Starting phenix.real_space_refine on Sun Sep 29 15:53:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/09_2024/3j9c_6224.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/09_2024/3j9c_6224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/09_2024/3j9c_6224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/09_2024/3j9c_6224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/09_2024/3j9c_6224.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/09_2024/3j9c_6224.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 14504 2.51 5 N 4046 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23296 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3326 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 7.84, per 1000 atoms: 0.34 Number of scatterers: 23296 At special positions: 0 Unit cell: (143.36, 140.8, 199.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4697 8.00 N 4046 7.00 C 14504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 2.9 seconds 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 63 sheets defined 20.8% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 578 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.610A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 578 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 578 " --> pdb=" O TYR D 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Proline residue: E 482 - end of helix Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU E 578 " --> pdb=" O TYR E 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 Processing helix chain 'F' and resid 555 through 569 Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 578 " --> pdb=" O TYR F 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 578 " --> pdb=" O TYR G 575 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=2, first strand: chain 'A' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL A 264 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 367 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET A 266 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A 365 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 268 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 276 through 299 Processing sheet with id=5, first strand: chain 'A' and resid 302 through 311 Processing sheet with id=6, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN A 376 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN A 458 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 454 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER A 382 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR A 452 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 384 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 450 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=8, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=10, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=11, first strand: chain 'B' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL B 264 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 367 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET B 266 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 365 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 268 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 276 through 299 Processing sheet with id=14, first strand: chain 'B' and resid 302 through 311 Processing sheet with id=15, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN B 376 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN B 458 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 454 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER B 382 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR B 452 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 384 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 450 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=17, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=19, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=20, first strand: chain 'C' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL C 264 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 367 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET C 266 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 365 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 268 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 276 through 299 Processing sheet with id=23, first strand: chain 'C' and resid 302 through 311 Processing sheet with id=24, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN C 376 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN C 458 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 454 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER C 382 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C 452 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 384 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 450 " --> pdb=" O VAL C 384 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=26, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=28, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=29, first strand: chain 'D' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL D 264 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 367 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET D 266 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG D 365 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 268 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'D' and resid 276 through 299 Processing sheet with id=32, first strand: chain 'D' and resid 302 through 311 Processing sheet with id=33, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN D 376 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN D 458 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 454 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER D 382 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR D 452 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 384 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 450 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'D' and resid 460 through 462 Processing sheet with id=35, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=37, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=38, first strand: chain 'E' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL E 264 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E 367 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET E 266 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG E 365 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 268 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'E' and resid 276 through 299 Processing sheet with id=41, first strand: chain 'E' and resid 302 through 311 Processing sheet with id=42, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN E 376 " --> pdb=" O ASN E 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN E 458 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN E 454 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER E 382 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR E 452 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL E 384 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU E 450 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=44, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=46, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=47, first strand: chain 'F' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL F 264 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 367 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET F 266 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG F 365 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 268 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'F' and resid 276 through 299 Processing sheet with id=50, first strand: chain 'F' and resid 302 through 311 Processing sheet with id=51, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN F 376 " --> pdb=" O ASN F 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN F 458 " --> pdb=" O ASN F 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN F 454 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER F 382 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR F 452 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 384 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU F 450 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'F' and resid 460 through 462 Processing sheet with id=53, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=55, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=56, first strand: chain 'G' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'G' and resid 276 through 299 Processing sheet with id=59, first strand: chain 'G' and resid 302 through 311 Processing sheet with id=60, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN G 376 " --> pdb=" O ASN G 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN G 458 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN G 454 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER G 382 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR G 452 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL G 384 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU G 450 " --> pdb=" O VAL G 384 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'G' and resid 460 through 462 Processing sheet with id=62, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'G' and resid 541 through 542 805 hydrogen bonds defined for protein. 2184 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: 7.53 Time building geometry restraints manager: 5.88 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: 7766 1.34 - 1.45: 2866 1.45 - 1.57: 13000 1.57 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 23709 Sorted by residual: bond pdb=" CA LYS F 444 " pdb=" C LYS F 444 " ideal model delta sigma weight residual 1.523 1.606 -0.082 1.34e-02 5.57e+03 3.78e+01 bond pdb=" CA LYS D 444 " pdb=" C LYS D 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.75e+01 bond pdb=" CA LYS E 444 " pdb=" C LYS E 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS G 444 " pdb=" C LYS G 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS A 444 " pdb=" C LYS A 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.72e+01 ... (remaining 23704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 30274 2.17 - 4.33: 1721 4.33 - 6.50: 212 6.50 - 8.67: 14 8.67 - 10.83: 7 Bond angle restraints: 32228 Sorted by residual: angle pdb=" C ALA G 417 " pdb=" N PRO G 418 " pdb=" CA PRO G 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA B 417 " pdb=" N PRO B 418 " pdb=" CA PRO B 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA C 417 " pdb=" N PRO C 418 " pdb=" CA PRO C 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.96e+01 angle pdb=" C ALA A 417 " pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C ALA E 417 " pdb=" N PRO E 418 " pdb=" CA PRO E 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.94e+01 ... (remaining 32223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 12749 13.72 - 27.44: 1069 27.44 - 41.16: 378 41.16 - 54.88: 189 54.88 - 68.60: 84 Dihedral angle restraints: 14469 sinusoidal: 5768 harmonic: 8701 Sorted by residual: dihedral pdb=" CA SER D 413 " pdb=" C SER D 413 " pdb=" N LYS D 414 " pdb=" CA LYS D 414 " ideal model delta harmonic sigma weight residual 180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 413 " pdb=" C SER G 413 " pdb=" N LYS G 414 " pdb=" CA LYS G 414 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER B 413 " pdb=" C SER B 413 " pdb=" N LYS B 414 " pdb=" CA LYS B 414 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 14466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2893 0.050 - 0.100: 610 0.100 - 0.150: 172 0.150 - 0.200: 7 0.200 - 0.249: 14 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CA LYS E 444 " pdb=" N LYS E 444 " pdb=" C LYS E 444 " pdb=" CB LYS E 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS D 444 " pdb=" N LYS D 444 " pdb=" C LYS D 444 " pdb=" CB LYS D 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLN D 543 " pdb=" N GLN D 543 " pdb=" C GLN D 543 " pdb=" CB GLN D 543 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3693 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 378 " 0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO F 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 379 " 0.024 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6067 2.80 - 3.33: 21651 3.33 - 3.85: 40623 3.85 - 4.38: 48842 4.38 - 4.90: 82490 Nonbonded interactions: 199673 Sorted by model distance: nonbonded pdb=" O ILE C 183 " pdb="CA CA C 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE F 183 " pdb="CA CA F 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE E 183 " pdb="CA CA E 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE D 183 " pdb="CA CA D 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE A 183 " pdb="CA CA A 801 " model vdw 2.277 2.510 ... (remaining 199668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 43.310 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.005 0.082 23709 Z= 0.353 Angle : 1.112 10.831 32228 Z= 0.744 Chirality : 0.047 0.249 3696 Planarity : 0.004 0.043 4249 Dihedral : 14.410 68.597 8813 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.13 % Allowed : 8.27 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2947 helix: -1.67 (0.20), residues: 497 sheet: -0.98 (0.15), residues: 1001 loop : 0.51 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 226 HIS 0.003 0.001 HIS D 263 PHE 0.011 0.001 PHE D 493 TYR 0.013 0.002 TYR B 456 ARG 0.003 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 600 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6849 (mt0) cc_final: 0.6557 (mm110) REVERT: A 287 ARG cc_start: 0.6325 (mtt90) cc_final: 0.5455 (ttp-170) REVERT: A 291 LYS cc_start: 0.6378 (tptt) cc_final: 0.5327 (tmtt) REVERT: A 330 SER cc_start: 0.4698 (OUTLIER) cc_final: 0.4233 (p) REVERT: A 334 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6509 (mt) REVERT: A 343 GLU cc_start: 0.7844 (tt0) cc_final: 0.7613 (tt0) REVERT: A 344 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.6822 (ttp80) REVERT: A 348 GLU cc_start: 0.7973 (tt0) cc_final: 0.7746 (pt0) REVERT: A 350 MET cc_start: 0.8690 (mmm) cc_final: 0.7772 (ttp) REVERT: A 387 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: A 388 ASN cc_start: 0.8794 (p0) cc_final: 0.8302 (p0) REVERT: A 404 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 434 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8578 (ttp) REVERT: A 436 TYR cc_start: 0.8663 (t80) cc_final: 0.8337 (t80) REVERT: A 441 GLU cc_start: 0.8347 (tt0) cc_final: 0.7965 (mt-10) REVERT: A 447 GLN cc_start: 0.7028 (mt0) cc_final: 0.6791 (mp10) REVERT: A 465 GLU cc_start: 0.9131 (tt0) cc_final: 0.8657 (mm-30) REVERT: A 470 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8409 (ptp90) REVERT: A 486 GLU cc_start: 0.9036 (tp30) cc_final: 0.8790 (mm-30) REVERT: A 542 TYR cc_start: 0.8932 (t80) cc_final: 0.8319 (t80) REVERT: A 579 ASP cc_start: 0.8595 (p0) cc_final: 0.8303 (t0) REVERT: A 580 LYS cc_start: 0.8917 (mttp) cc_final: 0.8653 (mptt) REVERT: A 586 LYS cc_start: 0.8869 (mttm) cc_final: 0.8294 (mtpt) REVERT: A 595 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7417 (mtm180) REVERT: B 212 GLU cc_start: 0.8218 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 263 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8750 (p90) REVERT: B 285 GLN cc_start: 0.6923 (mt0) cc_final: 0.6677 (mm-40) REVERT: B 287 ARG cc_start: 0.6382 (mtt90) cc_final: 0.5504 (ttp-170) REVERT: B 291 LYS cc_start: 0.6358 (tptt) cc_final: 0.6106 (tmtm) REVERT: B 330 SER cc_start: 0.5150 (OUTLIER) cc_final: 0.4812 (p) REVERT: B 334 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6497 (mt) REVERT: B 344 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6430 (tmt170) REVERT: B 348 GLU cc_start: 0.8094 (tt0) cc_final: 0.7795 (pt0) REVERT: B 350 MET cc_start: 0.8513 (mmm) cc_final: 0.7413 (pp-130) REVERT: B 387 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8280 (tmmt) REVERT: B 403 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9079 (mt0) REVERT: B 404 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 414 LYS cc_start: 0.9060 (tptt) cc_final: 0.8793 (tppp) REVERT: B 434 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8726 (ttp) REVERT: B 436 TYR cc_start: 0.8613 (t80) cc_final: 0.8364 (t80) REVERT: B 441 GLU cc_start: 0.8208 (tt0) cc_final: 0.7619 (tp30) REVERT: B 446 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7124 (tptp) REVERT: B 447 GLN cc_start: 0.7238 (mt0) cc_final: 0.6675 (mp10) REVERT: B 462 TYR cc_start: 0.8981 (t80) cc_final: 0.8675 (t80) REVERT: B 465 GLU cc_start: 0.9093 (tt0) cc_final: 0.8583 (mm-30) REVERT: B 470 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8432 (mmm160) REVERT: B 500 LEU cc_start: 0.8730 (mt) cc_final: 0.8526 (mm) REVERT: B 545 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8032 (ttpp) REVERT: B 560 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8026 (tp40) REVERT: B 579 ASP cc_start: 0.8446 (p0) cc_final: 0.8124 (t0) REVERT: B 595 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7845 (mtm180) REVERT: C 285 GLN cc_start: 0.6860 (mt0) cc_final: 0.6548 (mm-40) REVERT: C 287 ARG cc_start: 0.6458 (mtt90) cc_final: 0.5597 (ttp-110) REVERT: C 291 LYS cc_start: 0.5830 (tptt) cc_final: 0.5430 (tttm) REVERT: C 330 SER cc_start: 0.4677 (OUTLIER) cc_final: 0.4134 (p) REVERT: C 344 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.6957 (ttp80) REVERT: C 350 MET cc_start: 0.8618 (mmm) cc_final: 0.7502 (tmt) REVERT: C 381 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8727 (p) REVERT: C 387 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (ttpp) REVERT: C 404 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8658 (tp) REVERT: C 434 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8743 (ttp) REVERT: C 436 TYR cc_start: 0.8803 (t80) cc_final: 0.8467 (t80) REVERT: C 441 GLU cc_start: 0.8416 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 447 GLN cc_start: 0.7330 (mt0) cc_final: 0.6789 (mp10) REVERT: C 465 GLU cc_start: 0.9147 (tt0) cc_final: 0.8642 (mm-30) REVERT: C 470 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8494 (ptm160) REVERT: C 521 MET cc_start: 0.8982 (tpp) cc_final: 0.8744 (tpp) REVERT: C 539 ASN cc_start: 0.7196 (m110) cc_final: 0.6955 (p0) REVERT: C 579 ASP cc_start: 0.8471 (p0) cc_final: 0.8186 (t0) REVERT: C 586 LYS cc_start: 0.8744 (mttm) cc_final: 0.8352 (mtpt) REVERT: C 587 MET cc_start: 0.8769 (mtt) cc_final: 0.8491 (mtp) REVERT: D 285 GLN cc_start: 0.7118 (mt0) cc_final: 0.6693 (mm-40) REVERT: D 287 ARG cc_start: 0.6525 (mtt90) cc_final: 0.5667 (ttp-110) REVERT: D 330 SER cc_start: 0.5099 (OUTLIER) cc_final: 0.4301 (p) REVERT: D 334 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6457 (mt) REVERT: D 340 LEU cc_start: 0.7542 (mt) cc_final: 0.7138 (mm) REVERT: D 344 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.6991 (ttp-170) REVERT: D 387 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: D 388 ASN cc_start: 0.8706 (p0) cc_final: 0.8490 (p0) REVERT: D 398 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8924 (pm20) REVERT: D 403 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.9108 (mt0) REVERT: D 404 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8829 (tp) REVERT: D 434 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: D 441 GLU cc_start: 0.8137 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 447 GLN cc_start: 0.6923 (mt0) cc_final: 0.6472 (mp10) REVERT: D 448 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8452 (tp) REVERT: D 465 GLU cc_start: 0.9117 (tt0) cc_final: 0.8670 (mm-30) REVERT: D 557 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (tp-100) REVERT: D 579 ASP cc_start: 0.8428 (p0) cc_final: 0.8206 (t0) REVERT: D 587 MET cc_start: 0.8855 (mtt) cc_final: 0.8415 (mtm) REVERT: E 209 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.6895 (p0) REVERT: E 285 GLN cc_start: 0.7089 (mt0) cc_final: 0.6840 (mm110) REVERT: E 287 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5446 (ttp-110) REVERT: E 291 LYS cc_start: 0.6195 (tptt) cc_final: 0.5264 (tttt) REVERT: E 294 SER cc_start: 0.6522 (OUTLIER) cc_final: 0.6026 (t) REVERT: E 330 SER cc_start: 0.5382 (OUTLIER) cc_final: 0.4531 (p) REVERT: E 344 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6388 (ttp80) REVERT: E 348 GLU cc_start: 0.8101 (tt0) cc_final: 0.7892 (pt0) REVERT: E 350 MET cc_start: 0.8752 (mmm) cc_final: 0.7947 (ttp) REVERT: E 404 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8768 (tp) REVERT: E 434 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8678 (ttp) REVERT: E 441 GLU cc_start: 0.8344 (tt0) cc_final: 0.8007 (mt-10) REVERT: E 447 GLN cc_start: 0.7191 (mt0) cc_final: 0.6753 (mp10) REVERT: E 465 GLU cc_start: 0.9114 (tt0) cc_final: 0.8728 (mm-30) REVERT: E 470 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8376 (mmm160) REVERT: E 542 TYR cc_start: 0.8790 (t80) cc_final: 0.8490 (t80) REVERT: E 545 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7437 (ttpt) REVERT: E 551 ASP cc_start: 0.8890 (p0) cc_final: 0.8519 (t0) REVERT: E 557 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7968 (tp-100) REVERT: E 560 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7409 (tm-30) REVERT: E 579 ASP cc_start: 0.8570 (p0) cc_final: 0.8214 (t0) REVERT: E 580 LYS cc_start: 0.8932 (mttp) cc_final: 0.8575 (mptt) REVERT: F 209 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7567 (p0) REVERT: F 212 GLU cc_start: 0.8409 (tt0) cc_final: 0.8184 (tm-30) REVERT: F 263 HIS cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (p90) REVERT: F 285 GLN cc_start: 0.6997 (mt0) cc_final: 0.6574 (mm-40) REVERT: F 287 ARG cc_start: 0.6452 (mtt90) cc_final: 0.5227 (tmt170) REVERT: F 294 SER cc_start: 0.6083 (OUTLIER) cc_final: 0.5649 (t) REVERT: F 330 SER cc_start: 0.4669 (OUTLIER) cc_final: 0.4152 (p) REVERT: F 344 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.6669 (ttp80) REVERT: F 350 MET cc_start: 0.8731 (mmm) cc_final: 0.7853 (ttp) REVERT: F 404 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8793 (tp) REVERT: F 434 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8637 (ttp) REVERT: F 441 GLU cc_start: 0.8511 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 444 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7643 (mtpp) REVERT: F 447 GLN cc_start: 0.7104 (mt0) cc_final: 0.6758 (mp10) REVERT: F 465 GLU cc_start: 0.9112 (tt0) cc_final: 0.8646 (mm-30) REVERT: F 486 GLU cc_start: 0.9079 (tp30) cc_final: 0.8857 (mm-30) REVERT: F 579 ASP cc_start: 0.8521 (p0) cc_final: 0.8216 (t0) REVERT: F 586 LYS cc_start: 0.8708 (mttm) cc_final: 0.8230 (mtpt) REVERT: G 285 GLN cc_start: 0.6917 (mt0) cc_final: 0.6674 (mm110) REVERT: G 287 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5357 (ttp-170) REVERT: G 291 LYS cc_start: 0.6560 (tptt) cc_final: 0.6271 (tmtp) REVERT: G 294 SER cc_start: 0.5545 (OUTLIER) cc_final: 0.4889 (t) REVERT: G 334 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6720 (mt) REVERT: G 344 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6743 (ttp80) REVERT: G 350 MET cc_start: 0.8716 (mmm) cc_final: 0.7857 (ttp) REVERT: G 387 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: G 404 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 434 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: G 441 GLU cc_start: 0.8407 (tt0) cc_final: 0.8039 (mt-10) REVERT: G 447 GLN cc_start: 0.6833 (mt0) cc_final: 0.6484 (mp10) REVERT: G 448 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 465 GLU cc_start: 0.9108 (tt0) cc_final: 0.8718 (mm-30) REVERT: G 500 LEU cc_start: 0.8851 (mt) cc_final: 0.8591 (mm) REVERT: G 579 ASP cc_start: 0.8757 (p0) cc_final: 0.8297 (t0) REVERT: G 580 LYS cc_start: 0.8985 (mttp) cc_final: 0.8773 (mmtm) REVERT: G 587 MET cc_start: 0.8768 (mtt) cc_final: 0.8526 (mtm) outliers start: 161 outliers final: 17 residues processed: 706 average time/residue: 1.3654 time to fit residues: 1093.5425 Evaluate side-chains 415 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 355 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 557 GLN Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 1.9990 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 424 GLN A 483 GLN A 499 ASN A 541 GLN A 560 GLN B 198 ASN B 274 ASN B 483 GLN C 389 GLN C 483 GLN D 198 ASN D 274 ASN D 424 GLN D 499 ASN D 541 GLN E 263 HIS E 274 ASN E 389 GLN E 424 GLN E 483 GLN E 570 ASN F 274 ASN F 389 GLN F 483 GLN F 499 ASN G 198 ASN G 209 ASN G 274 ASN G 424 GLN G 483 GLN G 560 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23709 Z= 0.253 Angle : 0.568 5.077 32228 Z= 0.308 Chirality : 0.047 0.162 3696 Planarity : 0.004 0.034 4249 Dihedral : 7.808 57.439 3281 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.11 % Allowed : 14.93 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2947 helix: -0.29 (0.24), residues: 497 sheet: -0.17 (0.16), residues: 952 loop : 0.02 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 226 HIS 0.012 0.001 HIS E 263 PHE 0.014 0.002 PHE B 493 TYR 0.011 0.002 TYR D 575 ARG 0.004 0.000 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 347 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6895 (mt0) cc_final: 0.6610 (mm110) REVERT: A 287 ARG cc_start: 0.6230 (mtt90) cc_final: 0.5433 (tmt170) REVERT: A 294 SER cc_start: 0.6869 (OUTLIER) cc_final: 0.5969 (t) REVERT: A 334 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6256 (pp) REVERT: A 344 ARG cc_start: 0.7516 (ttp-110) cc_final: 0.6686 (ttp80) REVERT: A 348 GLU cc_start: 0.7991 (tt0) cc_final: 0.7579 (pt0) REVERT: A 350 MET cc_start: 0.8395 (mmm) cc_final: 0.7481 (tmt) REVERT: A 387 LYS cc_start: 0.8301 (tptm) cc_final: 0.8040 (ttpp) REVERT: A 404 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8803 (tp) REVERT: A 441 GLU cc_start: 0.8458 (tt0) cc_final: 0.8100 (mt-10) REVERT: A 447 GLN cc_start: 0.7280 (mt0) cc_final: 0.6959 (mp10) REVERT: A 465 GLU cc_start: 0.9026 (tt0) cc_final: 0.8635 (mm-30) REVERT: A 470 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8388 (ptt90) REVERT: A 497 ASP cc_start: 0.8009 (m-30) cc_final: 0.7763 (p0) REVERT: A 542 TYR cc_start: 0.8865 (t80) cc_final: 0.8372 (t80) REVERT: A 545 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7912 (mtpt) REVERT: A 560 GLN cc_start: 0.8648 (tp40) cc_final: 0.8355 (tp40) REVERT: A 579 ASP cc_start: 0.8710 (p0) cc_final: 0.8155 (t0) REVERT: A 586 LYS cc_start: 0.8998 (mttm) cc_final: 0.8560 (mtpp) REVERT: A 595 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7385 (mtm180) REVERT: B 285 GLN cc_start: 0.7002 (mt0) cc_final: 0.6793 (mm-40) REVERT: B 287 ARG cc_start: 0.6314 (mtt90) cc_final: 0.5399 (ttp-170) REVERT: B 334 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6166 (pp) REVERT: B 344 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.6571 (tmt170) REVERT: B 348 GLU cc_start: 0.7903 (tt0) cc_final: 0.7512 (pt0) REVERT: B 350 MET cc_start: 0.8293 (mmm) cc_final: 0.7610 (tmt) REVERT: B 387 LYS cc_start: 0.8570 (tptm) cc_final: 0.8319 (tmmt) REVERT: B 404 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8642 (tp) REVERT: B 441 GLU cc_start: 0.8378 (tt0) cc_final: 0.8107 (tt0) REVERT: B 447 GLN cc_start: 0.7407 (mt0) cc_final: 0.6884 (mp10) REVERT: B 465 GLU cc_start: 0.9084 (tt0) cc_final: 0.8604 (mm-30) REVERT: B 470 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8541 (mtp85) REVERT: B 545 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8260 (mtmt) REVERT: B 560 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8346 (tp40) REVERT: B 579 ASP cc_start: 0.8615 (p0) cc_final: 0.8264 (t0) REVERT: C 285 GLN cc_start: 0.6764 (mt0) cc_final: 0.6445 (mm-40) REVERT: C 287 ARG cc_start: 0.6337 (mtt90) cc_final: 0.5374 (ttp-110) REVERT: C 291 LYS cc_start: 0.5635 (tptt) cc_final: 0.5363 (tttm) REVERT: C 344 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6861 (ttp80) REVERT: C 350 MET cc_start: 0.8362 (mmm) cc_final: 0.7462 (tmt) REVERT: C 404 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8519 (tp) REVERT: C 441 GLU cc_start: 0.8609 (tt0) cc_final: 0.7965 (tm-30) REVERT: C 447 GLN cc_start: 0.7664 (mt0) cc_final: 0.7023 (mp10) REVERT: C 465 GLU cc_start: 0.9091 (tt0) cc_final: 0.8622 (mm-30) REVERT: C 470 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8492 (ptm160) REVERT: C 539 ASN cc_start: 0.7398 (m110) cc_final: 0.7082 (p0) REVERT: C 545 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7992 (mtpt) REVERT: C 579 ASP cc_start: 0.8814 (p0) cc_final: 0.8510 (t0) REVERT: C 586 LYS cc_start: 0.8950 (mttm) cc_final: 0.8552 (mtpt) REVERT: C 587 MET cc_start: 0.8929 (mtt) cc_final: 0.8586 (mtp) REVERT: C 595 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7434 (ptt180) REVERT: D 180 ASN cc_start: 0.9323 (t0) cc_final: 0.8952 (t0) REVERT: D 285 GLN cc_start: 0.6699 (mt0) cc_final: 0.6326 (mm110) REVERT: D 287 ARG cc_start: 0.6135 (mtt90) cc_final: 0.5250 (ttp-110) REVERT: D 294 SER cc_start: 0.6424 (OUTLIER) cc_final: 0.6013 (t) REVERT: D 334 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6011 (pp) REVERT: D 344 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.6764 (ttp-170) REVERT: D 387 LYS cc_start: 0.8580 (tptm) cc_final: 0.8364 (ttpt) REVERT: D 404 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8747 (tp) REVERT: D 441 GLU cc_start: 0.8238 (tt0) cc_final: 0.7776 (tm-30) REVERT: D 447 GLN cc_start: 0.7311 (mt0) cc_final: 0.6812 (mp10) REVERT: D 448 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8394 (tp) REVERT: D 465 GLU cc_start: 0.9104 (tt0) cc_final: 0.8891 (tm-30) REVERT: D 557 GLN cc_start: 0.8682 (mm-40) cc_final: 0.7996 (tp-100) REVERT: D 579 ASP cc_start: 0.8538 (p0) cc_final: 0.8222 (t0) REVERT: D 587 MET cc_start: 0.8804 (mtt) cc_final: 0.8599 (mtp) REVERT: E 209 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.6555 (p0) REVERT: E 271 LEU cc_start: 0.8691 (pt) cc_final: 0.8487 (pt) REVERT: E 285 GLN cc_start: 0.6756 (mt0) cc_final: 0.6541 (mm110) REVERT: E 287 ARG cc_start: 0.6327 (mtt90) cc_final: 0.5347 (ttp-110) REVERT: E 294 SER cc_start: 0.6917 (OUTLIER) cc_final: 0.6510 (t) REVERT: E 344 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6195 (ttp80) REVERT: E 348 GLU cc_start: 0.8056 (tt0) cc_final: 0.7208 (tm-30) REVERT: E 350 MET cc_start: 0.8550 (mmm) cc_final: 0.8041 (ttp) REVERT: E 357 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.8936 (t) REVERT: E 389 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: E 403 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.8792 (mt0) REVERT: E 404 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8609 (tp) REVERT: E 441 GLU cc_start: 0.8518 (tt0) cc_final: 0.7841 (tm-30) REVERT: E 447 GLN cc_start: 0.7235 (mt0) cc_final: 0.6790 (mp10) REVERT: E 465 GLU cc_start: 0.9119 (tt0) cc_final: 0.8660 (mm-30) REVERT: E 486 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8816 (mp0) REVERT: E 542 TYR cc_start: 0.8740 (t80) cc_final: 0.8444 (t80) REVERT: E 545 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7542 (mtpt) REVERT: E 557 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8237 (tp-100) REVERT: E 560 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8132 (tp40) REVERT: E 579 ASP cc_start: 0.8773 (p0) cc_final: 0.8309 (t0) REVERT: E 595 ARG cc_start: 0.7932 (mpp80) cc_final: 0.7549 (ptt-90) REVERT: F 209 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.6665 (p0) REVERT: F 263 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8753 (p90) REVERT: F 285 GLN cc_start: 0.6703 (mt0) cc_final: 0.6405 (mm110) REVERT: F 287 ARG cc_start: 0.6462 (mtt90) cc_final: 0.5322 (tmt170) REVERT: F 294 SER cc_start: 0.6387 (OUTLIER) cc_final: 0.6070 (t) REVERT: F 330 SER cc_start: 0.4332 (m) cc_final: 0.3907 (t) REVERT: F 344 ARG cc_start: 0.7311 (ttp-110) cc_final: 0.6578 (ttp80) REVERT: F 350 MET cc_start: 0.8476 (mmm) cc_final: 0.7704 (tmt) REVERT: F 404 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8668 (tp) REVERT: F 441 GLU cc_start: 0.8474 (tt0) cc_final: 0.7883 (tm-30) REVERT: F 444 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7761 (mtpp) REVERT: F 447 GLN cc_start: 0.7244 (mt0) cc_final: 0.6933 (mp10) REVERT: F 465 GLU cc_start: 0.9179 (tt0) cc_final: 0.8654 (mm-30) REVERT: F 497 ASP cc_start: 0.8283 (m-30) cc_final: 0.8056 (p0) REVERT: F 545 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7788 (mtpm) REVERT: F 560 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8212 (tp-100) REVERT: F 579 ASP cc_start: 0.8755 (p0) cc_final: 0.8287 (t0) REVERT: F 586 LYS cc_start: 0.8891 (mttm) cc_final: 0.8569 (mtpp) REVERT: F 595 ARG cc_start: 0.7364 (mtm180) cc_final: 0.6937 (ptt-90) REVERT: G 285 GLN cc_start: 0.6720 (mt0) cc_final: 0.6463 (mm110) REVERT: G 287 ARG cc_start: 0.6170 (mtt90) cc_final: 0.5054 (ttp-170) REVERT: G 294 SER cc_start: 0.6473 (OUTLIER) cc_final: 0.5601 (t) REVERT: G 334 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6338 (pp) REVERT: G 340 LEU cc_start: 0.7567 (mt) cc_final: 0.7232 (mm) REVERT: G 344 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.6677 (ttp-170) REVERT: G 350 MET cc_start: 0.8555 (mmm) cc_final: 0.8160 (mmt) REVERT: G 357 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8783 (t) REVERT: G 403 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8980 (mt0) REVERT: G 404 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8771 (tp) REVERT: G 434 MET cc_start: 0.8760 (ttm) cc_final: 0.8535 (ttp) REVERT: G 441 GLU cc_start: 0.8501 (tt0) cc_final: 0.8129 (mt-10) REVERT: G 447 GLN cc_start: 0.7133 (mt0) cc_final: 0.6912 (mp10) REVERT: G 448 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8511 (tt) REVERT: G 465 GLU cc_start: 0.9130 (tt0) cc_final: 0.8761 (mm-30) REVERT: G 486 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: G 500 LEU cc_start: 0.8972 (mt) cc_final: 0.8684 (mm) REVERT: G 557 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8305 (tp-100) REVERT: G 560 GLN cc_start: 0.8514 (tp40) cc_final: 0.8307 (tp40) REVERT: G 579 ASP cc_start: 0.8717 (p0) cc_final: 0.8371 (t70) REVERT: G 586 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8891 (mtpt) REVERT: G 587 MET cc_start: 0.8855 (mtt) cc_final: 0.8565 (mtm) REVERT: G 595 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7205 (ptt-90) outliers start: 108 outliers final: 40 residues processed: 419 average time/residue: 1.5274 time to fit residues: 720.6193 Evaluate side-chains 378 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 310 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 40.0000 chunk 181 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 288 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 265 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 422 ASN A 424 GLN A 476 ASN B 424 GLN B 476 ASN B 557 GLN C 389 GLN C 476 ASN D 476 ASN E 424 GLN E 476 ASN E 570 ASN F 198 ASN F 389 GLN F 476 ASN F 541 GLN G 424 GLN G 541 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 23709 Z= 0.394 Angle : 0.590 5.351 32228 Z= 0.315 Chirality : 0.049 0.166 3696 Planarity : 0.005 0.043 4249 Dihedral : 6.731 51.487 3213 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.91 % Allowed : 15.58 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2947 helix: -0.19 (0.24), residues: 497 sheet: 0.36 (0.16), residues: 903 loop : -0.54 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 226 HIS 0.006 0.001 HIS C 263 PHE 0.014 0.002 PHE A 493 TYR 0.013 0.002 TYR G 410 ARG 0.004 0.001 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 308 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6911 (mt0) cc_final: 0.6590 (mm110) REVERT: A 287 ARG cc_start: 0.6103 (mtt90) cc_final: 0.5297 (tmt170) REVERT: A 294 SER cc_start: 0.6774 (OUTLIER) cc_final: 0.5827 (t) REVERT: A 297 ARG cc_start: 0.4522 (OUTLIER) cc_final: 0.4076 (mmt90) REVERT: A 344 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.6723 (ttp80) REVERT: A 350 MET cc_start: 0.8457 (mmm) cc_final: 0.7565 (tmt) REVERT: A 387 LYS cc_start: 0.8283 (tptm) cc_final: 0.8005 (ttpp) REVERT: A 404 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 441 GLU cc_start: 0.8417 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 447 GLN cc_start: 0.7416 (mt0) cc_final: 0.6978 (mp10) REVERT: A 465 GLU cc_start: 0.9032 (tt0) cc_final: 0.8690 (mm-30) REVERT: A 470 ARG cc_start: 0.9014 (mtt180) cc_final: 0.8417 (ptp90) REVERT: A 496 LYS cc_start: 0.7625 (tptm) cc_final: 0.7374 (tttp) REVERT: A 497 ASP cc_start: 0.8222 (m-30) cc_final: 0.7879 (p0) REVERT: A 545 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8095 (mtpt) REVERT: A 560 GLN cc_start: 0.8645 (tp40) cc_final: 0.8254 (tp40) REVERT: A 579 ASP cc_start: 0.8794 (p0) cc_final: 0.8376 (t70) REVERT: A 586 LYS cc_start: 0.9055 (mttm) cc_final: 0.8506 (mtpt) REVERT: A 595 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7508 (mtm180) REVERT: B 285 GLN cc_start: 0.6970 (mt0) cc_final: 0.6703 (mm-40) REVERT: B 287 ARG cc_start: 0.6329 (mtt90) cc_final: 0.5413 (ttp-170) REVERT: B 294 SER cc_start: 0.6409 (OUTLIER) cc_final: 0.5716 (t) REVERT: B 334 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6461 (pp) REVERT: B 344 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.6318 (tmt170) REVERT: B 348 GLU cc_start: 0.8102 (tt0) cc_final: 0.7787 (pt0) REVERT: B 350 MET cc_start: 0.8336 (mmm) cc_final: 0.7662 (tmt) REVERT: B 403 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.9103 (mt0) REVERT: B 404 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8763 (tp) REVERT: B 441 GLU cc_start: 0.8322 (tt0) cc_final: 0.8080 (tt0) REVERT: B 447 GLN cc_start: 0.7420 (mt0) cc_final: 0.6883 (mp10) REVERT: B 465 GLU cc_start: 0.9061 (tt0) cc_final: 0.8655 (mm-30) REVERT: B 470 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8582 (mtp-110) REVERT: B 541 GLN cc_start: 0.8318 (mt0) cc_final: 0.7794 (mt0) REVERT: B 557 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8199 (mp10) REVERT: B 560 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8089 (tp40) REVERT: B 579 ASP cc_start: 0.8757 (p0) cc_final: 0.8394 (t0) REVERT: C 285 GLN cc_start: 0.6825 (mt0) cc_final: 0.6452 (mm-40) REVERT: C 287 ARG cc_start: 0.6101 (mtt90) cc_final: 0.5201 (ttp-110) REVERT: C 344 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.6964 (ttp80) REVERT: C 350 MET cc_start: 0.8397 (mmm) cc_final: 0.7527 (tmt) REVERT: C 394 ILE cc_start: 0.9372 (mp) cc_final: 0.9161 (mm) REVERT: C 404 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8692 (tp) REVERT: C 441 GLU cc_start: 0.8530 (tt0) cc_final: 0.7908 (tm-30) REVERT: C 447 GLN cc_start: 0.7726 (mt0) cc_final: 0.7109 (mp10) REVERT: C 465 GLU cc_start: 0.9124 (tt0) cc_final: 0.8683 (mm-30) REVERT: C 470 ARG cc_start: 0.8838 (mtt180) cc_final: 0.8520 (ptm160) REVERT: C 539 ASN cc_start: 0.7224 (m110) cc_final: 0.6725 (m-40) REVERT: C 541 GLN cc_start: 0.8711 (mt0) cc_final: 0.8105 (mt0) REVERT: C 545 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8163 (mtpt) REVERT: C 579 ASP cc_start: 0.8852 (p0) cc_final: 0.8584 (t0) REVERT: C 586 LYS cc_start: 0.9082 (mttm) cc_final: 0.8759 (mtpp) REVERT: C 587 MET cc_start: 0.9048 (mtt) cc_final: 0.8700 (mtp) REVERT: D 180 ASN cc_start: 0.9337 (t0) cc_final: 0.8964 (t0) REVERT: D 285 GLN cc_start: 0.6879 (mt0) cc_final: 0.6542 (mm110) REVERT: D 287 ARG cc_start: 0.6157 (mtt90) cc_final: 0.5265 (ttp-110) REVERT: D 297 ARG cc_start: 0.5173 (OUTLIER) cc_final: 0.4852 (mmt90) REVERT: D 340 LEU cc_start: 0.7427 (mt) cc_final: 0.7150 (mm) REVERT: D 344 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.6733 (ttp-170) REVERT: D 403 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.9002 (mt0) REVERT: D 441 GLU cc_start: 0.8201 (tt0) cc_final: 0.7756 (tm-30) REVERT: D 447 GLN cc_start: 0.7367 (mt0) cc_final: 0.6874 (mp10) REVERT: D 465 GLU cc_start: 0.9070 (tt0) cc_final: 0.8702 (mm-30) REVERT: D 545 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7895 (mtpt) REVERT: D 557 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8170 (mp10) REVERT: D 579 ASP cc_start: 0.8656 (p0) cc_final: 0.8276 (t0) REVERT: E 209 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.6509 (p0) REVERT: E 285 GLN cc_start: 0.6514 (mt0) cc_final: 0.6268 (mm110) REVERT: E 287 ARG cc_start: 0.6216 (mtt90) cc_final: 0.5295 (ttp-110) REVERT: E 294 SER cc_start: 0.6862 (OUTLIER) cc_final: 0.6400 (t) REVERT: E 344 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.6456 (ttp80) REVERT: E 348 GLU cc_start: 0.7964 (tt0) cc_final: 0.7589 (pt0) REVERT: E 350 MET cc_start: 0.8577 (mmm) cc_final: 0.7932 (ttp) REVERT: E 389 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: E 403 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.8871 (mt0) REVERT: E 404 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8597 (tp) REVERT: E 441 GLU cc_start: 0.8370 (tt0) cc_final: 0.7732 (tm-30) REVERT: E 447 GLN cc_start: 0.7436 (mt0) cc_final: 0.6937 (mp10) REVERT: E 465 GLU cc_start: 0.9113 (tt0) cc_final: 0.8761 (mm-30) REVERT: E 486 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: E 545 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7788 (mtpm) REVERT: E 557 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8260 (tp-100) REVERT: E 560 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8055 (tp40) REVERT: E 579 ASP cc_start: 0.8815 (p0) cc_final: 0.8418 (t0) REVERT: F 209 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.6848 (p0) REVERT: F 212 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8359 (mt-10) REVERT: F 285 GLN cc_start: 0.6514 (mt0) cc_final: 0.6172 (mm110) REVERT: F 287 ARG cc_start: 0.6347 (mtt90) cc_final: 0.5267 (tmt170) REVERT: F 330 SER cc_start: 0.4292 (m) cc_final: 0.3630 (p) REVERT: F 344 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.6612 (ttp80) REVERT: F 350 MET cc_start: 0.8574 (mmm) cc_final: 0.7780 (tmt) REVERT: F 404 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8802 (tp) REVERT: F 441 GLU cc_start: 0.8535 (tt0) cc_final: 0.7925 (tm-30) REVERT: F 444 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7853 (mtpp) REVERT: F 447 GLN cc_start: 0.7324 (mt0) cc_final: 0.6826 (mp10) REVERT: F 465 GLU cc_start: 0.9175 (tt0) cc_final: 0.8655 (mm-30) REVERT: F 486 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.9017 (mp0) REVERT: F 579 ASP cc_start: 0.8899 (p0) cc_final: 0.8508 (t0) REVERT: F 586 LYS cc_start: 0.8998 (mttm) cc_final: 0.8589 (mtpt) REVERT: G 271 LEU cc_start: 0.8708 (pt) cc_final: 0.8467 (pt) REVERT: G 285 GLN cc_start: 0.6733 (mt0) cc_final: 0.6490 (mm110) REVERT: G 287 ARG cc_start: 0.6190 (mtt90) cc_final: 0.5019 (ttp-170) REVERT: G 340 LEU cc_start: 0.7615 (mt) cc_final: 0.7273 (mm) REVERT: G 344 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.6761 (ttp-170) REVERT: G 350 MET cc_start: 0.8589 (mmm) cc_final: 0.7851 (ttp) REVERT: G 357 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.8841 (t) REVERT: G 403 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8966 (mt0) REVERT: G 404 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8806 (tp) REVERT: G 441 GLU cc_start: 0.8602 (tt0) cc_final: 0.8243 (mt-10) REVERT: G 447 GLN cc_start: 0.7177 (mt0) cc_final: 0.6918 (mp10) REVERT: G 448 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8516 (tp) REVERT: G 465 GLU cc_start: 0.9125 (tt0) cc_final: 0.8813 (mm-30) REVERT: G 541 GLN cc_start: 0.8394 (mt0) cc_final: 0.7797 (mt0) REVERT: G 555 ASP cc_start: 0.8269 (p0) cc_final: 0.7965 (p0) REVERT: G 557 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8226 (mp10) REVERT: G 560 GLN cc_start: 0.8397 (tp40) cc_final: 0.8099 (tp40) REVERT: G 579 ASP cc_start: 0.8688 (p0) cc_final: 0.8359 (t70) REVERT: G 587 MET cc_start: 0.9043 (mtt) cc_final: 0.8803 (mtm) outliers start: 129 outliers final: 63 residues processed: 387 average time/residue: 1.5065 time to fit residues: 656.9609 Evaluate side-chains 379 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 293 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 40.0000 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 30.0000 chunk 284 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 476 ASN E 389 GLN E 424 GLN E 476 ASN F 389 GLN F 422 ASN F 476 ASN G 424 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 23709 Z= 0.361 Angle : 0.567 6.107 32228 Z= 0.301 Chirality : 0.048 0.168 3696 Planarity : 0.005 0.044 4249 Dihedral : 6.357 47.164 3199 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.33 % Allowed : 15.66 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 2947 helix: -0.16 (0.24), residues: 497 sheet: 0.40 (0.16), residues: 910 loop : -0.62 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 226 HIS 0.005 0.001 HIS C 263 PHE 0.014 0.002 PHE B 493 TYR 0.012 0.002 TYR C 411 ARG 0.003 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 298 time to evaluate : 2.669 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 285 GLN cc_start: 0.6763 (mt0) cc_final: 0.6546 (mm-40) REVERT: A 287 ARG cc_start: 0.6118 (mtt90) cc_final: 0.5301 (tmt170) REVERT: A 344 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.6729 (ttp80) REVERT: A 348 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: A 350 MET cc_start: 0.8485 (mmm) cc_final: 0.7550 (tmt) REVERT: A 403 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.8872 (mt0) REVERT: A 404 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.8864 (tp) REVERT: A 441 GLU cc_start: 0.8380 (tt0) cc_final: 0.7906 (tm-30) REVERT: A 447 GLN cc_start: 0.7438 (mt0) cc_final: 0.7007 (mp10) REVERT: A 465 GLU cc_start: 0.9058 (tt0) cc_final: 0.8679 (mm-30) REVERT: A 470 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8413 (ptp90) REVERT: A 541 GLN cc_start: 0.8338 (mt0) cc_final: 0.7977 (mt0) REVERT: A 557 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8291 (mp10) REVERT: A 560 GLN cc_start: 0.8715 (tp40) cc_final: 0.8266 (tp40) REVERT: A 579 ASP cc_start: 0.8705 (p0) cc_final: 0.8275 (t70) REVERT: A 586 LYS cc_start: 0.9085 (mttm) cc_final: 0.8708 (mtpt) REVERT: A 595 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7449 (ttp-110) REVERT: B 287 ARG cc_start: 0.6306 (mtt90) cc_final: 0.5408 (ttp-170) REVERT: B 294 SER cc_start: 0.6440 (OUTLIER) cc_final: 0.5614 (t) REVERT: B 344 ARG cc_start: 0.7387 (ttp-110) cc_final: 0.6430 (tmt170) REVERT: B 348 GLU cc_start: 0.8149 (tt0) cc_final: 0.7788 (pt0) REVERT: B 350 MET cc_start: 0.8353 (mmm) cc_final: 0.7666 (tmt) REVERT: B 404 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8756 (tp) REVERT: B 441 GLU cc_start: 0.8305 (tt0) cc_final: 0.8090 (tt0) REVERT: B 447 GLN cc_start: 0.7513 (mt0) cc_final: 0.6938 (mp10) REVERT: B 465 GLU cc_start: 0.9039 (tt0) cc_final: 0.8651 (mm-30) REVERT: B 470 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8596 (mtp-110) REVERT: B 541 GLN cc_start: 0.8344 (mt0) cc_final: 0.7723 (mt0) REVERT: B 543 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8327 (mm-40) REVERT: B 557 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8225 (mp10) REVERT: B 560 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8045 (tp40) REVERT: B 579 ASP cc_start: 0.8775 (p0) cc_final: 0.8396 (t0) REVERT: C 276 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: C 285 GLN cc_start: 0.6772 (mt0) cc_final: 0.6444 (mm-40) REVERT: C 287 ARG cc_start: 0.6061 (mtt90) cc_final: 0.5202 (ttp-110) REVERT: C 344 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6757 (ttp80) REVERT: C 350 MET cc_start: 0.8421 (mmm) cc_final: 0.7552 (tmt) REVERT: C 394 ILE cc_start: 0.9439 (mp) cc_final: 0.9175 (mm) REVERT: C 404 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8720 (tp) REVERT: C 441 GLU cc_start: 0.8512 (tt0) cc_final: 0.7994 (tm-30) REVERT: C 447 GLN cc_start: 0.7735 (mt0) cc_final: 0.7115 (mp10) REVERT: C 465 GLU cc_start: 0.9034 (tt0) cc_final: 0.8687 (mm-30) REVERT: C 470 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8518 (ptm160) REVERT: C 539 ASN cc_start: 0.7224 (m110) cc_final: 0.6725 (m-40) REVERT: C 541 GLN cc_start: 0.8695 (mt0) cc_final: 0.8233 (mt0) REVERT: C 545 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8111 (mtpt) REVERT: C 557 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8314 (mp10) REVERT: C 579 ASP cc_start: 0.8856 (p0) cc_final: 0.8603 (t0) REVERT: C 587 MET cc_start: 0.9073 (mtt) cc_final: 0.8713 (mtp) REVERT: D 180 ASN cc_start: 0.9321 (t0) cc_final: 0.8927 (t0) REVERT: D 285 GLN cc_start: 0.7088 (mt0) cc_final: 0.6793 (mm110) REVERT: D 287 ARG cc_start: 0.6069 (mtt90) cc_final: 0.5140 (ttp-110) REVERT: D 294 SER cc_start: 0.6457 (OUTLIER) cc_final: 0.6123 (t) REVERT: D 297 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4868 (mmt90) REVERT: D 340 LEU cc_start: 0.7409 (mt) cc_final: 0.7172 (mm) REVERT: D 344 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.6659 (ttp-170) REVERT: D 403 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.8997 (mt0) REVERT: D 441 GLU cc_start: 0.8249 (tt0) cc_final: 0.7732 (tm-30) REVERT: D 447 GLN cc_start: 0.7390 (mt0) cc_final: 0.6893 (mp10) REVERT: D 465 GLU cc_start: 0.9015 (tt0) cc_final: 0.8685 (mm-30) REVERT: D 557 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8167 (mp10) REVERT: D 579 ASP cc_start: 0.8749 (p0) cc_final: 0.8385 (t0) REVERT: E 285 GLN cc_start: 0.6514 (mt0) cc_final: 0.6261 (mm-40) REVERT: E 287 ARG cc_start: 0.6246 (mtt90) cc_final: 0.5330 (ttp-110) REVERT: E 294 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6687 (t) REVERT: E 344 ARG cc_start: 0.7383 (ttp-110) cc_final: 0.6461 (ttp80) REVERT: E 348 GLU cc_start: 0.8173 (tt0) cc_final: 0.7790 (pt0) REVERT: E 350 MET cc_start: 0.8572 (mmm) cc_final: 0.7932 (ttp) REVERT: E 403 GLN cc_start: 0.9469 (OUTLIER) cc_final: 0.8835 (mt0) REVERT: E 404 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8590 (tp) REVERT: E 441 GLU cc_start: 0.8382 (tt0) cc_final: 0.7778 (tm-30) REVERT: E 447 GLN cc_start: 0.7484 (mt0) cc_final: 0.6965 (mp10) REVERT: E 465 GLU cc_start: 0.9096 (tt0) cc_final: 0.8819 (mm-30) REVERT: E 486 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8712 (mp0) REVERT: E 541 GLN cc_start: 0.8418 (mt0) cc_final: 0.7896 (mt0) REVERT: E 557 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8121 (mp10) REVERT: E 579 ASP cc_start: 0.8872 (p0) cc_final: 0.8455 (t0) REVERT: F 285 GLN cc_start: 0.6488 (mt0) cc_final: 0.6131 (mm110) REVERT: F 287 ARG cc_start: 0.6276 (mtt90) cc_final: 0.5122 (tmt170) REVERT: F 294 SER cc_start: 0.6505 (OUTLIER) cc_final: 0.6171 (t) REVERT: F 330 SER cc_start: 0.4195 (m) cc_final: 0.3743 (t) REVERT: F 344 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.6600 (ttp80) REVERT: F 350 MET cc_start: 0.8609 (mmm) cc_final: 0.7718 (tmt) REVERT: F 404 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8823 (tp) REVERT: F 441 GLU cc_start: 0.8500 (tt0) cc_final: 0.7887 (tm-30) REVERT: F 444 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7936 (mtpp) REVERT: F 447 GLN cc_start: 0.7356 (mt0) cc_final: 0.6870 (mp10) REVERT: F 465 GLU cc_start: 0.9104 (tt0) cc_final: 0.8643 (mm-30) REVERT: F 555 ASP cc_start: 0.7974 (p0) cc_final: 0.7394 (p0) REVERT: F 557 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8257 (mp10) REVERT: F 579 ASP cc_start: 0.8919 (p0) cc_final: 0.8536 (t0) REVERT: F 586 LYS cc_start: 0.9015 (mttm) cc_final: 0.8617 (mtpt) REVERT: F 595 ARG cc_start: 0.7652 (mpp80) cc_final: 0.7264 (ptt-90) REVERT: G 271 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8413 (pt) REVERT: G 285 GLN cc_start: 0.6644 (mt0) cc_final: 0.6430 (mm-40) REVERT: G 287 ARG cc_start: 0.6185 (mtt90) cc_final: 0.5010 (ttp-170) REVERT: G 340 LEU cc_start: 0.7604 (mt) cc_final: 0.7254 (mm) REVERT: G 344 ARG cc_start: 0.7579 (ttp-110) cc_final: 0.6780 (ttp-170) REVERT: G 350 MET cc_start: 0.8638 (mmm) cc_final: 0.7869 (ttp) REVERT: G 357 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.8785 (t) REVERT: G 403 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8953 (mt0) REVERT: G 404 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8778 (tp) REVERT: G 441 GLU cc_start: 0.8586 (tt0) cc_final: 0.8267 (mt-10) REVERT: G 447 GLN cc_start: 0.7351 (mt0) cc_final: 0.7029 (mp10) REVERT: G 448 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8477 (tp) REVERT: G 465 GLU cc_start: 0.9082 (tt0) cc_final: 0.8794 (mm-30) REVERT: G 500 LEU cc_start: 0.9071 (mt) cc_final: 0.8857 (mm) REVERT: G 541 GLN cc_start: 0.8405 (mt0) cc_final: 0.7938 (mt0) REVERT: G 545 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7546 (mtpt) REVERT: G 555 ASP cc_start: 0.8271 (p0) cc_final: 0.8008 (p0) REVERT: G 557 GLN cc_start: 0.8615 (tp-100) cc_final: 0.8257 (mp10) REVERT: G 579 ASP cc_start: 0.8643 (p0) cc_final: 0.8314 (t0) REVERT: G 587 MET cc_start: 0.9062 (mtt) cc_final: 0.8826 (mtm) outliers start: 140 outliers final: 68 residues processed: 391 average time/residue: 1.5264 time to fit residues: 678.3362 Evaluate side-chains 372 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 282 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 211 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN E 476 ASN F 422 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23709 Z= 0.176 Angle : 0.494 6.303 32228 Z= 0.262 Chirality : 0.045 0.160 3696 Planarity : 0.004 0.036 4249 Dihedral : 5.703 40.948 3192 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.73 % Allowed : 17.30 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2947 helix: 0.21 (0.25), residues: 497 sheet: 0.52 (0.16), residues: 910 loop : -0.50 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 226 HIS 0.002 0.001 HIS G 263 PHE 0.012 0.001 PHE A 493 TYR 0.012 0.001 TYR C 411 ARG 0.002 0.000 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 308 time to evaluate : 2.868 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 285 GLN cc_start: 0.6629 (mt0) cc_final: 0.6416 (mm-40) REVERT: A 287 ARG cc_start: 0.6185 (mtt90) cc_final: 0.5348 (tmt170) REVERT: A 344 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.6704 (ttp80) REVERT: A 350 MET cc_start: 0.8380 (mmm) cc_final: 0.7411 (tmt) REVERT: A 403 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.8846 (mt0) REVERT: A 404 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8801 (tp) REVERT: A 436 TYR cc_start: 0.8708 (t80) cc_final: 0.8489 (t80) REVERT: A 441 GLU cc_start: 0.8334 (tt0) cc_final: 0.8061 (mt-10) REVERT: A 447 GLN cc_start: 0.7462 (mt0) cc_final: 0.7038 (mp10) REVERT: A 465 GLU cc_start: 0.9086 (tt0) cc_final: 0.8691 (mm-30) REVERT: A 470 ARG cc_start: 0.9002 (mtt180) cc_final: 0.8406 (ptp90) REVERT: A 541 GLN cc_start: 0.8283 (mt0) cc_final: 0.7878 (mt0) REVERT: A 545 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7936 (mtpt) REVERT: A 557 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8334 (mp10) REVERT: A 560 GLN cc_start: 0.8620 (tp40) cc_final: 0.8140 (tp40) REVERT: A 579 ASP cc_start: 0.8749 (p0) cc_final: 0.8317 (t70) REVERT: A 586 LYS cc_start: 0.9034 (mttm) cc_final: 0.8509 (mtpt) REVERT: A 595 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7451 (ttp-110) REVERT: B 287 ARG cc_start: 0.6197 (mtt90) cc_final: 0.5347 (ttp-170) REVERT: B 334 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6445 (pp) REVERT: B 344 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.6457 (tmt170) REVERT: B 348 GLU cc_start: 0.8082 (tt0) cc_final: 0.7768 (pt0) REVERT: B 350 MET cc_start: 0.8385 (mmm) cc_final: 0.7753 (tmt) REVERT: B 403 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.9077 (mt0) REVERT: B 404 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B 436 TYR cc_start: 0.8693 (t80) cc_final: 0.8489 (t80) REVERT: B 447 GLN cc_start: 0.7491 (mt0) cc_final: 0.6920 (mp10) REVERT: B 465 GLU cc_start: 0.9151 (tt0) cc_final: 0.8720 (mm-30) REVERT: B 470 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8604 (mtp-110) REVERT: B 541 GLN cc_start: 0.8394 (mt0) cc_final: 0.7796 (mt0) REVERT: B 557 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8244 (mp10) REVERT: B 560 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7983 (tp40) REVERT: B 579 ASP cc_start: 0.8776 (p0) cc_final: 0.8416 (t0) REVERT: C 276 ASP cc_start: 0.8606 (m-30) cc_final: 0.8394 (m-30) REVERT: C 285 GLN cc_start: 0.6706 (mt0) cc_final: 0.6419 (mm-40) REVERT: C 287 ARG cc_start: 0.6300 (mtt90) cc_final: 0.5383 (ttp-110) REVERT: C 344 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.6681 (ttp80) REVERT: C 350 MET cc_start: 0.8286 (mmm) cc_final: 0.7381 (tmt) REVERT: C 389 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: C 394 ILE cc_start: 0.9340 (mp) cc_final: 0.9137 (mm) REVERT: C 398 GLU cc_start: 0.9195 (pt0) cc_final: 0.8765 (pm20) REVERT: C 404 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8666 (tp) REVERT: C 436 TYR cc_start: 0.8779 (t80) cc_final: 0.8539 (t80) REVERT: C 441 GLU cc_start: 0.8547 (tt0) cc_final: 0.8073 (mt-10) REVERT: C 447 GLN cc_start: 0.7716 (mt0) cc_final: 0.7116 (mp10) REVERT: C 465 GLU cc_start: 0.9037 (tt0) cc_final: 0.8694 (mm-30) REVERT: C 470 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8502 (ptm160) REVERT: C 539 ASN cc_start: 0.7136 (m110) cc_final: 0.6596 (m-40) REVERT: C 541 GLN cc_start: 0.8587 (mt0) cc_final: 0.8163 (mt0) REVERT: C 545 LYS cc_start: 0.8315 (mtpp) cc_final: 0.8035 (mtpt) REVERT: C 557 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8354 (mp10) REVERT: C 579 ASP cc_start: 0.8846 (p0) cc_final: 0.8617 (t0) REVERT: C 587 MET cc_start: 0.9001 (mtt) cc_final: 0.8662 (mtp) REVERT: D 180 ASN cc_start: 0.9294 (t0) cc_final: 0.8917 (t0) REVERT: D 285 GLN cc_start: 0.6885 (mt0) cc_final: 0.6552 (mm110) REVERT: D 287 ARG cc_start: 0.6101 (mtt90) cc_final: 0.5159 (ttp-110) REVERT: D 344 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.6631 (ttp-170) REVERT: D 404 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8767 (tp) REVERT: D 441 GLU cc_start: 0.8243 (tt0) cc_final: 0.7682 (tm-30) REVERT: D 447 GLN cc_start: 0.7342 (mt0) cc_final: 0.6876 (mp10) REVERT: D 465 GLU cc_start: 0.9001 (tt0) cc_final: 0.8707 (mm-30) REVERT: D 543 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: D 557 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8186 (mp10) REVERT: D 579 ASP cc_start: 0.8709 (p0) cc_final: 0.8322 (t0) REVERT: E 285 GLN cc_start: 0.6422 (mt0) cc_final: 0.6181 (mm-40) REVERT: E 287 ARG cc_start: 0.6249 (mtt90) cc_final: 0.5302 (ttp-110) REVERT: E 344 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6336 (ttp80) REVERT: E 348 GLU cc_start: 0.8157 (tt0) cc_final: 0.7270 (tm-30) REVERT: E 350 MET cc_start: 0.8444 (mmm) cc_final: 0.7980 (ttp) REVERT: E 403 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.8826 (mt0) REVERT: E 404 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8519 (tp) REVERT: E 441 GLU cc_start: 0.8416 (tt0) cc_final: 0.7949 (mm-30) REVERT: E 446 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8343 (mmtm) REVERT: E 447 GLN cc_start: 0.7444 (mt0) cc_final: 0.6893 (mp10) REVERT: E 465 GLU cc_start: 0.9103 (tt0) cc_final: 0.8835 (mm-30) REVERT: E 541 GLN cc_start: 0.8391 (mt0) cc_final: 0.7894 (mt0) REVERT: E 557 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8111 (mp10) REVERT: E 579 ASP cc_start: 0.8767 (p0) cc_final: 0.8337 (t0) REVERT: E 595 ARG cc_start: 0.7966 (mpp80) cc_final: 0.7542 (ptt-90) REVERT: F 271 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8394 (pp) REVERT: F 285 GLN cc_start: 0.6365 (mt0) cc_final: 0.6027 (mm110) REVERT: F 287 ARG cc_start: 0.6262 (mtt90) cc_final: 0.5099 (tmt170) REVERT: F 344 ARG cc_start: 0.7366 (ttp-110) cc_final: 0.6602 (ttp80) REVERT: F 350 MET cc_start: 0.8505 (mmm) cc_final: 0.7663 (tmt) REVERT: F 404 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8699 (tp) REVERT: F 441 GLU cc_start: 0.8522 (tt0) cc_final: 0.7885 (mm-30) REVERT: F 444 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8017 (mtpp) REVERT: F 447 GLN cc_start: 0.7335 (mt0) cc_final: 0.6856 (mp10) REVERT: F 465 GLU cc_start: 0.9161 (tt0) cc_final: 0.8702 (mm-30) REVERT: F 545 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8014 (mtpt) REVERT: F 555 ASP cc_start: 0.7947 (p0) cc_final: 0.7489 (p0) REVERT: F 557 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8287 (mp10) REVERT: F 579 ASP cc_start: 0.8895 (p0) cc_final: 0.8476 (t0) REVERT: F 595 ARG cc_start: 0.7707 (mpp80) cc_final: 0.7336 (ptt-90) REVERT: G 271 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8392 (pt) REVERT: G 285 GLN cc_start: 0.6447 (mt0) cc_final: 0.6232 (mm-40) REVERT: G 287 ARG cc_start: 0.6216 (mtt90) cc_final: 0.5038 (ttp-170) REVERT: G 340 LEU cc_start: 0.7512 (mt) cc_final: 0.7165 (mm) REVERT: G 344 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.6714 (ttp-170) REVERT: G 350 MET cc_start: 0.8548 (mmm) cc_final: 0.7848 (ttp) REVERT: G 357 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.8786 (t) REVERT: G 403 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8930 (mt0) REVERT: G 404 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 441 GLU cc_start: 0.8499 (tt0) cc_final: 0.8206 (mt-10) REVERT: G 447 GLN cc_start: 0.7510 (mt0) cc_final: 0.7190 (mp10) REVERT: G 465 GLU cc_start: 0.9065 (tt0) cc_final: 0.8786 (mm-30) REVERT: G 500 LEU cc_start: 0.9104 (mt) cc_final: 0.8857 (mm) REVERT: G 541 GLN cc_start: 0.8389 (mt0) cc_final: 0.7937 (mt0) REVERT: G 545 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7543 (mtpt) REVERT: G 557 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8203 (mp10) REVERT: G 579 ASP cc_start: 0.8741 (p0) cc_final: 0.8358 (t0) REVERT: G 587 MET cc_start: 0.8982 (mtt) cc_final: 0.8699 (mtm) outliers start: 98 outliers final: 40 residues processed: 362 average time/residue: 1.5507 time to fit residues: 630.5719 Evaluate side-chains 355 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 296 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 543 GLN Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN E 476 ASN E 499 ASN F 422 ASN F 476 ASN G 424 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23709 Z= 0.238 Angle : 0.513 6.865 32228 Z= 0.269 Chirality : 0.046 0.162 3696 Planarity : 0.004 0.038 4249 Dihedral : 5.608 40.086 3186 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.11 % Allowed : 17.56 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2947 helix: 0.21 (0.25), residues: 497 sheet: 0.88 (0.16), residues: 903 loop : -0.59 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 226 HIS 0.003 0.001 HIS A 263 PHE 0.012 0.001 PHE E 493 TYR 0.013 0.001 TYR C 411 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 300 time to evaluate : 2.645 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 283 ASP cc_start: 0.7864 (m-30) cc_final: 0.7487 (t0) REVERT: A 285 GLN cc_start: 0.6787 (mt0) cc_final: 0.6581 (mm-40) REVERT: A 287 ARG cc_start: 0.6108 (mtt90) cc_final: 0.5307 (tmt170) REVERT: A 344 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.6767 (ttp-170) REVERT: A 350 MET cc_start: 0.8434 (mmm) cc_final: 0.7564 (tmt) REVERT: A 403 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.8830 (mt0) REVERT: A 404 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8815 (tp) REVERT: A 441 GLU cc_start: 0.8341 (tt0) cc_final: 0.8062 (mt-10) REVERT: A 447 GLN cc_start: 0.7450 (mt0) cc_final: 0.7032 (mp10) REVERT: A 465 GLU cc_start: 0.9098 (tt0) cc_final: 0.8695 (mm-30) REVERT: A 470 ARG cc_start: 0.9018 (mtt180) cc_final: 0.8549 (mmm160) REVERT: A 541 GLN cc_start: 0.8392 (mt0) cc_final: 0.8049 (mt0) REVERT: A 560 GLN cc_start: 0.8657 (tp40) cc_final: 0.8170 (tp40) REVERT: A 579 ASP cc_start: 0.8724 (p0) cc_final: 0.8271 (t70) REVERT: A 586 LYS cc_start: 0.9093 (mttm) cc_final: 0.8569 (mtpt) REVERT: A 595 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7300 (ttp-110) REVERT: B 180 ASN cc_start: 0.9234 (t0) cc_final: 0.8873 (t0) REVERT: B 287 ARG cc_start: 0.6226 (mtt90) cc_final: 0.5359 (ttp-170) REVERT: B 334 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6405 (pp) REVERT: B 344 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.6443 (tmt170) REVERT: B 348 GLU cc_start: 0.8052 (tt0) cc_final: 0.7742 (pt0) REVERT: B 350 MET cc_start: 0.8393 (mmm) cc_final: 0.7624 (tmt) REVERT: B 403 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.9100 (mt0) REVERT: B 404 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8635 (tp) REVERT: B 436 TYR cc_start: 0.8711 (t80) cc_final: 0.8505 (t80) REVERT: B 447 GLN cc_start: 0.7524 (mt0) cc_final: 0.6947 (mp10) REVERT: B 465 GLU cc_start: 0.9159 (tt0) cc_final: 0.8716 (mm-30) REVERT: B 470 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8560 (ptm160) REVERT: B 541 GLN cc_start: 0.8394 (mt0) cc_final: 0.7842 (mt0) REVERT: B 557 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8223 (mp10) REVERT: B 579 ASP cc_start: 0.8773 (p0) cc_final: 0.8421 (t0) REVERT: B 595 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7668 (ptt180) REVERT: C 285 GLN cc_start: 0.6689 (mt0) cc_final: 0.6388 (mm-40) REVERT: C 287 ARG cc_start: 0.6325 (mtt90) cc_final: 0.5271 (tmt170) REVERT: C 344 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.6669 (ttp80) REVERT: C 350 MET cc_start: 0.8307 (mmm) cc_final: 0.7402 (tmt) REVERT: C 394 ILE cc_start: 0.9386 (mp) cc_final: 0.9128 (mm) REVERT: C 398 GLU cc_start: 0.9216 (pt0) cc_final: 0.8781 (pm20) REVERT: C 404 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8663 (tp) REVERT: C 441 GLU cc_start: 0.8513 (tt0) cc_final: 0.8061 (mt-10) REVERT: C 447 GLN cc_start: 0.7713 (mt0) cc_final: 0.7110 (mp10) REVERT: C 465 GLU cc_start: 0.9086 (tt0) cc_final: 0.8701 (mm-30) REVERT: C 470 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8478 (ptm160) REVERT: C 496 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6889 (tptm) REVERT: C 539 ASN cc_start: 0.7115 (m110) cc_final: 0.6581 (m-40) REVERT: C 541 GLN cc_start: 0.8620 (mt0) cc_final: 0.8279 (mt0) REVERT: C 545 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8025 (mtpt) REVERT: C 557 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8374 (mp10) REVERT: C 579 ASP cc_start: 0.8836 (p0) cc_final: 0.8629 (t0) REVERT: C 587 MET cc_start: 0.9019 (mtt) cc_final: 0.8677 (mtp) REVERT: D 180 ASN cc_start: 0.9283 (t0) cc_final: 0.8909 (t0) REVERT: D 285 GLN cc_start: 0.6783 (mt0) cc_final: 0.6483 (mm110) REVERT: D 287 ARG cc_start: 0.6293 (mtt90) cc_final: 0.5403 (ttp-110) REVERT: D 294 SER cc_start: 0.6413 (OUTLIER) cc_final: 0.6116 (t) REVERT: D 297 ARG cc_start: 0.5238 (OUTLIER) cc_final: 0.4840 (mmt90) REVERT: D 344 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.6654 (ttp-170) REVERT: D 403 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9021 (mt0) REVERT: D 404 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.8816 (tp) REVERT: D 441 GLU cc_start: 0.8272 (tt0) cc_final: 0.7695 (tm-30) REVERT: D 447 GLN cc_start: 0.7328 (mt0) cc_final: 0.6832 (mp10) REVERT: D 465 GLU cc_start: 0.8988 (tt0) cc_final: 0.8696 (mm-30) REVERT: D 557 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8191 (mp10) REVERT: D 579 ASP cc_start: 0.8765 (p0) cc_final: 0.8410 (t0) REVERT: E 285 GLN cc_start: 0.6355 (mt0) cc_final: 0.6142 (mm-40) REVERT: E 287 ARG cc_start: 0.6270 (mtt90) cc_final: 0.5319 (ttp-110) REVERT: E 344 ARG cc_start: 0.7135 (ttp-110) cc_final: 0.6301 (ttp80) REVERT: E 348 GLU cc_start: 0.8230 (tt0) cc_final: 0.7356 (tm-30) REVERT: E 350 MET cc_start: 0.8463 (mmm) cc_final: 0.8013 (ttp) REVERT: E 403 GLN cc_start: 0.9452 (OUTLIER) cc_final: 0.8821 (mt0) REVERT: E 404 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8606 (tp) REVERT: E 441 GLU cc_start: 0.8343 (tt0) cc_final: 0.7679 (tm-30) REVERT: E 447 GLN cc_start: 0.7331 (mt0) cc_final: 0.6813 (mm-40) REVERT: E 465 GLU cc_start: 0.9080 (tt0) cc_final: 0.8779 (mm-30) REVERT: E 557 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8114 (mp10) REVERT: E 579 ASP cc_start: 0.8812 (p0) cc_final: 0.8368 (t0) REVERT: E 595 ARG cc_start: 0.7946 (mpp80) cc_final: 0.7494 (ptt-90) REVERT: F 271 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8487 (pp) REVERT: F 285 GLN cc_start: 0.6504 (mt0) cc_final: 0.6124 (mm110) REVERT: F 287 ARG cc_start: 0.6265 (mtt90) cc_final: 0.5068 (tmt170) REVERT: F 294 SER cc_start: 0.6454 (OUTLIER) cc_final: 0.6162 (t) REVERT: F 344 ARG cc_start: 0.7348 (ttp-110) cc_final: 0.6588 (ttp80) REVERT: F 350 MET cc_start: 0.8550 (mmm) cc_final: 0.7690 (tmt) REVERT: F 389 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: F 404 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8698 (tp) REVERT: F 441 GLU cc_start: 0.8462 (tt0) cc_final: 0.7849 (mm-30) REVERT: F 444 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8024 (mtpp) REVERT: F 447 GLN cc_start: 0.7324 (mt0) cc_final: 0.6838 (mp10) REVERT: F 465 GLU cc_start: 0.9167 (tt0) cc_final: 0.8704 (mm-30) REVERT: F 545 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7985 (mtmt) REVERT: F 555 ASP cc_start: 0.7970 (p0) cc_final: 0.7523 (p0) REVERT: F 557 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8346 (mp10) REVERT: F 579 ASP cc_start: 0.8873 (p0) cc_final: 0.8434 (t0) REVERT: G 271 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8432 (pt) REVERT: G 285 GLN cc_start: 0.6425 (mt0) cc_final: 0.6190 (mm-40) REVERT: G 287 ARG cc_start: 0.6195 (mtt90) cc_final: 0.4956 (ttp-170) REVERT: G 299 HIS cc_start: 0.3714 (OUTLIER) cc_final: 0.3510 (p-80) REVERT: G 344 ARG cc_start: 0.7501 (ttp-110) cc_final: 0.6704 (ttp-170) REVERT: G 350 MET cc_start: 0.8576 (mmm) cc_final: 0.8158 (mmt) REVERT: G 357 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8814 (t) REVERT: G 403 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8930 (mt0) REVERT: G 404 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8663 (tp) REVERT: G 441 GLU cc_start: 0.8484 (tt0) cc_final: 0.8190 (mt-10) REVERT: G 447 GLN cc_start: 0.7431 (mt0) cc_final: 0.7027 (mp10) REVERT: G 448 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8489 (tp) REVERT: G 465 GLU cc_start: 0.9042 (tt0) cc_final: 0.8755 (mm-30) REVERT: G 500 LEU cc_start: 0.9131 (mt) cc_final: 0.8895 (mm) REVERT: G 545 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7634 (mtpt) REVERT: G 557 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8208 (mp10) REVERT: G 560 GLN cc_start: 0.8257 (tp40) cc_final: 0.8030 (tp40) REVERT: G 579 ASP cc_start: 0.8737 (p0) cc_final: 0.8346 (t0) REVERT: G 587 MET cc_start: 0.9027 (mtt) cc_final: 0.8729 (mtm) outliers start: 108 outliers final: 62 residues processed: 362 average time/residue: 1.5691 time to fit residues: 638.5708 Evaluate side-chains 376 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 291 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 239 optimal weight: 0.0870 chunk 158 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 overall best weight: 4.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 476 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN G 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23709 Z= 0.337 Angle : 0.554 6.600 32228 Z= 0.291 Chirality : 0.047 0.165 3696 Planarity : 0.004 0.041 4249 Dihedral : 5.734 40.712 3185 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.76 % Allowed : 17.41 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2947 helix: 0.11 (0.25), residues: 497 sheet: 0.96 (0.16), residues: 889 loop : -0.62 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 226 HIS 0.004 0.001 HIS C 263 PHE 0.013 0.001 PHE B 493 TYR 0.013 0.002 TYR C 411 ARG 0.002 0.000 ARG G 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 291 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7891 (m-30) cc_final: 0.7525 (t0) REVERT: A 285 GLN cc_start: 0.6902 (mt0) cc_final: 0.6683 (mm-40) REVERT: A 287 ARG cc_start: 0.6050 (mtt90) cc_final: 0.5292 (tmt170) REVERT: A 344 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.6767 (ttp-170) REVERT: A 350 MET cc_start: 0.8510 (mmm) cc_final: 0.7635 (tmt) REVERT: A 403 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.8850 (mt0) REVERT: A 404 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.8869 (tp) REVERT: A 441 GLU cc_start: 0.8349 (tt0) cc_final: 0.8094 (mt-10) REVERT: A 447 GLN cc_start: 0.7438 (mt0) cc_final: 0.6988 (mp10) REVERT: A 465 GLU cc_start: 0.9092 (tt0) cc_final: 0.8705 (mm-30) REVERT: A 470 ARG cc_start: 0.9031 (mtt180) cc_final: 0.8550 (mmm160) REVERT: A 541 GLN cc_start: 0.8419 (mt0) cc_final: 0.8064 (mt0) REVERT: A 557 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8371 (mp10) REVERT: A 560 GLN cc_start: 0.8661 (tp40) cc_final: 0.8205 (tp40) REVERT: A 579 ASP cc_start: 0.8751 (p0) cc_final: 0.8323 (t70) REVERT: A 586 LYS cc_start: 0.9146 (mttm) cc_final: 0.8652 (mtpt) REVERT: A 595 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7216 (ttp-110) REVERT: B 287 ARG cc_start: 0.6349 (mtt180) cc_final: 0.5380 (ttp-170) REVERT: B 299 HIS cc_start: 0.3649 (OUTLIER) cc_final: 0.3350 (p90) REVERT: B 334 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6419 (pp) REVERT: B 344 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.6457 (tmt170) REVERT: B 350 MET cc_start: 0.8438 (mmm) cc_final: 0.7643 (tmt) REVERT: B 403 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.9101 (mt0) REVERT: B 404 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8697 (tp) REVERT: B 447 GLN cc_start: 0.7590 (mt0) cc_final: 0.6995 (mp10) REVERT: B 465 GLU cc_start: 0.9167 (tt0) cc_final: 0.8726 (mm-30) REVERT: B 470 ARG cc_start: 0.8874 (mtt180) cc_final: 0.8524 (mtp-110) REVERT: B 541 GLN cc_start: 0.8437 (mt0) cc_final: 0.7499 (mm-40) REVERT: B 557 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8286 (mp10) REVERT: B 579 ASP cc_start: 0.8762 (p0) cc_final: 0.8386 (t0) REVERT: C 285 GLN cc_start: 0.6641 (mt0) cc_final: 0.6417 (mm-40) REVERT: C 287 ARG cc_start: 0.6312 (mtt180) cc_final: 0.5267 (tmt170) REVERT: C 344 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.6709 (ttp80) REVERT: C 350 MET cc_start: 0.8367 (mmm) cc_final: 0.7455 (tmt) REVERT: C 389 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8907 (tt0) REVERT: C 394 ILE cc_start: 0.9453 (mp) cc_final: 0.9171 (mm) REVERT: C 404 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8720 (tp) REVERT: C 441 GLU cc_start: 0.8455 (tt0) cc_final: 0.8080 (mt-10) REVERT: C 447 GLN cc_start: 0.7725 (mt0) cc_final: 0.7134 (mp10) REVERT: C 465 GLU cc_start: 0.9089 (tt0) cc_final: 0.8707 (mm-30) REVERT: C 470 ARG cc_start: 0.8755 (mtt180) cc_final: 0.8486 (ptm160) REVERT: C 496 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6873 (tptm) REVERT: C 539 ASN cc_start: 0.7130 (m110) cc_final: 0.6606 (m-40) REVERT: C 541 GLN cc_start: 0.8498 (mt0) cc_final: 0.8194 (mt0) REVERT: C 545 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8010 (mtpt) REVERT: C 557 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8373 (mp10) REVERT: C 587 MET cc_start: 0.9045 (mtt) cc_final: 0.8831 (mtp) REVERT: D 180 ASN cc_start: 0.9297 (t0) cc_final: 0.8927 (t0) REVERT: D 285 GLN cc_start: 0.6751 (mt0) cc_final: 0.6449 (mm110) REVERT: D 287 ARG cc_start: 0.6307 (mtt180) cc_final: 0.5421 (ttp-110) REVERT: D 294 SER cc_start: 0.6434 (OUTLIER) cc_final: 0.6053 (t) REVERT: D 297 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.4807 (mmt90) REVERT: D 299 HIS cc_start: 0.3403 (OUTLIER) cc_final: 0.3186 (p-80) REVERT: D 344 ARG cc_start: 0.7402 (ttp-110) cc_final: 0.6658 (ttp-170) REVERT: D 403 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.9057 (mt0) REVERT: D 404 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.8878 (tp) REVERT: D 441 GLU cc_start: 0.8231 (tt0) cc_final: 0.7700 (tm-30) REVERT: D 447 GLN cc_start: 0.7364 (mt0) cc_final: 0.6859 (mp10) REVERT: D 465 GLU cc_start: 0.8978 (tt0) cc_final: 0.8686 (mm-30) REVERT: D 557 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8189 (mp10) REVERT: D 579 ASP cc_start: 0.8924 (p0) cc_final: 0.8506 (t0) REVERT: E 285 GLN cc_start: 0.6421 (mt0) cc_final: 0.6218 (mm-40) REVERT: E 287 ARG cc_start: 0.6169 (mtt90) cc_final: 0.5263 (ttp-110) REVERT: E 299 HIS cc_start: 0.3860 (OUTLIER) cc_final: 0.3587 (p90) REVERT: E 344 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6401 (ttp80) REVERT: E 348 GLU cc_start: 0.8262 (tt0) cc_final: 0.7456 (tm-30) REVERT: E 350 MET cc_start: 0.8527 (mmm) cc_final: 0.8040 (ttp) REVERT: E 403 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.8857 (mt0) REVERT: E 404 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8567 (tp) REVERT: E 441 GLU cc_start: 0.8351 (tt0) cc_final: 0.7725 (tm-30) REVERT: E 447 GLN cc_start: 0.7348 (mt0) cc_final: 0.6894 (mp10) REVERT: E 465 GLU cc_start: 0.9070 (tt0) cc_final: 0.8835 (mm-30) REVERT: E 486 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: E 557 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8069 (mp10) REVERT: E 579 ASP cc_start: 0.8801 (p0) cc_final: 0.8342 (t0) REVERT: F 285 GLN cc_start: 0.6609 (mt0) cc_final: 0.6257 (mm110) REVERT: F 287 ARG cc_start: 0.6337 (mtt90) cc_final: 0.5122 (tmt170) REVERT: F 294 SER cc_start: 0.6471 (OUTLIER) cc_final: 0.6205 (t) REVERT: F 297 ARG cc_start: 0.4549 (OUTLIER) cc_final: 0.4063 (mmt90) REVERT: F 344 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6492 (ttp80) REVERT: F 350 MET cc_start: 0.8613 (mmm) cc_final: 0.7761 (tmt) REVERT: F 389 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: F 404 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8787 (tp) REVERT: F 441 GLU cc_start: 0.8464 (tt0) cc_final: 0.7882 (tm-30) REVERT: F 447 GLN cc_start: 0.7362 (mt0) cc_final: 0.6789 (mp10) REVERT: F 465 GLU cc_start: 0.9156 (tt0) cc_final: 0.8700 (mm-30) REVERT: F 555 ASP cc_start: 0.7963 (p0) cc_final: 0.7578 (p0) REVERT: F 557 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8339 (mp10) REVERT: F 579 ASP cc_start: 0.8885 (p0) cc_final: 0.8440 (t0) REVERT: F 595 ARG cc_start: 0.7706 (mpp80) cc_final: 0.7455 (ptt-90) REVERT: G 271 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8388 (pt) REVERT: G 285 GLN cc_start: 0.6561 (mt0) cc_final: 0.6306 (mm-40) REVERT: G 287 ARG cc_start: 0.6233 (mtt90) cc_final: 0.5076 (ttp-170) REVERT: G 299 HIS cc_start: 0.3721 (OUTLIER) cc_final: 0.3507 (p-80) REVERT: G 344 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.6696 (ttp-170) REVERT: G 350 MET cc_start: 0.8641 (mmm) cc_final: 0.8242 (mmt) REVERT: G 357 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8796 (t) REVERT: G 403 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8957 (mt0) REVERT: G 404 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8778 (tp) REVERT: G 441 GLU cc_start: 0.8555 (tt0) cc_final: 0.8238 (mt-10) REVERT: G 447 GLN cc_start: 0.7470 (mt0) cc_final: 0.7144 (mp10) REVERT: G 448 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8441 (tp) REVERT: G 465 GLU cc_start: 0.9075 (tt0) cc_final: 0.8737 (mm-30) REVERT: G 500 LEU cc_start: 0.9073 (mt) cc_final: 0.8871 (mm) REVERT: G 557 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8328 (mp10) REVERT: G 579 ASP cc_start: 0.8723 (p0) cc_final: 0.8368 (t0) REVERT: G 587 MET cc_start: 0.9072 (mtt) cc_final: 0.8834 (mtm) outliers start: 125 outliers final: 69 residues processed: 369 average time/residue: 1.4962 time to fit residues: 621.8837 Evaluate side-chains 374 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 277 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 0.0770 chunk 54 optimal weight: 40.0000 chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23709 Z= 0.336 Angle : 0.565 7.744 32228 Z= 0.296 Chirality : 0.048 0.165 3696 Planarity : 0.004 0.040 4249 Dihedral : 5.734 40.384 3185 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.80 % Allowed : 17.75 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 2947 helix: 0.10 (0.25), residues: 497 sheet: 0.94 (0.16), residues: 889 loop : -0.69 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 226 HIS 0.004 0.001 HIS C 263 PHE 0.013 0.001 PHE B 493 TYR 0.013 0.002 TYR C 411 ARG 0.002 0.000 ARG F 595 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 274 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7871 (m-30) cc_final: 0.7518 (t0) REVERT: A 287 ARG cc_start: 0.6151 (mtt90) cc_final: 0.5372 (tmt170) REVERT: A 344 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.6709 (ttp-170) REVERT: A 348 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7532 (pt0) REVERT: A 350 MET cc_start: 0.8572 (mmm) cc_final: 0.7753 (tmt) REVERT: A 403 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.8835 (mt0) REVERT: A 404 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.8867 (tp) REVERT: A 441 GLU cc_start: 0.8360 (tt0) cc_final: 0.8102 (mt-10) REVERT: A 447 GLN cc_start: 0.7397 (mt0) cc_final: 0.6924 (mp10) REVERT: A 465 GLU cc_start: 0.9087 (tt0) cc_final: 0.8723 (mm-30) REVERT: A 470 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8544 (mmm160) REVERT: A 541 GLN cc_start: 0.8466 (mt0) cc_final: 0.8102 (mt0) REVERT: A 557 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8398 (mp10) REVERT: A 560 GLN cc_start: 0.8662 (tp40) cc_final: 0.8186 (tp40) REVERT: A 579 ASP cc_start: 0.8757 (p0) cc_final: 0.8305 (t70) REVERT: A 586 LYS cc_start: 0.9147 (mttm) cc_final: 0.8709 (mtpt) REVERT: A 595 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7251 (ttp-110) REVERT: B 287 ARG cc_start: 0.6338 (mtt180) cc_final: 0.5422 (ttp-170) REVERT: B 299 HIS cc_start: 0.3580 (OUTLIER) cc_final: 0.3283 (p90) REVERT: B 334 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6417 (pp) REVERT: B 344 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.6411 (tmt170) REVERT: B 350 MET cc_start: 0.8329 (mmm) cc_final: 0.7475 (tmt) REVERT: B 403 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9101 (mt0) REVERT: B 404 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8673 (tp) REVERT: B 447 GLN cc_start: 0.7594 (mt0) cc_final: 0.7008 (mp10) REVERT: B 465 GLU cc_start: 0.9121 (tt0) cc_final: 0.8683 (mm-30) REVERT: B 470 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8567 (ptm160) REVERT: B 541 GLN cc_start: 0.8447 (mt0) cc_final: 0.7471 (mm-40) REVERT: B 557 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8292 (mp10) REVERT: B 579 ASP cc_start: 0.8793 (p0) cc_final: 0.8344 (t0) REVERT: B 595 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7694 (ptt180) REVERT: C 285 GLN cc_start: 0.6626 (mt0) cc_final: 0.6332 (mm-40) REVERT: C 287 ARG cc_start: 0.6315 (mtt180) cc_final: 0.5270 (tmt170) REVERT: C 344 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.6728 (ttp-170) REVERT: C 350 MET cc_start: 0.8398 (mmm) cc_final: 0.7446 (tmt) REVERT: C 389 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (tt0) REVERT: C 394 ILE cc_start: 0.9446 (mp) cc_final: 0.9163 (mm) REVERT: C 404 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8713 (tp) REVERT: C 441 GLU cc_start: 0.8465 (tt0) cc_final: 0.8055 (mt-10) REVERT: C 447 GLN cc_start: 0.7731 (mt0) cc_final: 0.7148 (mp10) REVERT: C 465 GLU cc_start: 0.9091 (tt0) cc_final: 0.8711 (mm-30) REVERT: C 470 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8486 (ptm160) REVERT: C 496 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6854 (tptm) REVERT: C 539 ASN cc_start: 0.7136 (m110) cc_final: 0.6554 (m-40) REVERT: C 541 GLN cc_start: 0.8457 (mt0) cc_final: 0.8160 (mt0) REVERT: C 545 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8069 (mtpt) REVERT: C 557 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8374 (mp10) REVERT: C 586 LYS cc_start: 0.9019 (mttm) cc_final: 0.8736 (mtpp) REVERT: D 180 ASN cc_start: 0.9304 (t0) cc_final: 0.8924 (t0) REVERT: D 285 GLN cc_start: 0.6758 (mt0) cc_final: 0.6509 (mm-40) REVERT: D 287 ARG cc_start: 0.6301 (mtt180) cc_final: 0.5337 (tmt170) REVERT: D 294 SER cc_start: 0.6465 (OUTLIER) cc_final: 0.6064 (t) REVERT: D 297 ARG cc_start: 0.5160 (OUTLIER) cc_final: 0.4806 (mmt90) REVERT: D 344 ARG cc_start: 0.7296 (ttp-110) cc_final: 0.6524 (ttp-170) REVERT: D 403 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9045 (mt0) REVERT: D 404 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.8874 (tp) REVERT: D 441 GLU cc_start: 0.8215 (tt0) cc_final: 0.7704 (tm-30) REVERT: D 447 GLN cc_start: 0.7310 (mt0) cc_final: 0.6870 (mp10) REVERT: D 465 GLU cc_start: 0.8976 (tt0) cc_final: 0.8689 (mm-30) REVERT: D 557 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8188 (mp10) REVERT: D 579 ASP cc_start: 0.8931 (p0) cc_final: 0.8511 (t0) REVERT: E 285 GLN cc_start: 0.6407 (mt0) cc_final: 0.6184 (mm-40) REVERT: E 287 ARG cc_start: 0.6178 (mtt180) cc_final: 0.5253 (ttp-110) REVERT: E 299 HIS cc_start: 0.3798 (OUTLIER) cc_final: 0.3535 (p90) REVERT: E 344 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.6402 (ttp80) REVERT: E 348 GLU cc_start: 0.8251 (tt0) cc_final: 0.7397 (tm-30) REVERT: E 350 MET cc_start: 0.8516 (mmm) cc_final: 0.8041 (ttp) REVERT: E 403 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.8852 (mt0) REVERT: E 404 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8559 (tp) REVERT: E 441 GLU cc_start: 0.8340 (tt0) cc_final: 0.7720 (tm-30) REVERT: E 446 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8234 (mmtm) REVERT: E 447 GLN cc_start: 0.7276 (mt0) cc_final: 0.6796 (mp10) REVERT: E 465 GLU cc_start: 0.9057 (tt0) cc_final: 0.8845 (mm-30) REVERT: E 557 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8036 (mp10) REVERT: E 579 ASP cc_start: 0.8797 (p0) cc_final: 0.8356 (t0) REVERT: F 285 GLN cc_start: 0.6636 (mt0) cc_final: 0.6244 (mm110) REVERT: F 287 ARG cc_start: 0.6373 (mtt90) cc_final: 0.5209 (tmt170) REVERT: F 294 SER cc_start: 0.6508 (OUTLIER) cc_final: 0.6218 (t) REVERT: F 297 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.4098 (mmt90) REVERT: F 344 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.6611 (ttp80) REVERT: F 350 MET cc_start: 0.8623 (mmm) cc_final: 0.7771 (tmt) REVERT: F 389 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: F 404 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8795 (tp) REVERT: F 441 GLU cc_start: 0.8484 (tt0) cc_final: 0.7960 (tm-30) REVERT: F 447 GLN cc_start: 0.7275 (mt0) cc_final: 0.6733 (mp10) REVERT: F 465 GLU cc_start: 0.9154 (tt0) cc_final: 0.8707 (mm-30) REVERT: F 555 ASP cc_start: 0.8004 (p0) cc_final: 0.7650 (p0) REVERT: F 557 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8320 (mp10) REVERT: F 579 ASP cc_start: 0.8886 (p0) cc_final: 0.8444 (t0) REVERT: F 595 ARG cc_start: 0.7609 (mpp80) cc_final: 0.7390 (mpp80) REVERT: G 271 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8413 (pt) REVERT: G 285 GLN cc_start: 0.6605 (mt0) cc_final: 0.6383 (mm-40) REVERT: G 287 ARG cc_start: 0.6218 (mtt90) cc_final: 0.5056 (ttp-170) REVERT: G 299 HIS cc_start: 0.3751 (OUTLIER) cc_final: 0.3543 (p-80) REVERT: G 344 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.6703 (ttp-170) REVERT: G 350 MET cc_start: 0.8662 (mmm) cc_final: 0.8286 (mmt) REVERT: G 357 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8829 (t) REVERT: G 403 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8939 (mt0) REVERT: G 404 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.8779 (tp) REVERT: G 434 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8288 (ttp) REVERT: G 441 GLU cc_start: 0.8561 (tt0) cc_final: 0.8275 (mt-10) REVERT: G 447 GLN cc_start: 0.7624 (mt0) cc_final: 0.7152 (mp10) REVERT: G 448 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8434 (tp) REVERT: G 465 GLU cc_start: 0.9149 (tt0) cc_final: 0.8787 (mm-30) REVERT: G 512 ASP cc_start: 0.9002 (t0) cc_final: 0.8761 (t70) REVERT: G 557 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8336 (mp10) REVERT: G 560 GLN cc_start: 0.8207 (tp40) cc_final: 0.7987 (tp40) REVERT: G 579 ASP cc_start: 0.8723 (p0) cc_final: 0.8359 (t0) REVERT: G 587 MET cc_start: 0.9074 (mtt) cc_final: 0.8839 (mtm) outliers start: 126 outliers final: 75 residues processed: 351 average time/residue: 1.5111 time to fit residues: 599.0051 Evaluate side-chains 372 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 268 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 264 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 299 HIS D 476 ASN E 292 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN G 422 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 23709 Z= 0.435 Angle : 0.616 12.336 32228 Z= 0.322 Chirality : 0.050 0.166 3696 Planarity : 0.005 0.043 4249 Dihedral : 5.930 40.643 3185 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.72 % Allowed : 17.90 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 2947 helix: -0.04 (0.24), residues: 497 sheet: 0.65 (0.15), residues: 945 loop : -0.78 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 226 HIS 0.010 0.001 HIS D 299 PHE 0.015 0.002 PHE B 493 TYR 0.015 0.002 TYR G 462 ARG 0.003 0.000 ARG F 595 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 264 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7894 (m-30) cc_final: 0.7513 (t0) REVERT: A 287 ARG cc_start: 0.6229 (mtt90) cc_final: 0.5381 (tmt170) REVERT: A 344 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.6736 (ttp-170) REVERT: A 348 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: A 350 MET cc_start: 0.8617 (mmm) cc_final: 0.7787 (tmt) REVERT: A 403 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.8885 (mt0) REVERT: A 404 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.8883 (tp) REVERT: A 441 GLU cc_start: 0.8350 (tt0) cc_final: 0.7954 (tm-30) REVERT: A 447 GLN cc_start: 0.7412 (mt0) cc_final: 0.6953 (mp10) REVERT: A 465 GLU cc_start: 0.9076 (tt0) cc_final: 0.8716 (mm-30) REVERT: A 470 ARG cc_start: 0.9029 (mtt180) cc_final: 0.8545 (mmm160) REVERT: A 557 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8364 (mp10) REVERT: A 560 GLN cc_start: 0.8663 (tp40) cc_final: 0.8198 (tp40) REVERT: A 579 ASP cc_start: 0.8743 (p0) cc_final: 0.8294 (t70) REVERT: A 586 LYS cc_start: 0.9154 (mttm) cc_final: 0.8719 (mtpt) REVERT: A 595 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7270 (ttp-110) REVERT: B 287 ARG cc_start: 0.6406 (mtt180) cc_final: 0.5445 (ttp-170) REVERT: B 299 HIS cc_start: 0.3687 (OUTLIER) cc_final: 0.3365 (p90) REVERT: B 334 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6377 (pp) REVERT: B 344 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.6539 (ttp80) REVERT: B 350 MET cc_start: 0.8367 (mmm) cc_final: 0.7498 (tmt) REVERT: B 403 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.9152 (mt0) REVERT: B 404 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8774 (tp) REVERT: B 447 GLN cc_start: 0.7491 (mt0) cc_final: 0.6945 (mp10) REVERT: B 465 GLU cc_start: 0.9132 (tt0) cc_final: 0.8701 (mm-30) REVERT: B 470 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8566 (ptm160) REVERT: B 541 GLN cc_start: 0.8473 (mt0) cc_final: 0.7533 (mm-40) REVERT: B 557 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8259 (mp10) REVERT: B 579 ASP cc_start: 0.8778 (p0) cc_final: 0.8303 (t0) REVERT: C 285 GLN cc_start: 0.6779 (mt0) cc_final: 0.6513 (mm-40) REVERT: C 287 ARG cc_start: 0.6274 (mtt180) cc_final: 0.5198 (tmt170) REVERT: C 344 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.6713 (ttp-170) REVERT: C 350 MET cc_start: 0.8461 (mmm) cc_final: 0.7500 (tmt) REVERT: C 394 ILE cc_start: 0.9475 (mp) cc_final: 0.9177 (mm) REVERT: C 398 GLU cc_start: 0.9165 (pt0) cc_final: 0.8732 (pm20) REVERT: C 404 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8746 (tp) REVERT: C 436 TYR cc_start: 0.8740 (t80) cc_final: 0.8498 (t80) REVERT: C 441 GLU cc_start: 0.8455 (tt0) cc_final: 0.7984 (tm-30) REVERT: C 447 GLN cc_start: 0.7736 (mt0) cc_final: 0.7179 (mp10) REVERT: C 465 GLU cc_start: 0.9059 (tt0) cc_final: 0.8721 (mm-30) REVERT: C 470 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8501 (ptm160) REVERT: C 496 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6894 (tptm) REVERT: C 539 ASN cc_start: 0.7054 (m110) cc_final: 0.6484 (m-40) REVERT: C 541 GLN cc_start: 0.8457 (mt0) cc_final: 0.8161 (mt0) REVERT: C 545 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8014 (mtpt) REVERT: C 557 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8360 (mp10) REVERT: C 586 LYS cc_start: 0.9071 (mttm) cc_final: 0.8781 (mtpp) REVERT: D 180 ASN cc_start: 0.9321 (t0) cc_final: 0.8935 (t0) REVERT: D 285 GLN cc_start: 0.6833 (mt0) cc_final: 0.6532 (mm-40) REVERT: D 287 ARG cc_start: 0.6304 (mtt180) cc_final: 0.5343 (tmt170) REVERT: D 294 SER cc_start: 0.6528 (OUTLIER) cc_final: 0.6072 (t) REVERT: D 297 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4846 (mmt90) REVERT: D 344 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.6753 (ttp-170) REVERT: D 403 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.9080 (mt0) REVERT: D 441 GLU cc_start: 0.8230 (tt0) cc_final: 0.7733 (tm-30) REVERT: D 447 GLN cc_start: 0.7351 (mt0) cc_final: 0.6874 (mp10) REVERT: D 465 GLU cc_start: 0.8973 (tt0) cc_final: 0.8695 (mm-30) REVERT: D 557 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8188 (mp10) REVERT: D 579 ASP cc_start: 0.8942 (p0) cc_final: 0.8512 (t0) REVERT: E 285 GLN cc_start: 0.6505 (mt0) cc_final: 0.6257 (mm-40) REVERT: E 287 ARG cc_start: 0.6266 (mtt180) cc_final: 0.5319 (ttp-110) REVERT: E 344 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.6434 (ttp80) REVERT: E 350 MET cc_start: 0.8590 (mmm) cc_final: 0.7976 (ttp) REVERT: E 403 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: E 404 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8620 (tp) REVERT: E 441 GLU cc_start: 0.8363 (tt0) cc_final: 0.7734 (tm-30) REVERT: E 446 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8300 (mmtm) REVERT: E 447 GLN cc_start: 0.7418 (mt0) cc_final: 0.6930 (mp10) REVERT: E 465 GLU cc_start: 0.9039 (tt0) cc_final: 0.8829 (mm-30) REVERT: E 486 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: E 557 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8040 (mp10) REVERT: E 579 ASP cc_start: 0.8751 (p0) cc_final: 0.8285 (t0) REVERT: F 285 GLN cc_start: 0.6729 (mt0) cc_final: 0.6363 (mm110) REVERT: F 287 ARG cc_start: 0.6374 (mtt180) cc_final: 0.5164 (tmt170) REVERT: F 294 SER cc_start: 0.6575 (OUTLIER) cc_final: 0.6251 (t) REVERT: F 297 ARG cc_start: 0.4592 (OUTLIER) cc_final: 0.4111 (mmt90) REVERT: F 344 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.6625 (ttp80) REVERT: F 350 MET cc_start: 0.8684 (mmm) cc_final: 0.7808 (tmt) REVERT: F 389 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: F 404 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8848 (tp) REVERT: F 441 GLU cc_start: 0.8427 (tt0) cc_final: 0.7924 (tm-30) REVERT: F 447 GLN cc_start: 0.7277 (mt0) cc_final: 0.6732 (mp10) REVERT: F 465 GLU cc_start: 0.9150 (tt0) cc_final: 0.8717 (mm-30) REVERT: F 555 ASP cc_start: 0.8086 (p0) cc_final: 0.7786 (p0) REVERT: F 557 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8365 (mp10) REVERT: F 579 ASP cc_start: 0.8920 (p0) cc_final: 0.8534 (t0) REVERT: F 586 LYS cc_start: 0.9050 (mttm) cc_final: 0.8724 (mtpt) REVERT: F 595 ARG cc_start: 0.7561 (mpp80) cc_final: 0.7175 (ptt-90) REVERT: G 271 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8367 (pt) REVERT: G 285 GLN cc_start: 0.6754 (mt0) cc_final: 0.6506 (mm-40) REVERT: G 287 ARG cc_start: 0.6205 (mtt90) cc_final: 0.4939 (ttp-170) REVERT: G 344 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6443 (ttp80) REVERT: G 350 MET cc_start: 0.8695 (mmm) cc_final: 0.7910 (ttp) REVERT: G 357 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8804 (t) REVERT: G 403 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8975 (mt0) REVERT: G 441 GLU cc_start: 0.8623 (tt0) cc_final: 0.8289 (mt-10) REVERT: G 447 GLN cc_start: 0.7588 (mt0) cc_final: 0.7179 (mp10) REVERT: G 448 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8529 (tp) REVERT: G 465 GLU cc_start: 0.9148 (tt0) cc_final: 0.8792 (mm-30) REVERT: G 512 ASP cc_start: 0.9016 (t0) cc_final: 0.8781 (t70) REVERT: G 557 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8155 (mp10) REVERT: G 579 ASP cc_start: 0.8726 (p0) cc_final: 0.8377 (t0) REVERT: G 587 MET cc_start: 0.9115 (mtt) cc_final: 0.8844 (mtm) outliers start: 124 outliers final: 81 residues processed: 344 average time/residue: 1.4891 time to fit residues: 578.1789 Evaluate side-chains 368 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 263 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.1980 chunk 279 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS E 299 HIS ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS G 422 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23709 Z= 0.209 Angle : 0.533 9.332 32228 Z= 0.280 Chirality : 0.045 0.161 3696 Planarity : 0.004 0.037 4249 Dihedral : 5.510 39.529 3185 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.89 % Allowed : 19.01 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2947 helix: 0.29 (0.26), residues: 497 sheet: 0.93 (0.16), residues: 889 loop : -0.67 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 226 HIS 0.011 0.001 HIS E 299 PHE 0.012 0.001 PHE B 493 TYR 0.012 0.001 TYR C 411 ARG 0.002 0.000 ARG D 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 281 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7950 (m-30) cc_final: 0.7547 (t0) REVERT: A 287 ARG cc_start: 0.6167 (mtt90) cc_final: 0.5359 (tmt170) REVERT: A 344 ARG cc_start: 0.7326 (ttp-110) cc_final: 0.6618 (ttp-170) REVERT: A 350 MET cc_start: 0.8507 (mmm) cc_final: 0.7565 (tmt) REVERT: A 403 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.8824 (mt0) REVERT: A 404 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8819 (tp) REVERT: A 441 GLU cc_start: 0.8357 (tt0) cc_final: 0.8093 (mt-10) REVERT: A 447 GLN cc_start: 0.7408 (mt0) cc_final: 0.6942 (mp10) REVERT: A 465 GLU cc_start: 0.9067 (tt0) cc_final: 0.8715 (mm-30) REVERT: A 470 ARG cc_start: 0.9018 (mtt180) cc_final: 0.8540 (mmm160) REVERT: A 557 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8462 (mp10) REVERT: A 560 GLN cc_start: 0.8599 (tp40) cc_final: 0.8118 (tp40) REVERT: A 570 ASN cc_start: 0.8715 (m-40) cc_final: 0.8466 (p0) REVERT: A 579 ASP cc_start: 0.8774 (p0) cc_final: 0.8284 (t70) REVERT: A 586 LYS cc_start: 0.9161 (mttm) cc_final: 0.8748 (mtpt) REVERT: A 595 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7221 (ttp-110) REVERT: B 287 ARG cc_start: 0.6389 (mtt180) cc_final: 0.5431 (ttp-170) REVERT: B 299 HIS cc_start: 0.3650 (OUTLIER) cc_final: 0.3358 (p90) REVERT: B 334 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6370 (pp) REVERT: B 344 ARG cc_start: 0.7426 (ttp-110) cc_final: 0.6476 (ttp80) REVERT: B 350 MET cc_start: 0.8293 (mmm) cc_final: 0.7461 (tmt) REVERT: B 403 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.9096 (mt0) REVERT: B 404 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8640 (tp) REVERT: B 447 GLN cc_start: 0.7520 (mt0) cc_final: 0.6955 (mp10) REVERT: B 465 GLU cc_start: 0.9130 (tt0) cc_final: 0.8720 (mm-30) REVERT: B 470 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8556 (ptm160) REVERT: B 541 GLN cc_start: 0.8456 (mt0) cc_final: 0.7467 (mm-40) REVERT: B 579 ASP cc_start: 0.8794 (p0) cc_final: 0.8336 (t0) REVERT: B 595 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7668 (ptt180) REVERT: C 285 GLN cc_start: 0.6710 (mt0) cc_final: 0.6469 (mm-40) REVERT: C 287 ARG cc_start: 0.6300 (mtt180) cc_final: 0.5242 (tmt170) REVERT: C 344 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6581 (ttp80) REVERT: C 350 MET cc_start: 0.8387 (mmm) cc_final: 0.7378 (tmt) REVERT: C 394 ILE cc_start: 0.9411 (mp) cc_final: 0.9155 (mm) REVERT: C 398 GLU cc_start: 0.9164 (pt0) cc_final: 0.8787 (pm20) REVERT: C 404 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8693 (tp) REVERT: C 436 TYR cc_start: 0.8700 (t80) cc_final: 0.8471 (t80) REVERT: C 441 GLU cc_start: 0.8329 (tt0) cc_final: 0.7913 (mt-10) REVERT: C 447 GLN cc_start: 0.7722 (mt0) cc_final: 0.7141 (mp10) REVERT: C 465 GLU cc_start: 0.9060 (tt0) cc_final: 0.8716 (mm-30) REVERT: C 470 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8474 (ptm160) REVERT: C 496 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6889 (tptm) REVERT: C 539 ASN cc_start: 0.7009 (m110) cc_final: 0.6442 (m-40) REVERT: C 541 GLN cc_start: 0.8413 (mt0) cc_final: 0.8129 (mt0) REVERT: C 545 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7992 (mtpt) REVERT: C 557 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8432 (mp10) REVERT: C 586 LYS cc_start: 0.9009 (mttm) cc_final: 0.8732 (mtpp) REVERT: D 180 ASN cc_start: 0.9301 (t0) cc_final: 0.8917 (t0) REVERT: D 285 GLN cc_start: 0.6882 (mt0) cc_final: 0.6591 (mm-40) REVERT: D 287 ARG cc_start: 0.6277 (mtt180) cc_final: 0.5343 (tmt170) REVERT: D 344 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.6605 (ttp-170) REVERT: D 403 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8996 (mt0) REVERT: D 404 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 441 GLU cc_start: 0.8310 (tt0) cc_final: 0.7794 (tm-30) REVERT: D 447 GLN cc_start: 0.7282 (mt0) cc_final: 0.6872 (mp10) REVERT: D 465 GLU cc_start: 0.8956 (tt0) cc_final: 0.8684 (mm-30) REVERT: D 557 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8187 (mp10) REVERT: D 579 ASP cc_start: 0.8948 (p0) cc_final: 0.8527 (t0) REVERT: E 285 GLN cc_start: 0.6418 (mt0) cc_final: 0.6195 (mm-40) REVERT: E 287 ARG cc_start: 0.6260 (mtt180) cc_final: 0.5328 (ttp-110) REVERT: E 344 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.6345 (ttp80) REVERT: E 348 GLU cc_start: 0.8229 (tt0) cc_final: 0.7368 (tm-30) REVERT: E 350 MET cc_start: 0.8482 (mmm) cc_final: 0.8033 (ttp) REVERT: E 403 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.8812 (mt0) REVERT: E 404 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8553 (tp) REVERT: E 441 GLU cc_start: 0.8345 (tt0) cc_final: 0.7714 (tm-30) REVERT: E 447 GLN cc_start: 0.7266 (mt0) cc_final: 0.6737 (mm-40) REVERT: E 465 GLU cc_start: 0.9002 (tt0) cc_final: 0.8802 (mm-30) REVERT: E 557 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8060 (mp10) REVERT: E 579 ASP cc_start: 0.8848 (p0) cc_final: 0.8349 (t0) REVERT: F 285 GLN cc_start: 0.6678 (mt0) cc_final: 0.6403 (mm110) REVERT: F 287 ARG cc_start: 0.6369 (mtt180) cc_final: 0.5177 (tmt170) REVERT: F 294 SER cc_start: 0.6554 (OUTLIER) cc_final: 0.6272 (t) REVERT: F 297 ARG cc_start: 0.4566 (OUTLIER) cc_final: 0.4069 (mmt90) REVERT: F 344 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.6587 (ttp80) REVERT: F 350 MET cc_start: 0.8615 (mmm) cc_final: 0.7703 (tmt) REVERT: F 389 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: F 404 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8784 (tp) REVERT: F 441 GLU cc_start: 0.8474 (tt0) cc_final: 0.7983 (tm-30) REVERT: F 447 GLN cc_start: 0.7244 (mt0) cc_final: 0.6706 (mp10) REVERT: F 465 GLU cc_start: 0.9151 (tt0) cc_final: 0.8716 (mm-30) REVERT: F 557 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8372 (mp10) REVERT: F 579 ASP cc_start: 0.8882 (p0) cc_final: 0.8425 (t0) REVERT: F 595 ARG cc_start: 0.7692 (mpp80) cc_final: 0.7364 (ptt-90) REVERT: G 271 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8424 (pt) REVERT: G 285 GLN cc_start: 0.6604 (mt0) cc_final: 0.6347 (mm-40) REVERT: G 287 ARG cc_start: 0.6165 (mtt90) cc_final: 0.4909 (ttp-170) REVERT: G 344 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.6593 (ttp80) REVERT: G 350 MET cc_start: 0.8624 (mmm) cc_final: 0.8224 (mmt) REVERT: G 403 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8958 (mt0) REVERT: G 404 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8681 (tp) REVERT: G 434 MET cc_start: 0.8535 (ttm) cc_final: 0.8313 (ttp) REVERT: G 441 GLU cc_start: 0.8565 (tt0) cc_final: 0.8279 (mt-10) REVERT: G 447 GLN cc_start: 0.7569 (mt0) cc_final: 0.7146 (mp10) REVERT: G 465 GLU cc_start: 0.9075 (tt0) cc_final: 0.8793 (mm-30) REVERT: G 512 ASP cc_start: 0.8989 (t0) cc_final: 0.8770 (t70) REVERT: G 557 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8350 (mp10) REVERT: G 562 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8808 (tp) REVERT: G 579 ASP cc_start: 0.8693 (p0) cc_final: 0.8312 (t0) REVERT: G 587 MET cc_start: 0.9063 (mtt) cc_final: 0.8814 (mtm) REVERT: G 595 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7262 (ptt-90) outliers start: 102 outliers final: 66 residues processed: 343 average time/residue: 1.5239 time to fit residues: 588.5525 Evaluate side-chains 361 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 275 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 233 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN B 499 ASN C 299 HIS ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 476 ASN D 274 ASN D 299 HIS E 299 HIS E 422 ASN F 422 ASN G 299 HIS G 422 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101753 restraints weight = 32151.413| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.78 r_work: 0.3080 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23709 Z= 0.289 Angle : 0.559 10.216 32228 Z= 0.292 Chirality : 0.047 0.163 3696 Planarity : 0.004 0.040 4249 Dihedral : 5.521 40.195 3182 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.96 % Allowed : 19.01 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2947 helix: 0.27 (0.25), residues: 497 sheet: 0.93 (0.16), residues: 889 loop : -0.70 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 226 HIS 0.012 0.001 HIS D 299 PHE 0.013 0.001 PHE B 493 TYR 0.013 0.001 TYR C 411 ARG 0.002 0.000 ARG G 449 =============================================================================== Job complete usr+sys time: 9954.92 seconds wall clock time: 174 minutes 22.54 seconds (10462.54 seconds total)