 Z= 0.157 Angle : 0.721 13.973 26868 Z= 0.350 Chirality : 0.044 0.201 3056 Planarity : 0.004 0.041 3396 Dihedral : 5.170 46.024 2639 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.83 % Allowed : 21.08 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2396 helix: 0.10 (0.14), residues: 1388 sheet: -1.10 (0.50), residues: 84 loop : -3.03 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 180 TYR 0.015 0.001 TYR C 622 PHE 0.036 0.002 PHE B 492 TRP 0.015 0.001 TRP C 612 HIS 0.020 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00364 (19788) covalent geometry : angle 0.72074 (26868) hydrogen bonds : bond 0.03823 ( 844) hydrogen bonds : angle 4.71179 ( 2436) *********************** 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 488 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 387 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8862 (p) cc_final: 0.8315 (t) REVERT: A 329 CYS cc_start: 0.7718 (m) cc_final: 0.7452 (m) REVERT: A 492 PHE cc_start: 0.8457 (t80) cc_final: 0.8190 (t80) REVERT: A 522 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.7132 (p90) REVERT: A 595 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8226 (mm-40) REVERT: B 144 SER cc_start: 0.8919 (p) cc_final: 0.8324 (t) REVERT: B 521 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8279 (t70) REVERT: B 522 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.6989 (p90) REVERT: B 553 MET cc_start: 0.8544 (mmm) cc_final: 0.8052 (tpt) REVERT: C 144 SER cc_start: 0.8809 (p) cc_final: 0.8208 (t) REVERT: C 161 TYR cc_start: 0.8812 (t80) cc_final: 0.8473 (t80) REVERT: C 177 GLU cc_start: 0.8173 (mp0) cc_final: 0.7704 (mp0) REVERT: C 522 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7114 (p90) REVERT: C 540 ILE cc_start: 0.9152 (pt) cc_final: 0.8543 (mt) REVERT: C 553 MET cc_start: 0.8042 (mmm) cc_final: 0.7621 (tpp) REVERT: D 144 SER cc_start: 0.8871 (p) cc_final: 0.8243 (t) REVERT: D 473 MET cc_start: 0.5901 (ptp) cc_final: 0.5685 (ptp) REVERT: D 492 PHE cc_start: 0.8455 (t80) cc_final: 0.7973 (t80) REVERT: D 522 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7227 (p90) REVERT: D 553 MET cc_start: 0.8116 (mmm) cc_final: 0.7737 (tpp) outliers start: 101 outliers final: 52 residues processed: 450 average time/residue: 0.1365 time to fit residues: 97.3417 Evaluate side-chains 415 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 358 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LEU 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 443 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 LEU 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 A residue 591 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 215 MET Chi-restraints excluded: chain B residue 294 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 344 MET Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU 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 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 LEU 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 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 522 PHE Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 626 ASP 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 329 CYS Chi-restraints excluded: chain D residue 389 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 519 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 572 LEU 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 102 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 463 ASN B 463 ASN B 521 HIS C 40 GLN C 96 GLN C 118 GLN C 445 ASN C 463 ASN D 122 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119355 restraints weight = 32402.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121629 restraints weight = 22037.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123063 restraints weight = 17154.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124096 restraints weight = 14635.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124471 restraints weight = 13225.255| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19788 Z= 0.129 Angle : 0.722 12.767 26868 Z= 0.345 Chirality : 0.045 0.275 3056 Planarity : 0.004 0.051 3396 Dihedral : 4.956 46.141 2639 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.30 % Allowed : 22.04 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2396 helix: 0.26 (0.14), residues: 1384 sheet: -1.25 (0.49), residues: 84 loop : -2.98 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 354 TYR 0.014 0.001 TYR A 554 PHE 0.053 0.001 PHE B 492 TRP 0.016 0.001 TRP D 29 HIS 0.012 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00289 (19788) covalent geometry : angle 0.72185 (26868) hydrogen bonds : bond 0.03624 ( 844) hydrogen bonds : angle 4.56343 ( 2436) *********************** 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 474 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 384 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8844 (p) cc_final: 0.8305 (t) REVERT: A 177 GLU cc_start: 0.8225 (mp0) cc_final: 0.7888 (mp0) REVERT: A 189 ILE cc_start: 0.8424 (mm) cc_final: 0.8164 (mm) REVERT: A 216 TYR cc_start: 0.7300 (t80) cc_final: 0.7060 (t80) REVERT: A 329 CYS cc_start: 0.7569 (m) cc_final: 0.7290 (m) REVERT: A 492 PHE cc_start: 0.8541 (t80) cc_final: 0.8172 (t80) REVERT: A 521 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.7546 (t-90) REVERT: A 595 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8163 (mm-40) REVERT: B 144 SER cc_start: 0.8896 (p) cc_final: 0.8303 (t) REVERT: B 175 SER cc_start: 0.7346 (t) cc_final: 0.7135 (t) REVERT: B 216 TYR cc_start: 0.7027 (t80) cc_final: 0.6788 (t80) REVERT: B 338 TYR cc_start: 0.9164 (t80) cc_final: 0.8945 (t80) REVERT: B 521 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.7994 (t70) REVERT: B 522 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.6637 (p90) REVERT: B 553 MET cc_start: 0.8525 (mmm) cc_final: 0.8317 (tpt) REVERT: C 144 SER cc_start: 0.8739 (p) cc_final: 0.8150 (t) REVERT: C 161 TYR cc_start: 0.8791 (t80) cc_final: 0.8472 (t80) REVERT: C 177 GLU cc_start: 0.7901 (mp0) cc_final: 0.7684 (mp0) REVERT: C 368 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: C 522 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.6932 (p90) REVERT: C 540 ILE cc_start: 0.9040 (pt) cc_final: 0.8501 (mt) REVERT: C 553 MET cc_start: 0.8065 (mmm) cc_final: 0.7685 (tpp) REVERT: D 144 SER cc_start: 0.8814 (p) cc_final: 0.8200 (t) REVERT: D 175 SER cc_start: 0.7639 (t) cc_final: 0.7342 (t) REVERT: D 473 MET cc_start: 0.6070 (ptp) cc_final: 0.5808 (ptp) REVERT: D 522 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7104 (p90) REVERT: D 553 MET cc_start: 0.8073 (mmm) cc_final: 0.7716 (tpp) outliers start: 90 outliers final: 49 residues processed: 447 average time/residue: 0.1383 time to fit residues: 97.6183 Evaluate side-chains 414 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 359 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 390 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 495 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 591 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 215 MET Chi-restraints excluded: chain B residue 219 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 389 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 96 GLN 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 227 HIS 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 368 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 522 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 197 ASN 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 522 PHE Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 114 optimal weight: 0.0470 chunk 4 optimal weight: 0.0970 chunk 150 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 305 GLN B 463 ASN C 40 GLN C 96 GLN C 305 GLN C 463 ASN D 206 GLN D 305 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121313 restraints weight = 32402.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123591 restraints weight = 21919.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125028 restraints weight = 17050.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126099 restraints weight = 14557.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126618 restraints weight = 13094.836| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19788 Z= 0.123 Angle : 0.729 14.673 26868 Z= 0.343 Chirality : 0.045 0.290 3056 Planarity : 0.004 0.039 3396 Dihedral : 4.815 46.260 2639 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.68 % Allowed : 24.04 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2396 helix: 0.29 (0.14), residues: 1396 sheet: 0.12 (0.50), residues: 64 loop : -2.90 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.014 0.001 TYR A 554 PHE 0.052 0.001 PHE B 492 TRP 0.015 0.001 TRP D 612 HIS 0.017 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00270 (19788) covalent geometry : angle 0.72923 (26868) hydrogen bonds : bond 0.03547 ( 844) hydrogen bonds : angle 4.50599 ( 2436) *********************** 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 470 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 393 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8856 (m110) cc_final: 0.8649 (m110) REVERT: A 144 SER cc_start: 0.8769 (p) cc_final: 0.8211 (t) REVERT: A 177 GLU cc_start: 0.8028 (mp0) cc_final: 0.7761 (mp0) REVERT: A 189 ILE cc_start: 0.8355 (mm) cc_final: 0.8107 (mm) REVERT: A 222 TYR cc_start: 0.7727 (m-80) cc_final: 0.7405 (m-10) REVERT: A 492 PHE cc_start: 0.8522 (t80) cc_final: 0.8178 (t80) REVERT: A 521 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.7396 (t-90) REVERT: A 522 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.6954 (p90) REVERT: A 595 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8124 (mm-40) REVERT: A 602 MET cc_start: 0.8373 (ttp) cc_final: 0.8165 (ttp) REVERT: B 40 GLN cc_start: 0.7885 (mm110) cc_final: 0.7561 (mm110) REVERT: B 144 SER cc_start: 0.8768 (p) cc_final: 0.8158 (t) REVERT: B 175 SER cc_start: 0.7570 (t) cc_final: 0.7333 (t) REVERT: B 473 MET cc_start: 0.5835 (ptp) cc_final: 0.5594 (ptp) REVERT: B 490 MET cc_start: 0.7635 (mtt) cc_final: 0.6674 (tpt) REVERT: B 521 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7795 (t-90) REVERT: B 522 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.6675 (p90) REVERT: B 553 MET cc_start: 0.8492 (mmm) cc_final: 0.8256 (tpt) REVERT: C 144 SER cc_start: 0.8723 (p) cc_final: 0.8142 (t) REVERT: C 177 GLU cc_start: 0.7888 (mp0) cc_final: 0.7601 (mp0) REVERT: C 522 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.6862 (p90) REVERT: C 540 ILE cc_start: 0.8991 (pt) cc_final: 0.8466 (mt) REVERT: C 553 MET cc_start: 0.8023 (mmm) cc_final: 0.7694 (tpp) REVERT: D 144 SER cc_start: 0.8833 (p) cc_final: 0.8232 (t) REVERT: D 175 SER cc_start: 0.7764 (t) cc_final: 0.7329 (t) REVERT: D 490 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7229 (mtt) REVERT: D 553 MET cc_start: 0.7980 (mmm) cc_final: 0.7638 (tpp) outliers start: 77 outliers final: 45 residues processed: 443 average time/residue: 0.1257 time to fit residues: 88.9624 Evaluate side-chains 413 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 362 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 296 VAL 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 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 389 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 572 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 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 389 LEU Chi-restraints excluded: chain C residue 522 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 626 ASP 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 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 308 ASP 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 474 LEU Chi-restraints excluded: chain D residue 490 MET 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 18 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.0050 chunk 158 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 B 571 ASN C 41 GLN C 463 ASN D 84 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120509 restraints weight = 32288.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122657 restraints weight = 21716.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124109 restraints weight = 16952.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124959 restraints weight = 14513.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125696 restraints weight = 13149.974| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19788 Z= 0.135 Angle : 0.764 15.111 26868 Z= 0.355 Chirality : 0.046 0.356 3056 Planarity : 0.004 0.039 3396 Dihedral : 4.731 45.952 2637 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.35 % Allowed : 24.90 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2396 helix: 0.32 (0.14), residues: 1396 sheet: 0.03 (0.50), residues: 64 loop : -2.92 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.013 0.001 TYR A 554 PHE 0.056 0.002 PHE B 492 TRP 0.014 0.001 TRP D 612 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00311 (19788) covalent geometry : angle 0.76363 (26868) hydrogen bonds : bond 0.03635 ( 844) hydrogen bonds : angle 4.54453 ( 2436) *********************** 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 448 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 378 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8797 (m110) cc_final: 0.8578 (m110) REVERT: A 144 SER cc_start: 0.8791 (p) cc_final: 0.8248 (t) REVERT: A 189 ILE cc_start: 0.8359 (mm) cc_final: 0.8092 (mm) REVERT: A 492 PHE cc_start: 0.8552 (t80) cc_final: 0.8190 (t80) REVERT: A 521 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.7447 (t-90) REVERT: A 522 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.7910 (p90) REVERT: A 595 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8123 (mm-40) REVERT: A 602 MET cc_start: 0.8388 (ttp) cc_final: 0.8150 (ttp) REVERT: B 144 SER cc_start: 0.8710 (p) cc_final: 0.8054 (t) REVERT: B 175 SER cc_start: 0.7541 (t) cc_final: 0.7197 (t) REVERT: B 383 LEU cc_start: 0.8563 (tt) cc_final: 0.8188 (tp) REVERT: B 490 MET cc_start: 0.7641 (mtt) cc_final: 0.6660 (tpt) REVERT: B 521 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: B 522 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.6779 (p90) REVERT: B 553 MET cc_start: 0.8504 (mmm) cc_final: 0.8248 (tpt) REVERT: C 144 SER cc_start: 0.8713 (p) cc_final: 0.8100 (t) REVERT: C 368 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: C 522 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7154 (p90) REVERT: C 540 ILE cc_start: 0.8985 (pt) cc_final: 0.8460 (mt) REVERT: C 553 MET cc_start: 0.8078 (mmm) cc_final: 0.7774 (tpp) REVERT: C 571 ASN cc_start: 0.8030 (m110) cc_final: 0.7642 (m-40) REVERT: D 144 SER cc_start: 0.8819 (p) cc_final: 0.8225 (t) REVERT: D 490 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: D 522 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.7043 (p90) REVERT: D 553 MET cc_start: 0.8046 (mmm) cc_final: 0.7721 (tpp) outliers start: 70 outliers final: 47 residues processed: 425 average time/residue: 0.1259 time to fit residues: 85.8305 Evaluate side-chains 418 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 LEU 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 A residue 591 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 389 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 572 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 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 339 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 522 PHE 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 215 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 280 THR 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 454 SER Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 522 PHE 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 154 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 161 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 463 ASN B 122 HIS B 305 GLN B 463 ASN C 305 GLN C 463 ASN D 305 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121857 restraints weight = 32317.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124114 restraints weight = 22030.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125672 restraints weight = 17187.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126700 restraints weight = 14562.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127190 restraints weight = 13088.921| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19788 Z= 0.126 Angle : 0.768 14.396 26868 Z= 0.353 Chirality : 0.045 0.333 3056 Planarity : 0.004 0.043 3396 Dihedral : 4.656 46.044 2637 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.30 % Allowed : 25.43 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2396 helix: 0.35 (0.14), residues: 1396 sheet: 0.07 (0.50), residues: 64 loop : -2.86 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 354 TYR 0.013 0.001 TYR A 554 PHE 0.052 0.001 PHE B 492 TRP 0.013 0.001 TRP D 612 HIS 0.003 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00283 (19788) covalent geometry : angle 0.76805 (26868) hydrogen bonds : bond 0.03622 ( 844) hydrogen bonds : angle 4.50217 ( 2436) *********************** 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 462 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 393 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8726 (p) cc_final: 0.8182 (t) REVERT: A 222 TYR cc_start: 0.7553 (m-80) cc_final: 0.7350 (m-10) REVERT: A 492 PHE cc_start: 0.8507 (t80) cc_final: 0.8147 (t80) REVERT: A 521 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7362 (t-90) REVERT: A 522 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.6926 (p90) REVERT: A 595 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8182 (mm-40) REVERT: A 602 MET cc_start: 0.8363 (ttp) cc_final: 0.8078 (ttp) REVERT: B 144 SER cc_start: 0.8688 (p) cc_final: 0.8036 (t) REVERT: B 175 SER cc_start: 0.7389 (t) cc_final: 0.6976 (t) REVERT: B 354 ARG cc_start: 0.5371 (OUTLIER) cc_final: 0.3218 (ptt180) REVERT: B 362 ARG cc_start: 0.7892 (ppt170) cc_final: 0.7626 (ptt-90) REVERT: B 383 LEU cc_start: 0.8592 (tt) cc_final: 0.8200 (tp) REVERT: B 490 MET cc_start: 0.7620 (mtt) cc_final: 0.6677 (tpt) REVERT: B 521 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.7797 (t-90) REVERT: B 553 MET cc_start: 0.8447 (mmm) cc_final: 0.8185 (tpt) REVERT: B 571 ASN cc_start: 0.8272 (m110) cc_final: 0.8031 (m-40) REVERT: C 144 SER cc_start: 0.8737 (p) cc_final: 0.8137 (t) REVERT: C 368 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: C 383 LEU cc_start: 0.8475 (tt) cc_final: 0.8110 (tp) REVERT: C 522 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7106 (p90) REVERT: C 540 ILE cc_start: 0.8952 (pt) cc_final: 0.8425 (mt) REVERT: C 553 MET cc_start: 0.8121 (mmm) cc_final: 0.7777 (tpp) REVERT: C 571 ASN cc_start: 0.8071 (m110) cc_final: 0.7737 (m-40) REVERT: C 595 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8057 (mm-40) REVERT: D 144 SER cc_start: 0.8798 (p) cc_final: 0.8201 (t) REVERT: D 490 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7206 (mtt) REVERT: D 521 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.7481 (t-90) REVERT: D 522 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.6937 (p90) REVERT: D 553 MET cc_start: 0.7950 (mmm) cc_final: 0.7633 (tpp) outliers start: 69 outliers final: 42 residues processed: 436 average time/residue: 0.1326 time to fit residues: 91.5903 Evaluate side-chains 416 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 451 VAL 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 A residue 612 TRP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 296 VAL 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 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 116 GLU 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 366 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 522 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 626 ASP 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 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 280 THR 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 454 SER Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 522 PHE 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 178 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 11 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 463 ASN B 463 ASN C 122 HIS C 463 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120919 restraints weight = 32404.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123010 restraints weight = 22425.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124449 restraints weight = 17689.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125261 restraints weight = 15155.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125424 restraints weight = 13794.618| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19788 Z= 0.140 Angle : 0.791 14.443 26868 Z= 0.367 Chirality : 0.046 0.317 3056 Planarity : 0.004 0.039 3396 Dihedral : 4.681 45.744 2637 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.15 % Allowed : 25.67 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.17), residues: 2396 helix: 0.34 (0.14), residues: 1388 sheet: -0.07 (0.49), residues: 64 loop : -2.66 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.019 0.001 TYR A 554 PHE 0.046 0.002 PHE B 492 TRP 0.014 0.001 TRP D 612 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00326 (19788) covalent geometry : angle 0.79141 (26868) hydrogen bonds : bond 0.03729 ( 844) hydrogen bonds : angle 4.56718 ( 2436) ********************** 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 431 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 365 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8774 (m110) cc_final: 0.8557 (m110) REVERT: A 144 SER cc_start: 0.8724 (p) cc_final: 0.8183 (t) REVERT: A 492 PHE cc_start: 0.8423 (t80) cc_final: 0.8064 (t80) REVERT: A 521 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.7387 (t-90) REVERT: A 522 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8266 (p90) REVERT: A 595 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8218 (mm-40) REVERT: A 602 MET cc_start: 0.8352 (ttp) cc_final: 0.8046 (ttp) REVERT: B 144 SER cc_start: 0.8691 (p) cc_final: 0.8081 (t) REVERT: B 175 SER cc_start: 0.7402 (t) cc_final: 0.7154 (t) REVERT: B 354 ARG cc_start: 0.5155 (OUTLIER) cc_final: 0.3004 (ptt180) REVERT: B 358 ARG cc_start: 0.7249 (ptp-170) cc_final: 0.7015 (ptp-170) REVERT: B 362 ARG cc_start: 0.7930 (ppt170) cc_final: 0.7660 (ptt-90) REVERT: B 490 MET cc_start: 0.7722 (mtt) cc_final: 0.6582 (tpt) REVERT: B 492 PHE cc_start: 0.8162 (t80) cc_final: 0.7787 (t80) REVERT: B 521 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.7627 (t-90) REVERT: B 522 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.6919 (p90) REVERT: B 553 MET cc_start: 0.8446 (mmm) cc_final: 0.8203 (tpt) REVERT: B 581 HIS cc_start: 0.5988 (t70) cc_final: 0.5484 (t70) REVERT: C 144 SER cc_start: 0.8695 (p) cc_final: 0.8070 (t) REVERT: C 383 LEU cc_start: 0.8516 (tt) cc_final: 0.8144 (tp) REVERT: C 522 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7313 (p90) REVERT: C 540 ILE cc_start: 0.8981 (pt) cc_final: 0.8468 (mt) REVERT: C 553 MET cc_start: 0.8022 (mmm) cc_final: 0.7687 (tpp) REVERT: D 144 SER cc_start: 0.8787 (p) cc_final: 0.8194 (t) REVERT: D 522 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7225 (p90) REVERT: D 553 MET cc_start: 0.7928 (mmm) cc_final: 0.7620 (tpp) outliers start: 66 outliers final: 46 residues processed: 409 average time/residue: 0.1288 time to fit residues: 83.9946 Evaluate side-chains 412 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 451 VAL 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 A residue 550 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 294 LEU 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 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 116 GLU Chi-restraints excluded: chain C residue 197 ASN 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 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 522 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 200 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 280 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 522 PHE 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 194 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 96 GLN A 305 GLN A 463 ASN B 305 GLN B 463 ASN B 521 HIS B 581 HIS C 305 GLN C 463 ASN C 521 HIS C 581 HIS D 305 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 521 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116652 restraints weight = 32769.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118750 restraints weight = 23081.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120150 restraints weight = 18321.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121093 restraints weight = 15780.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121535 restraints weight = 14322.597| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19788 Z= 0.171 Angle : 0.810 13.795 26868 Z= 0.378 Chirality : 0.047 0.305 3056 Planarity : 0.004 0.040 3396 Dihedral : 4.862 45.292 2637 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.25 % Allowed : 26.10 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2396 helix: 0.18 (0.14), residues: 1396 sheet: -0.35 (0.47), residues: 64 loop : -2.52 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.017 0.002 TYR A 554 PHE 0.052 0.002 PHE C 492 TRP 0.018 0.002 TRP D 612 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00405 (19788) covalent geometry : angle 0.80960 (26868) hydrogen bonds : bond 0.04035 ( 844) hydrogen bonds : angle 4.72155 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.83 seconds wall clock time: 57 minutes 44.02 seconds (3464.02 seconds total)