Starting phenix.real_space_refine on Sun Sep 13 11:00:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.cif" model { file = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2026/3j9c_6224.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: B, C, D, E, F, G Time building chain proxies: 3.91, per 1000 atoms: 0.17 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: 1.65 Conformation dependent library (CDL) restraints added in 994.6 milliseconds 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: 0.79 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: 4.61 Time building geometry restraints manager: 2.28 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: 0.08 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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= 0.360 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.003 0.001 ARG D 359 TYR 0.013 0.002 TYR B 456 PHE 0.011 0.001 PHE D 493 TRP 0.012 0.002 TRP G 226 HIS 0.003 0.001 HIS D 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.36 (23709) covalent geometry : angle 1.11209 / 0.74 (32228) hydrogen bonds : bond 0.10893 / 7.19 ( 805) hydrogen bonds : angle 10.38417 / 7.17 ( 2184) *********************** 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 to be fit. rotamer outliers: 161 poor density : 600 time to evaluate : 0.909 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: 0.8925 (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: 0.6521 time to fit residues: 523.0736 Evaluate side-chains 415 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0270 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 389 GLN A 424 GLN A 483 GLN A 499 ASN A 541 GLN A 560 GLN B 198 ASN B 268 ASN B 274 ASN B 483 GLN B 557 GLN C 263 HIS C 268 ASN C 389 GLN C 483 GLN D 198 ASN D 268 ASN D 274 ASN D 424 GLN D 499 ASN D 541 GLN E 263 HIS E 268 ASN E 274 ASN E 389 GLN E 424 GLN E 483 GLN E 570 ASN F 268 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105721 restraints weight = 32541.540| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.84 r_work: 0.3150 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23709 Z= 0.125 Angle : 0.542 5.367 32228 Z= 0.295 Chirality : 0.046 0.160 3696 Planarity : 0.004 0.033 4249 Dihedral : 7.543 56.820 3281 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.24 % Allowed : 16.00 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2947 helix: -0.26 (0.25), residues: 497 sheet: -0.20 (0.15), residues: 980 loop : 0.08 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 365 TYR 0.011 0.001 TYR C 410 PHE 0.013 0.001 PHE B 493 TRP 0.018 0.002 TRP A 226 HIS 0.012 0.001 HIS E 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (23709) covalent geometry : angle 0.54208 / 0.29 (32228) hydrogen bonds : bond 0.03015 / 2.03 ( 805) hydrogen bonds : angle 6.98139 / 4.83 ( 2184) *********************** 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 451 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 366 time to evaluate : 0.918 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 287 ARG cc_start: 0.6391 (mtt90) cc_final: 0.5796 (tmt170) REVERT: A 291 LYS cc_start: 0.6629 (tptt) cc_final: 0.6162 (tptt) REVERT: A 294 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.6718 (t) REVERT: A 343 GLU cc_start: 0.7767 (tt0) cc_final: 0.7475 (tt0) REVERT: A 344 ARG cc_start: 0.7062 (ttp-110) cc_final: 0.6728 (ttp80) REVERT: A 350 MET cc_start: 0.7866 (mmm) cc_final: 0.7288 (tmt) REVERT: A 542 TYR cc_start: 0.8571 (t80) cc_final: 0.8115 (t80) REVERT: A 560 GLN cc_start: 0.8416 (tp40) cc_final: 0.8162 (tp40) REVERT: A 586 LYS cc_start: 0.8807 (mttm) cc_final: 0.8582 (mtpp) REVERT: B 287 ARG cc_start: 0.6285 (mtt90) cc_final: 0.5775 (ttp-170) REVERT: B 294 SER cc_start: 0.7112 (OUTLIER) cc_final: 0.6403 (t) REVERT: B 334 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6967 (mt) REVERT: B 350 MET cc_start: 0.7766 (mmm) cc_final: 0.7508 (tmt) REVERT: B 356 ASP cc_start: 0.8018 (t0) cc_final: 0.7709 (t0) REVERT: B 447 GLN cc_start: 0.7483 (mt0) cc_final: 0.7224 (mp10) REVERT: C 287 ARG cc_start: 0.6524 (mtt90) cc_final: 0.5882 (ttp-110) REVERT: C 291 LYS cc_start: 0.6218 (tptt) cc_final: 0.6017 (tttm) REVERT: C 344 ARG cc_start: 0.7073 (ttp-110) cc_final: 0.6839 (ttp80) REVERT: C 350 MET cc_start: 0.7711 (mmm) cc_final: 0.7121 (tmt) REVERT: C 356 ASP cc_start: 0.7901 (t0) cc_final: 0.7563 (t0) REVERT: C 426 ASP cc_start: 0.8417 (m-30) cc_final: 0.8173 (m-30) REVERT: C 447 GLN cc_start: 0.7589 (mt0) cc_final: 0.7297 (mp10) REVERT: C 545 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7681 (mtpt) REVERT: C 587 MET cc_start: 0.8295 (mtt) cc_final: 0.8033 (mtp) REVERT: C 595 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7451 (ptt180) REVERT: D 180 ASN cc_start: 0.8630 (t0) cc_final: 0.8084 (t0) REVERT: D 287 ARG cc_start: 0.6520 (mtt90) cc_final: 0.5998 (ttp-110) REVERT: D 334 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6616 (pp) REVERT: D 344 ARG cc_start: 0.7015 (ttp-110) cc_final: 0.6805 (ttp-170) REVERT: D 350 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7509 (OUTLIER) REVERT: D 356 ASP cc_start: 0.8019 (t0) cc_final: 0.7648 (t70) REVERT: D 447 GLN cc_start: 0.7256 (mt0) cc_final: 0.7053 (mp10) REVERT: D 557 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7644 (tp-100) REVERT: D 587 MET cc_start: 0.8177 (mtt) cc_final: 0.7953 (mtp) REVERT: D 595 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7170 (ptt-90) REVERT: E 209 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6800 (p0) REVERT: E 271 LEU cc_start: 0.8465 (pt) cc_final: 0.8250 (pt) REVERT: E 287 ARG cc_start: 0.6552 (mtt90) cc_final: 0.5793 (ttp-110) REVERT: E 294 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.7098 (t) REVERT: E 344 ARG cc_start: 0.6587 (ttp-110) cc_final: 0.6255 (ttp80) REVERT: E 348 GLU cc_start: 0.7885 (tt0) cc_final: 0.7066 (tm-30) REVERT: E 356 ASP cc_start: 0.7637 (t0) cc_final: 0.7340 (t0) REVERT: E 357 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8593 (t) REVERT: E 389 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: E 542 TYR cc_start: 0.8330 (t80) cc_final: 0.8026 (t80) REVERT: E 545 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7791 (mtpp) REVERT: E 557 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7864 (tp-100) REVERT: E 560 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7948 (tp40) REVERT: E 563 LYS cc_start: 0.8555 (tppp) cc_final: 0.8354 (ttmm) REVERT: E 595 ARG cc_start: 0.7831 (mpp80) cc_final: 0.7535 (ptt-90) REVERT: F 209 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.6807 (p0) REVERT: F 263 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8529 (p90) REVERT: F 271 LEU cc_start: 0.8532 (pt) cc_final: 0.8266 (pp) REVERT: F 287 ARG cc_start: 0.6535 (mtt90) cc_final: 0.5671 (tmt170) REVERT: F 330 SER cc_start: 0.6412 (m) cc_final: 0.5791 (t) REVERT: F 344 ARG cc_start: 0.6819 (ttp-110) cc_final: 0.6584 (ttp80) REVERT: F 350 MET cc_start: 0.7798 (mmm) cc_final: 0.7383 (tmt) REVERT: F 356 ASP cc_start: 0.7717 (t0) cc_final: 0.7450 (t0) REVERT: F 441 GLU cc_start: 0.7940 (tt0) cc_final: 0.7681 (tm-30) REVERT: F 444 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7677 (mtpp) REVERT: F 545 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7708 (mtpt) REVERT: F 560 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7940 (tp-100) REVERT: F 587 MET cc_start: 0.8373 (mtp) cc_final: 0.8172 (ttp) REVERT: F 595 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7026 (ptt-90) REVERT: G 287 ARG cc_start: 0.6474 (mtt90) cc_final: 0.5599 (ttp-170) REVERT: G 334 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7036 (mt) REVERT: G 344 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6679 (ttp-170) REVERT: G 350 MET cc_start: 0.7952 (mmm) cc_final: 0.7629 (mmt) REVERT: G 357 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8472 (t) REVERT: G 448 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (tt) REVERT: G 486 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: G 557 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7950 (tp-100) REVERT: G 586 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8743 (mtpt) REVERT: G 595 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7088 (ptt180) outliers start: 85 outliers final: 31 residues processed: 422 average time/residue: 0.7171 time to fit residues: 341.0242 Evaluate side-chains 351 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 569 LEU 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 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 448 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 334 ILE 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 433 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 209 ASN 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 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 263 HIS 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 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR 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 251 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 114 optimal weight: 0.2980 chunk 225 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 ASN A 285 GLN A 422 ASN A 424 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 476 ASN B 557 GLN C 389 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN D 285 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 422 ASN E 424 GLN E 476 ASN F 285 GLN F 389 GLN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 GLN G 285 GLN G 424 GLN G 541 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105130 restraints weight = 32374.318| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.81 r_work: 0.3113 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23709 Z= 0.134 Angle : 0.523 5.824 32228 Z= 0.280 Chirality : 0.045 0.163 3696 Planarity : 0.004 0.032 4249 Dihedral : 5.710 51.461 3192 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.54 % Allowed : 17.26 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2947 helix: 0.25 (0.26), residues: 497 sheet: 0.63 (0.17), residues: 875 loop : -0.30 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 470 TYR 0.011 0.001 TYR C 411 PHE 0.012 0.001 PHE E 493 TRP 0.015 0.001 TRP A 226 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (23709) covalent geometry : angle 0.52342 / 0.28 (32228) hydrogen bonds : bond 0.02920 / 1.97 ( 805) hydrogen bonds : angle 6.39507 / 4.45 ( 2184) *********************** 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 401 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6444 (mtt90) cc_final: 0.5722 (tmt170) REVERT: A 343 GLU cc_start: 0.7823 (tt0) cc_final: 0.7528 (tt0) REVERT: A 344 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6672 (ttp80) REVERT: A 350 MET cc_start: 0.7811 (mmm) cc_final: 0.7252 (tmt) REVERT: A 479 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 545 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7989 (mtpt) REVERT: A 560 GLN cc_start: 0.8531 (tp40) cc_final: 0.8125 (tp40) REVERT: A 586 LYS cc_start: 0.8918 (mttm) cc_final: 0.8591 (mtpt) REVERT: B 287 ARG cc_start: 0.6286 (mtt90) cc_final: 0.5836 (ttp-170) REVERT: B 334 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6900 (pp) REVERT: B 350 MET cc_start: 0.7800 (mmm) cc_final: 0.7519 (tmt) REVERT: B 447 GLN cc_start: 0.7505 (mt0) cc_final: 0.7245 (mp10) REVERT: B 465 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 557 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8264 (mp10) REVERT: B 563 LYS cc_start: 0.8638 (tppp) cc_final: 0.8245 (mmtp) REVERT: C 287 ARG cc_start: 0.6570 (mtt90) cc_final: 0.5927 (ttp-110) REVERT: C 350 MET cc_start: 0.7578 (mmm) cc_final: 0.7103 (tmt) REVERT: C 398 GLU cc_start: 0.8152 (pt0) cc_final: 0.7929 (pm20) REVERT: C 447 GLN cc_start: 0.7647 (mt0) cc_final: 0.7365 (mp10) REVERT: C 545 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7797 (mtpt) REVERT: C 587 MET cc_start: 0.8464 (mtt) cc_final: 0.8216 (mtp) REVERT: C 595 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7425 (ptt180) REVERT: D 180 ASN cc_start: 0.8623 (t0) cc_final: 0.8117 (t0) REVERT: D 287 ARG cc_start: 0.6333 (mtt90) cc_final: 0.5719 (ttp-110) REVERT: D 294 SER cc_start: 0.6948 (OUTLIER) cc_final: 0.6623 (t) REVERT: D 344 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6790 (ttp-170) REVERT: D 350 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7508 (OUTLIER) REVERT: D 356 ASP cc_start: 0.7820 (t0) cc_final: 0.7584 (t70) REVERT: D 545 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7832 (mtpt) REVERT: D 595 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7289 (ptt-90) REVERT: E 209 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6694 (p0) REVERT: E 287 ARG cc_start: 0.6651 (mtt90) cc_final: 0.5864 (ttp-110) REVERT: E 344 ARG cc_start: 0.6480 (ttp-110) cc_final: 0.6164 (ttp80) REVERT: E 348 GLU cc_start: 0.7820 (tt0) cc_final: 0.7029 (tm-30) REVERT: E 486 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: E 545 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7557 (mtpt) REVERT: E 551 ASP cc_start: 0.7532 (p0) cc_final: 0.7323 (p0) REVERT: E 557 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7917 (tp-100) REVERT: E 595 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7484 (ptt-90) REVERT: F 209 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.6995 (p0) REVERT: F 287 ARG cc_start: 0.6561 (mtt90) cc_final: 0.5750 (tmt170) REVERT: F 330 SER cc_start: 0.6432 (m) cc_final: 0.5755 (t) REVERT: F 344 ARG cc_start: 0.6790 (ttp-110) cc_final: 0.6562 (ttp80) REVERT: F 350 MET cc_start: 0.7739 (mmm) cc_final: 0.7394 (tmt) REVERT: F 444 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7729 (mtpp) REVERT: F 545 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7654 (mtpt) REVERT: F 557 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8236 (mp10) REVERT: F 579 ASP cc_start: 0.7417 (p0) cc_final: 0.6929 (t0) REVERT: F 595 ARG cc_start: 0.7467 (mtm180) cc_final: 0.7051 (ptt-90) REVERT: G 287 ARG cc_start: 0.6479 (mtt90) cc_final: 0.5571 (ttp-170) REVERT: G 334 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6978 (pp) REVERT: G 344 ARG cc_start: 0.6972 (ttp-110) cc_final: 0.6732 (ttp-170) REVERT: G 350 MET cc_start: 0.8010 (mmm) cc_final: 0.7669 (ttp) REVERT: G 356 ASP cc_start: 0.7936 (t0) cc_final: 0.7637 (t0) REVERT: G 357 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8359 (t) REVERT: G 403 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8811 (mt0) REVERT: G 500 LEU cc_start: 0.8801 (mm) cc_final: 0.8586 (mt) REVERT: G 595 ARG cc_start: 0.7860 (mtp180) cc_final: 0.7198 (ptt-90) outliers start: 93 outliers final: 44 residues processed: 374 average time/residue: 0.7159 time to fit residues: 300.8844 Evaluate side-chains 331 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 381 THR 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 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 433 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR 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 294 SER 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 433 THR 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 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 595 ARG Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR 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 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 403 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 136 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 268 optimal weight: 40.0000 chunk 172 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN A 424 GLN A 476 ASN B 198 ASN B 285 GLN B 424 GLN B 476 ASN C 389 GLN C 409 ASN C 422 ASN D 285 GLN D 476 ASN E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN F 198 ASN F 389 GLN F 422 ASN F 476 ASN G 285 GLN G 424 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098257 restraints weight = 32713.854| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.79 r_work: 0.3020 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 23709 Z= 0.325 Angle : 0.644 7.956 32228 Z= 0.340 Chirality : 0.052 0.162 3696 Planarity : 0.005 0.046 4249 Dihedral : 6.144 54.174 3182 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.30 % Allowed : 16.50 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 2947 helix: -0.23 (0.24), residues: 497 sheet: 0.50 (0.15), residues: 931 loop : -0.66 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 470 TYR 0.018 0.002 TYR G 462 PHE 0.016 0.002 PHE B 493 TRP 0.018 0.003 TRP A 226 HIS 0.007 0.002 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.33 (23709) covalent geometry : angle 0.64410 / 0.34 (32228) hydrogen bonds : bond 0.03648 / 2.47 ( 805) hydrogen bonds : angle 6.75934 / 4.72 ( 2184) *********************** 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 410 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 271 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6344 (mtt90) cc_final: 0.5885 (tmt170) REVERT: A 297 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.5136 (mmt90) REVERT: A 343 GLU cc_start: 0.7930 (tt0) cc_final: 0.7614 (tt0) REVERT: A 344 ARG cc_start: 0.7205 (ttp-110) cc_final: 0.6811 (ttp80) REVERT: A 350 MET cc_start: 0.7949 (mmm) cc_final: 0.7548 (tmt) REVERT: A 541 GLN cc_start: 0.8063 (mt0) cc_final: 0.7783 (mt0) REVERT: A 560 GLN cc_start: 0.8438 (tp40) cc_final: 0.8040 (tp40) REVERT: B 287 ARG cc_start: 0.6508 (mtt90) cc_final: 0.5890 (ttp-170) REVERT: B 350 MET cc_start: 0.7998 (mmm) cc_final: 0.7229 (pp-130) REVERT: B 447 GLN cc_start: 0.7643 (mt0) cc_final: 0.7252 (mp10) REVERT: B 541 GLN cc_start: 0.7941 (mt0) cc_final: 0.7505 (mt0) REVERT: B 557 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8233 (mp10) REVERT: B 563 LYS cc_start: 0.8698 (tppp) cc_final: 0.8316 (mmtp) REVERT: B 580 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8620 (mptt) REVERT: C 287 ARG cc_start: 0.6445 (mtt90) cc_final: 0.5954 (ttp-110) REVERT: C 350 MET cc_start: 0.7773 (mmm) cc_final: 0.7355 (tmt) REVERT: C 404 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9100 (tp) REVERT: C 447 GLN cc_start: 0.7749 (mt0) cc_final: 0.7405 (mp10) REVERT: C 486 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: C 541 GLN cc_start: 0.8221 (mt0) cc_final: 0.7904 (mt0) REVERT: C 563 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8591 (mttm) REVERT: D 180 ASN cc_start: 0.8675 (t0) cc_final: 0.8144 (t0) REVERT: D 287 ARG cc_start: 0.6408 (mtt90) cc_final: 0.5786 (ttp-110) REVERT: D 294 SER cc_start: 0.7164 (OUTLIER) cc_final: 0.6801 (t) REVERT: D 297 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5737 (mmt90) REVERT: D 356 ASP cc_start: 0.7917 (t0) cc_final: 0.7673 (t70) REVERT: D 541 GLN cc_start: 0.8113 (mt0) cc_final: 0.7760 (mt0) REVERT: E 287 ARG cc_start: 0.6474 (mtt90) cc_final: 0.5874 (ttp-110) REVERT: E 344 ARG cc_start: 0.6941 (ttp-110) cc_final: 0.6551 (ttp80) REVERT: E 348 GLU cc_start: 0.8006 (tt0) cc_final: 0.7647 (pt0) REVERT: E 403 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8944 (mt0) REVERT: E 486 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: E 541 GLN cc_start: 0.8184 (mt0) cc_final: 0.7756 (mt0) REVERT: E 551 ASP cc_start: 0.7503 (p0) cc_final: 0.7269 (p0) REVERT: E 557 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7859 (tp-100) REVERT: F 287 ARG cc_start: 0.6619 (mtt90) cc_final: 0.5861 (tmt170) REVERT: F 330 SER cc_start: 0.6313 (m) cc_final: 0.5385 (p) REVERT: F 344 ARG cc_start: 0.6835 (ttp-110) cc_final: 0.6609 (ttp80) REVERT: F 398 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: F 444 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7813 (mtpp) REVERT: F 557 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8308 (mp10) REVERT: G 212 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: G 287 ARG cc_start: 0.6604 (mtt90) cc_final: 0.5701 (ttp-170) REVERT: G 294 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.6524 (t) REVERT: G 344 ARG cc_start: 0.7092 (ttp-110) cc_final: 0.6813 (ttp-170) REVERT: G 357 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8512 (t) REVERT: G 403 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8833 (mt0) REVERT: G 448 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8377 (tt) REVERT: G 465 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 541 GLN cc_start: 0.8153 (mt0) cc_final: 0.7892 (mt0) outliers start: 139 outliers final: 73 residues processed: 361 average time/residue: 0.7187 time to fit residues: 292.1273 Evaluate side-chains 336 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 248 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 297 ARG 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 447 GLN 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 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 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 B residue 580 LYS 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 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 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 LYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 187 LEU 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 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN 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 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 577 VAL 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 338 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 276 ASP 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 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 283 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 129 optimal weight: 0.0000 chunk 195 optimal weight: 8.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 476 ASN C 389 GLN C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 403 GLN E 409 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104923 restraints weight = 32052.671| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.80 r_work: 0.3098 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23709 Z= 0.106 Angle : 0.499 7.211 32228 Z= 0.265 Chirality : 0.045 0.160 3696 Planarity : 0.004 0.033 4249 Dihedral : 5.130 48.222 3174 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.01 % Allowed : 18.86 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2947 helix: 0.24 (0.25), residues: 497 sheet: 0.72 (0.16), residues: 896 loop : -0.44 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 470 TYR 0.011 0.001 TYR D 410 PHE 0.012 0.001 PHE E 493 TRP 0.014 0.001 TRP D 226 HIS 0.005 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23709) covalent geometry : angle 0.49911 / 0.26 (32228) hydrogen bonds : bond 0.02789 / 1.89 ( 805) hydrogen bonds : angle 6.09129 / 4.27 ( 2184) *********************** 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 357 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 278 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6308 (mtt90) cc_final: 0.5897 (tmt170) REVERT: A 343 GLU cc_start: 0.7792 (tt0) cc_final: 0.7432 (tt0) REVERT: A 344 ARG cc_start: 0.7015 (ttp-110) cc_final: 0.6631 (ttp80) REVERT: A 350 MET cc_start: 0.7860 (mmm) cc_final: 0.7117 (tmt) REVERT: A 388 ASN cc_start: 0.8584 (p0) cc_final: 0.8379 (p0) REVERT: A 479 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 541 GLN cc_start: 0.7862 (mt0) cc_final: 0.7577 (mt0) REVERT: A 545 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8038 (mtpt) REVERT: A 560 GLN cc_start: 0.8367 (tp40) cc_final: 0.7931 (tp40) REVERT: A 570 ASN cc_start: 0.8636 (m-40) cc_final: 0.8087 (p0) REVERT: A 595 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7009 (ptt180) REVERT: B 287 ARG cc_start: 0.6541 (mtt90) cc_final: 0.5861 (ttp-170) REVERT: B 334 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7090 (pp) REVERT: B 350 MET cc_start: 0.7876 (mmm) cc_final: 0.7549 (tmt) REVERT: B 447 GLN cc_start: 0.7595 (mt0) cc_final: 0.7228 (mp10) REVERT: B 465 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 557 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8311 (mp10) REVERT: B 563 LYS cc_start: 0.8626 (tppp) cc_final: 0.8326 (ttmm) REVERT: C 287 ARG cc_start: 0.6482 (mtt90) cc_final: 0.5905 (ttp-110) REVERT: C 350 MET cc_start: 0.7726 (mmm) cc_final: 0.7199 (tmt) REVERT: C 447 GLN cc_start: 0.7667 (mt0) cc_final: 0.7400 (mp10) REVERT: C 541 GLN cc_start: 0.8147 (mt0) cc_final: 0.7834 (mt0) REVERT: C 563 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8568 (mttm) REVERT: C 587 MET cc_start: 0.8674 (mtt) cc_final: 0.8377 (mtp) REVERT: C 595 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7307 (ptt180) REVERT: D 180 ASN cc_start: 0.8555 (t0) cc_final: 0.8078 (t0) REVERT: D 287 ARG cc_start: 0.6451 (mtt90) cc_final: 0.5813 (ttp-110) REVERT: D 465 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 586 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8808 (mtpp) REVERT: D 595 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7153 (ptp90) REVERT: E 287 ARG cc_start: 0.6435 (mtt90) cc_final: 0.5814 (ttp-110) REVERT: E 294 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7473 (t) REVERT: E 344 ARG cc_start: 0.6746 (ttp-110) cc_final: 0.6413 (ttp80) REVERT: E 348 GLU cc_start: 0.7818 (tt0) cc_final: 0.6934 (tm-30) REVERT: E 541 GLN cc_start: 0.8027 (mt0) cc_final: 0.7628 (mt0) REVERT: E 557 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8008 (mp10) REVERT: F 287 ARG cc_start: 0.6550 (mtt90) cc_final: 0.5733 (tmt170) REVERT: F 330 SER cc_start: 0.6326 (m) cc_final: 0.5636 (t) REVERT: F 344 ARG cc_start: 0.6825 (ttp-110) cc_final: 0.6588 (ttp80) REVERT: F 350 MET cc_start: 0.7970 (mtt) cc_final: 0.7495 (tmt) REVERT: F 444 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7908 (mtpp) REVERT: F 595 ARG cc_start: 0.7711 (mpp80) cc_final: 0.7385 (ptt-90) REVERT: G 287 ARG cc_start: 0.6578 (mtt90) cc_final: 0.5619 (ttp-170) REVERT: G 344 ARG cc_start: 0.7090 (ttp-110) cc_final: 0.6884 (ttp-170) REVERT: G 356 ASP cc_start: 0.7833 (t0) cc_final: 0.7584 (t0) REVERT: G 357 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8319 (t) REVERT: G 403 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8707 (mt0) REVERT: G 500 LEU cc_start: 0.8945 (mm) cc_final: 0.8688 (mt) REVERT: G 520 ASP cc_start: 0.8556 (m-30) cc_final: 0.8349 (m-30) REVERT: G 541 GLN cc_start: 0.8017 (mt0) cc_final: 0.7689 (mt0) REVERT: G 562 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8696 (tp) REVERT: G 563 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8562 (mttm) outliers start: 79 outliers final: 35 residues processed: 335 average time/residue: 0.7342 time to fit residues: 276.1224 Evaluate side-chains 299 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 497 ASP 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 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 357 THR 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 330 SER Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 563 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 253 optimal weight: 0.0770 chunk 183 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 197 optimal weight: 0.1980 chunk 287 optimal weight: 1.9990 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 476 ASN B 424 GLN B 476 ASN C 389 GLN C 403 GLN C 422 ASN C 424 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 403 GLN E 422 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN F 422 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105028 restraints weight = 32354.417| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.82 r_work: 0.3095 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23709 Z= 0.112 Angle : 0.501 6.868 32228 Z= 0.263 Chirality : 0.045 0.159 3696 Planarity : 0.004 0.033 4249 Dihedral : 4.830 42.627 3170 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.39 % Allowed : 19.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2947 helix: 0.65 (0.27), residues: 455 sheet: 0.95 (0.16), residues: 938 loop : -0.18 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 470 TYR 0.012 0.001 TYR F 410 PHE 0.012 0.001 PHE E 493 TRP 0.014 0.001 TRP D 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (23709) covalent geometry : angle 0.50052 / 0.26 (32228) hydrogen bonds : bond 0.02710 / 1.84 ( 805) hydrogen bonds : angle 5.88915 / 4.12 ( 2184) *********************** 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 358 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 269 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7869 (m-30) cc_final: 0.7278 (t70) REVERT: A 287 ARG cc_start: 0.6351 (mtt90) cc_final: 0.5819 (tmt170) REVERT: A 343 GLU cc_start: 0.7815 (tt0) cc_final: 0.7480 (tt0) REVERT: A 344 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6600 (ttp80) REVERT: A 350 MET cc_start: 0.7915 (mmm) cc_final: 0.7193 (tmt) REVERT: A 388 ASN cc_start: 0.8589 (p0) cc_final: 0.8375 (p0) REVERT: A 541 GLN cc_start: 0.7928 (mt0) cc_final: 0.7707 (mt0) REVERT: A 560 GLN cc_start: 0.8333 (tp40) cc_final: 0.7888 (tp40) REVERT: A 570 ASN cc_start: 0.8619 (m-40) cc_final: 0.8079 (p0) REVERT: A 595 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7059 (ptt180) REVERT: B 180 ASN cc_start: 0.8585 (t0) cc_final: 0.8058 (t0) REVERT: B 287 ARG cc_start: 0.6402 (mtt90) cc_final: 0.5855 (ttp-170) REVERT: B 334 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7075 (pp) REVERT: B 350 MET cc_start: 0.7857 (mmm) cc_final: 0.7298 (tmt) REVERT: B 447 GLN cc_start: 0.7544 (mt0) cc_final: 0.7192 (mp10) REVERT: B 465 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 541 GLN cc_start: 0.7934 (mt0) cc_final: 0.7592 (mt0) REVERT: B 557 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8398 (mp10) REVERT: B 563 LYS cc_start: 0.8641 (tppp) cc_final: 0.8331 (mmtp) REVERT: C 276 ASP cc_start: 0.8022 (m-30) cc_final: 0.7731 (t70) REVERT: C 287 ARG cc_start: 0.6480 (mtt90) cc_final: 0.5872 (ttp-110) REVERT: C 350 MET cc_start: 0.7699 (mmm) cc_final: 0.7167 (tmt) REVERT: C 356 ASP cc_start: 0.7695 (t0) cc_final: 0.7337 (t0) REVERT: C 394 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9128 (mm) REVERT: C 441 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7739 (pt0) REVERT: C 447 GLN cc_start: 0.7636 (mt0) cc_final: 0.7402 (mp10) REVERT: C 541 GLN cc_start: 0.8050 (mt0) cc_final: 0.7828 (mt0) REVERT: C 563 LYS cc_start: 0.8887 (tppp) cc_final: 0.8569 (mttm) REVERT: C 587 MET cc_start: 0.8691 (mtt) cc_final: 0.8389 (mtp) REVERT: C 595 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7363 (ptt180) REVERT: D 180 ASN cc_start: 0.8530 (t0) cc_final: 0.8092 (t0) REVERT: D 221 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8936 (p) REVERT: D 287 ARG cc_start: 0.6549 (mtt90) cc_final: 0.5974 (ttp-110) REVERT: D 335 ASP cc_start: 0.7613 (m-30) cc_final: 0.7365 (m-30) REVERT: D 398 GLU cc_start: 0.7784 (pm20) cc_final: 0.7521 (pm20) REVERT: D 595 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7057 (ptt-90) REVERT: E 287 ARG cc_start: 0.6462 (mtt90) cc_final: 0.5821 (ttp-110) REVERT: E 294 SER cc_start: 0.7726 (OUTLIER) cc_final: 0.7277 (t) REVERT: E 344 ARG cc_start: 0.6700 (ttp-110) cc_final: 0.6367 (ttp80) REVERT: E 348 GLU cc_start: 0.7878 (tt0) cc_final: 0.6980 (tm-30) REVERT: E 486 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: E 541 GLN cc_start: 0.8072 (mt0) cc_final: 0.7779 (tt0) REVERT: E 557 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8087 (mp10) REVERT: E 595 ARG cc_start: 0.7846 (mpp80) cc_final: 0.7550 (ptt-90) REVERT: F 271 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (pp) REVERT: F 287 ARG cc_start: 0.6526 (mtt90) cc_final: 0.5692 (tmt170) REVERT: F 330 SER cc_start: 0.6132 (m) cc_final: 0.5455 (t) REVERT: F 344 ARG cc_start: 0.6802 (ttp-110) cc_final: 0.6564 (ttp80) REVERT: F 350 MET cc_start: 0.7973 (mtt) cc_final: 0.7495 (tmt) REVERT: F 356 ASP cc_start: 0.7776 (t0) cc_final: 0.7470 (t0) REVERT: F 570 ASN cc_start: 0.8436 (m-40) cc_final: 0.8066 (p0) REVERT: F 587 MET cc_start: 0.8501 (mtp) cc_final: 0.8281 (mtp) REVERT: F 595 ARG cc_start: 0.7711 (mpp80) cc_final: 0.7367 (ptt-90) REVERT: G 212 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: G 287 ARG cc_start: 0.6580 (mtt90) cc_final: 0.5539 (ttp-170) REVERT: G 344 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6849 (ttp-170) REVERT: G 357 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8482 (t) REVERT: G 403 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8743 (mt0) REVERT: G 486 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: G 500 LEU cc_start: 0.8880 (mm) cc_final: 0.8672 (mt) REVERT: G 520 ASP cc_start: 0.8515 (m-30) cc_final: 0.8287 (m-30) REVERT: G 541 GLN cc_start: 0.8067 (mt0) cc_final: 0.7773 (mt0) REVERT: G 563 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8649 (mttm) REVERT: G 595 ARG cc_start: 0.7755 (mtp180) cc_final: 0.6903 (ptt180) outliers start: 89 outliers final: 48 residues processed: 328 average time/residue: 0.7617 time to fit residues: 280.2391 Evaluate side-chains 314 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 ASP 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 367 VAL Chi-restraints excluded: chain B residue 381 THR 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 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 394 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 187 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS 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 381 THR Chi-restraints excluded: chain E residue 413 SER 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 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain G residue 212 GLU 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 433 THR Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 563 LYS 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 153 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 476 ASN B 424 GLN B 476 ASN C 476 ASN E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN G 424 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101107 restraints weight = 32553.892| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.81 r_work: 0.3038 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 23709 Z= 0.261 Angle : 0.597 7.738 32228 Z= 0.312 Chirality : 0.049 0.165 3696 Planarity : 0.005 0.040 4249 Dihedral : 5.274 47.686 3168 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.57 % Allowed : 18.17 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 2947 helix: 0.05 (0.24), residues: 497 sheet: 0.70 (0.16), residues: 931 loop : -0.66 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 470 TYR 0.014 0.002 TYR G 462 PHE 0.014 0.002 PHE B 493 TRP 0.015 0.002 TRP E 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.26 (23709) covalent geometry : angle 0.59661 / 0.31 (32228) hydrogen bonds : bond 0.03303 / 2.24 ( 805) hydrogen bonds : angle 6.27940 / 4.40 ( 2184) *********************** 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 364 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 244 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7922 (m-30) cc_final: 0.7411 (t70) REVERT: A 287 ARG cc_start: 0.6283 (mtt90) cc_final: 0.5947 (tmt170) REVERT: A 299 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.6090 (p90) REVERT: A 343 GLU cc_start: 0.7882 (tt0) cc_final: 0.7533 (tt0) REVERT: A 344 ARG cc_start: 0.7174 (ttp-110) cc_final: 0.6886 (ttp-170) REVERT: A 350 MET cc_start: 0.8012 (mmm) cc_final: 0.7335 (tmt) REVERT: A 541 GLN cc_start: 0.8079 (mt0) cc_final: 0.7816 (mt0) REVERT: A 560 GLN cc_start: 0.8452 (tp40) cc_final: 0.8027 (tp40) REVERT: A 570 ASN cc_start: 0.8452 (m-40) cc_final: 0.8072 (p0) REVERT: B 287 ARG cc_start: 0.6529 (mtt90) cc_final: 0.5924 (ttp-170) REVERT: B 294 SER cc_start: 0.7435 (OUTLIER) cc_final: 0.6680 (t) REVERT: B 297 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5843 (mmt90) REVERT: B 334 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7093 (pp) REVERT: B 350 MET cc_start: 0.7973 (mmm) cc_final: 0.7411 (tmt) REVERT: B 447 GLN cc_start: 0.7597 (mt0) cc_final: 0.7262 (mp10) REVERT: B 465 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 541 GLN cc_start: 0.8083 (mt0) cc_final: 0.7740 (mt0) REVERT: B 557 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8260 (mp10) REVERT: B 563 LYS cc_start: 0.8682 (tppp) cc_final: 0.8324 (mmtp) REVERT: B 580 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8686 (mptt) REVERT: C 287 ARG cc_start: 0.6599 (mtt90) cc_final: 0.6043 (ttp-110) REVERT: C 299 HIS cc_start: 0.6388 (OUTLIER) cc_final: 0.6040 (p-80) REVERT: C 350 MET cc_start: 0.7795 (mmm) cc_final: 0.7297 (tmt) REVERT: C 389 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: C 394 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9107 (mm) REVERT: C 404 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9054 (tp) REVERT: C 441 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7701 (pt0) REVERT: C 447 GLN cc_start: 0.7749 (mt0) cc_final: 0.7446 (mp10) REVERT: C 496 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7248 (tptm) REVERT: C 587 MET cc_start: 0.8778 (mtt) cc_final: 0.8523 (mtp) REVERT: C 595 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7302 (ptt180) REVERT: D 180 ASN cc_start: 0.8647 (t0) cc_final: 0.8164 (t0) REVERT: D 221 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.9027 (p) REVERT: D 287 ARG cc_start: 0.6423 (mtt90) cc_final: 0.5961 (ttp-110) REVERT: D 294 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6864 (t) REVERT: D 297 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5617 (mmt90) REVERT: D 335 ASP cc_start: 0.7680 (m-30) cc_final: 0.7459 (m-30) REVERT: D 465 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7598 (mm-30) REVERT: E 287 ARG cc_start: 0.6568 (mtt90) cc_final: 0.5946 (ttp-110) REVERT: E 294 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7086 (t) REVERT: E 344 ARG cc_start: 0.6844 (ttp-110) cc_final: 0.6514 (ttp80) REVERT: E 348 GLU cc_start: 0.8017 (tt0) cc_final: 0.7215 (tm-30) REVERT: E 486 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: E 541 GLN cc_start: 0.8215 (mt0) cc_final: 0.7982 (tt0) REVERT: E 557 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8018 (mp10) REVERT: E 595 ARG cc_start: 0.7865 (mpp80) cc_final: 0.7499 (ptt-90) REVERT: F 287 ARG cc_start: 0.6711 (mtt90) cc_final: 0.5819 (tmt170) REVERT: F 297 ARG cc_start: 0.5919 (OUTLIER) cc_final: 0.5048 (mmt90) REVERT: F 330 SER cc_start: 0.6208 (m) cc_final: 0.5344 (p) REVERT: F 344 ARG cc_start: 0.6861 (ttp-110) cc_final: 0.6611 (ttp80) REVERT: F 350 MET cc_start: 0.8124 (mtt) cc_final: 0.7571 (tmt) REVERT: F 356 ASP cc_start: 0.7907 (t0) cc_final: 0.7608 (t0) REVERT: F 389 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: F 580 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8607 (mptt) REVERT: F 587 MET cc_start: 0.8596 (mtp) cc_final: 0.8377 (mtp) REVERT: G 287 ARG cc_start: 0.6597 (mtt90) cc_final: 0.5577 (ttp-170) REVERT: G 294 SER cc_start: 0.7321 (OUTLIER) cc_final: 0.6608 (t) REVERT: G 344 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6771 (ttp-170) REVERT: G 357 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8463 (t) REVERT: G 403 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8808 (mt0) REVERT: G 434 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7911 (ttp) REVERT: G 541 GLN cc_start: 0.8142 (mt0) cc_final: 0.7851 (mt0) REVERT: G 563 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8626 (mttm) outliers start: 120 outliers final: 66 residues processed: 322 average time/residue: 0.7445 time to fit residues: 269.8249 Evaluate side-chains 322 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 233 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 299 HIS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 ASP 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 297 ARG Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 THR 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 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 299 HIS 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 394 ILE 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 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 187 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 SER 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 338 LEU Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN 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 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 511 SER 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 297 ARG Chi-restraints excluded: chain F residue 338 LEU 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 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 580 LYS Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 297 ARG 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 433 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 563 LYS 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 72 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 57 optimal weight: 50.0000 chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 476 ASN B 403 GLN B 424 GLN ** B 476 ASN ** 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 285 GLN E 476 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104297 restraints weight = 32182.415| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.81 r_work: 0.3086 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23709 Z= 0.123 Angle : 0.519 7.592 32228 Z= 0.271 Chirality : 0.045 0.161 3696 Planarity : 0.004 0.035 4249 Dihedral : 4.804 44.142 3168 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.54 % Allowed : 19.12 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2947 helix: 0.62 (0.27), residues: 455 sheet: 1.21 (0.16), residues: 889 loop : -0.36 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 470 TYR 0.011 0.001 TYR C 411 PHE 0.012 0.001 PHE A 493 TRP 0.015 0.001 TRP D 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (23709) covalent geometry : angle 0.51936 / 0.27 (32228) hydrogen bonds : bond 0.02764 / 1.87 ( 805) hydrogen bonds : angle 5.92292 / 4.16 ( 2184) *********************** 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 348 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 255 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASP cc_start: 0.8142 (p0) cc_final: 0.7673 (p0) REVERT: A 283 ASP cc_start: 0.7784 (m-30) cc_final: 0.7262 (t0) REVERT: A 287 ARG cc_start: 0.6314 (mtt90) cc_final: 0.5723 (tmt170) REVERT: A 343 GLU cc_start: 0.7825 (tt0) cc_final: 0.7461 (tt0) REVERT: A 344 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6655 (ttp80) REVERT: A 350 MET cc_start: 0.7924 (mmm) cc_final: 0.7190 (tmt) REVERT: A 541 GLN cc_start: 0.7997 (mt0) cc_final: 0.7777 (mt0) REVERT: A 560 GLN cc_start: 0.8303 (tp40) cc_final: 0.7871 (tp40) REVERT: A 570 ASN cc_start: 0.8379 (m-40) cc_final: 0.7991 (p0) REVERT: A 595 ARG cc_start: 0.7597 (mtm180) cc_final: 0.7060 (ptt180) REVERT: B 180 ASN cc_start: 0.8602 (t0) cc_final: 0.8141 (t0) REVERT: B 287 ARG cc_start: 0.6535 (mtt90) cc_final: 0.5907 (ttp-170) REVERT: B 334 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.7044 (pp) REVERT: B 350 MET cc_start: 0.7892 (mmm) cc_final: 0.7307 (tmt) REVERT: B 403 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8892 (mt0) REVERT: B 447 GLN cc_start: 0.7565 (mt0) cc_final: 0.7243 (mp10) REVERT: B 465 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 541 GLN cc_start: 0.8029 (mt0) cc_final: 0.7660 (mt0) REVERT: B 557 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8276 (mp10) REVERT: B 563 LYS cc_start: 0.8651 (tppp) cc_final: 0.8397 (ttmm) REVERT: B 580 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8724 (mptt) REVERT: C 287 ARG cc_start: 0.6577 (mtt90) cc_final: 0.5984 (ttp-110) REVERT: C 299 HIS cc_start: 0.6323 (OUTLIER) cc_final: 0.6054 (p-80) REVERT: C 344 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7291 (tmt170) REVERT: C 350 MET cc_start: 0.7711 (mmm) cc_final: 0.7145 (tmt) REVERT: C 356 ASP cc_start: 0.7722 (t0) cc_final: 0.7520 (t0) REVERT: C 394 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9142 (mm) REVERT: C 404 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9017 (tp) REVERT: C 441 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7792 (pt0) REVERT: C 447 GLN cc_start: 0.7710 (mt0) cc_final: 0.7433 (mp10) REVERT: C 587 MET cc_start: 0.8767 (mtt) cc_final: 0.8486 (mtp) REVERT: C 595 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7337 (ptt180) REVERT: D 180 ASN cc_start: 0.8546 (t0) cc_final: 0.8087 (t0) REVERT: D 221 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8979 (p) REVERT: D 287 ARG cc_start: 0.6399 (mtt90) cc_final: 0.5928 (ttp-110) REVERT: D 294 SER cc_start: 0.7256 (OUTLIER) cc_final: 0.6830 (t) REVERT: D 335 ASP cc_start: 0.7563 (m-30) cc_final: 0.7360 (m-30) REVERT: D 465 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7649 (mm-30) REVERT: E 287 ARG cc_start: 0.6472 (mtt90) cc_final: 0.5841 (ttp-110) REVERT: E 294 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7294 (t) REVERT: E 344 ARG cc_start: 0.6683 (ttp-110) cc_final: 0.6408 (ttp80) REVERT: E 348 GLU cc_start: 0.7965 (tt0) cc_final: 0.7131 (tm-30) REVERT: E 486 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: E 541 GLN cc_start: 0.8082 (mt0) cc_final: 0.7800 (tt0) REVERT: E 557 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8042 (mp10) REVERT: E 570 ASN cc_start: 0.8308 (m-40) cc_final: 0.7935 (p0) REVERT: E 595 ARG cc_start: 0.7834 (mpp80) cc_final: 0.7484 (ptt-90) REVERT: F 287 ARG cc_start: 0.6683 (mtt90) cc_final: 0.5778 (tmt170) REVERT: F 330 SER cc_start: 0.6102 (m) cc_final: 0.5437 (t) REVERT: F 344 ARG cc_start: 0.6891 (ttp-110) cc_final: 0.6632 (ttp80) REVERT: F 350 MET cc_start: 0.8023 (mtt) cc_final: 0.7461 (tmt) REVERT: F 356 ASP cc_start: 0.7726 (t0) cc_final: 0.7445 (t0) REVERT: F 389 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: F 580 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8657 (mptt) REVERT: F 587 MET cc_start: 0.8436 (mtp) cc_final: 0.8148 (mtp) REVERT: G 287 ARG cc_start: 0.6598 (mtt90) cc_final: 0.5550 (ttp-170) REVERT: G 403 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: G 500 LEU cc_start: 0.8965 (mm) cc_final: 0.8730 (mt) REVERT: G 541 GLN cc_start: 0.8119 (mt0) cc_final: 0.7828 (mt0) REVERT: G 562 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8735 (tp) REVERT: G 563 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8584 (mttm) REVERT: G 595 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7036 (ptt-90) outliers start: 93 outliers final: 54 residues processed: 314 average time/residue: 0.7226 time to fit residues: 255.3872 Evaluate side-chains 311 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL 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 381 THR Chi-restraints excluded: chain B residue 403 GLN 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 B residue 580 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 394 ILE 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 187 LEU Chi-restraints excluded: chain D residue 221 SER 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 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS 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 381 THR Chi-restraints excluded: chain E residue 413 SER 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 357 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 389 GLN 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 F residue 580 LYS 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 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 563 LYS 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 231 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 180 optimal weight: 40.0000 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 476 ASN B 424 GLN B 476 ASN B 499 ASN C 422 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN F 422 ASN F 476 ASN G 424 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102885 restraints weight = 32390.244| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.81 r_work: 0.3065 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23709 Z= 0.172 Angle : 0.551 7.751 32228 Z= 0.286 Chirality : 0.046 0.161 3696 Planarity : 0.004 0.037 4249 Dihedral : 4.899 44.170 3167 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.89 % Allowed : 18.70 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2947 helix: 0.56 (0.26), residues: 455 sheet: 1.14 (0.16), residues: 903 loop : -0.44 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 470 TYR 0.014 0.001 TYR F 410 PHE 0.012 0.001 PHE B 493 TRP 0.014 0.002 TRP E 226 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (23709) covalent geometry : angle 0.55053 / 0.29 (32228) hydrogen bonds : bond 0.02930 / 1.98 ( 805) hydrogen bonds : angle 5.97539 / 4.19 ( 2184) *********************** 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 342 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 240 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7781 (m-30) cc_final: 0.7314 (t70) REVERT: A 287 ARG cc_start: 0.6352 (mtt90) cc_final: 0.5904 (tmt170) REVERT: A 299 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.6072 (p90) REVERT: A 343 GLU cc_start: 0.7851 (tt0) cc_final: 0.7517 (tt0) REVERT: A 344 ARG cc_start: 0.7120 (ttp-110) cc_final: 0.6837 (ttp-170) REVERT: A 350 MET cc_start: 0.7958 (mmm) cc_final: 0.7244 (tmt) REVERT: A 541 GLN cc_start: 0.8033 (mt0) cc_final: 0.7813 (mt0) REVERT: A 560 GLN cc_start: 0.8334 (tp40) cc_final: 0.7946 (tp40) REVERT: A 570 ASN cc_start: 0.8413 (m-40) cc_final: 0.8035 (p0) REVERT: A 595 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7058 (ptt180) REVERT: B 180 ASN cc_start: 0.8587 (t0) cc_final: 0.8117 (t0) REVERT: B 287 ARG cc_start: 0.6539 (mtt90) cc_final: 0.5937 (ttp-170) REVERT: B 294 SER cc_start: 0.7426 (OUTLIER) cc_final: 0.6672 (t) REVERT: B 334 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7073 (pp) REVERT: B 350 MET cc_start: 0.7977 (mmm) cc_final: 0.7293 (tmt) REVERT: B 447 GLN cc_start: 0.7534 (mt0) cc_final: 0.7217 (mp10) REVERT: B 465 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 541 GLN cc_start: 0.8078 (mt0) cc_final: 0.7732 (mt0) REVERT: B 557 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8282 (mp10) REVERT: B 563 LYS cc_start: 0.8664 (tppp) cc_final: 0.8404 (ttmm) REVERT: B 580 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8686 (mptt) REVERT: C 287 ARG cc_start: 0.6616 (mtt90) cc_final: 0.6045 (ttp-110) REVERT: C 299 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.6037 (p-80) REVERT: C 344 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7332 (tmt170) REVERT: C 350 MET cc_start: 0.7719 (mmm) cc_final: 0.7126 (tmt) REVERT: C 394 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9084 (mm) REVERT: C 404 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9056 (tp) REVERT: C 447 GLN cc_start: 0.7720 (mt0) cc_final: 0.7502 (mp10) REVERT: C 496 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7197 (tptm) REVERT: C 587 MET cc_start: 0.8775 (mtt) cc_final: 0.8513 (mtp) REVERT: C 595 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7338 (ptt180) REVERT: D 180 ASN cc_start: 0.8563 (t0) cc_final: 0.8097 (t0) REVERT: D 221 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.9001 (p) REVERT: D 287 ARG cc_start: 0.6450 (mtt90) cc_final: 0.5981 (ttp-110) REVERT: D 294 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.6852 (t) REVERT: D 335 ASP cc_start: 0.7628 (m-30) cc_final: 0.7419 (m-30) REVERT: D 465 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7669 (mm-30) REVERT: E 287 ARG cc_start: 0.6512 (mtt90) cc_final: 0.5920 (ttp-110) REVERT: E 294 SER cc_start: 0.7518 (OUTLIER) cc_final: 0.7053 (t) REVERT: E 344 ARG cc_start: 0.6832 (ttp-110) cc_final: 0.6440 (ttp80) REVERT: E 348 GLU cc_start: 0.7970 (tt0) cc_final: 0.7158 (tm-30) REVERT: E 486 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: E 541 GLN cc_start: 0.8186 (mt0) cc_final: 0.7928 (tt0) REVERT: E 557 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8078 (mp10) REVERT: E 570 ASN cc_start: 0.8329 (m-40) cc_final: 0.8108 (p0) REVERT: E 595 ARG cc_start: 0.7839 (mpp80) cc_final: 0.7465 (ptt-90) REVERT: F 287 ARG cc_start: 0.6728 (mtt90) cc_final: 0.5851 (tmt170) REVERT: F 330 SER cc_start: 0.6126 (m) cc_final: 0.5176 (p) REVERT: F 344 ARG cc_start: 0.6797 (ttp-110) cc_final: 0.6563 (ttp80) REVERT: F 350 MET cc_start: 0.8105 (mtt) cc_final: 0.7564 (tmt) REVERT: F 356 ASP cc_start: 0.7840 (t0) cc_final: 0.7576 (t0) REVERT: F 389 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: F 580 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8584 (mptt) REVERT: F 587 MET cc_start: 0.8485 (mtp) cc_final: 0.8211 (mtp) REVERT: G 287 ARG cc_start: 0.6587 (mtt90) cc_final: 0.5568 (ttp-170) REVERT: G 299 HIS cc_start: 0.6286 (OUTLIER) cc_final: 0.5574 (p-80) REVERT: G 403 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8659 (mt0) REVERT: G 500 LEU cc_start: 0.9004 (mm) cc_final: 0.8762 (mt) REVERT: G 562 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8758 (tp) REVERT: G 563 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (mttm) REVERT: G 595 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7103 (ptt180) outliers start: 102 outliers final: 69 residues processed: 309 average time/residue: 0.7170 time to fit residues: 249.8912 Evaluate side-chains 323 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 236 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 HIS 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 433 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL 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 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 381 THR 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 B residue 580 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 394 ILE 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 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 187 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 SER 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 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain D residue 469 VAL 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 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 511 SER 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 338 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 389 GLN 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 F residue 580 LYS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 297 ARG 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 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 563 LYS 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 176 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 272 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 476 ASN B 403 GLN B 424 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105833 restraints weight = 32292.875| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.81 r_work: 0.3109 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23709 Z= 0.104 Angle : 0.511 7.681 32228 Z= 0.266 Chirality : 0.045 0.158 3696 Planarity : 0.004 0.033 4249 Dihedral : 4.531 39.343 3167 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.82 % Allowed : 19.77 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 2947 helix: 0.74 (0.27), residues: 462 sheet: 1.37 (0.16), residues: 875 loop : -0.25 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 470 TYR 0.012 0.001 TYR F 410 PHE 0.011 0.001 PHE A 493 TRP 0.014 0.001 TRP D 226 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (23709) covalent geometry : angle 0.51142 / 0.27 (32228) hydrogen bonds : bond 0.02588 / 1.75 ( 805) hydrogen bonds : angle 5.69503 / 4.00 ( 2184) ********************** 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 335 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 261 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8680 (t0) cc_final: 0.8195 (t0) REVERT: A 283 ASP cc_start: 0.7820 (m-30) cc_final: 0.7353 (t0) REVERT: A 287 ARG cc_start: 0.6288 (mtt90) cc_final: 0.5821 (tmt170) REVERT: A 299 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.6063 (p90) REVERT: A 343 GLU cc_start: 0.7807 (tt0) cc_final: 0.7443 (tt0) REVERT: A 344 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6793 (ttp-170) REVERT: A 350 MET cc_start: 0.7934 (mmm) cc_final: 0.7087 (tmt) REVERT: A 560 GLN cc_start: 0.8237 (tp40) cc_final: 0.7793 (tp40) REVERT: A 570 ASN cc_start: 0.8261 (m-40) cc_final: 0.7965 (p0) REVERT: A 595 ARG cc_start: 0.7644 (mtm180) cc_final: 0.7087 (ptt180) REVERT: B 180 ASN cc_start: 0.8587 (t0) cc_final: 0.8115 (t0) REVERT: B 287 ARG cc_start: 0.6565 (mtt90) cc_final: 0.5929 (ttp-170) REVERT: B 294 SER cc_start: 0.7397 (OUTLIER) cc_final: 0.6644 (t) REVERT: B 335 ASP cc_start: 0.7509 (m-30) cc_final: 0.7214 (t0) REVERT: B 350 MET cc_start: 0.7904 (mmm) cc_final: 0.7212 (tmt) REVERT: B 403 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8873 (mt0) REVERT: B 447 GLN cc_start: 0.7576 (mt0) cc_final: 0.7249 (mp10) REVERT: B 465 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7627 (mm-30) REVERT: B 541 GLN cc_start: 0.7987 (mt0) cc_final: 0.7630 (mt0) REVERT: B 563 LYS cc_start: 0.8648 (tppp) cc_final: 0.8364 (mmtp) REVERT: B 580 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8719 (mptt) REVERT: C 287 ARG cc_start: 0.6613 (mtt90) cc_final: 0.6047 (ttp-110) REVERT: C 299 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.5851 (p-80) REVERT: C 344 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7314 (tmt170) REVERT: C 350 MET cc_start: 0.7623 (mmm) cc_final: 0.7061 (tmt) REVERT: C 394 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8984 (mp) REVERT: C 441 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7742 (pt0) REVERT: C 496 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7118 (tptm) REVERT: C 557 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8259 (mp10) REVERT: C 587 MET cc_start: 0.8729 (mtt) cc_final: 0.8441 (mtp) REVERT: C 595 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7352 (ptt180) REVERT: D 180 ASN cc_start: 0.8456 (t0) cc_final: 0.8038 (t0) REVERT: D 287 ARG cc_start: 0.6448 (mtt90) cc_final: 0.5958 (ttp-110) REVERT: D 294 SER cc_start: 0.7233 (OUTLIER) cc_final: 0.6775 (t) REVERT: D 563 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8490 (ttmm) REVERT: D 595 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7316 (ptt-90) REVERT: E 180 ASN cc_start: 0.8433 (t0) cc_final: 0.8022 (t0) REVERT: E 287 ARG cc_start: 0.6449 (mtt90) cc_final: 0.5839 (ttp-110) REVERT: E 344 ARG cc_start: 0.6681 (ttp-110) cc_final: 0.6308 (ttp80) REVERT: E 348 GLU cc_start: 0.8000 (tt0) cc_final: 0.7156 (tm-30) REVERT: E 541 GLN cc_start: 0.8119 (mt0) cc_final: 0.7856 (tt0) REVERT: E 595 ARG cc_start: 0.7800 (mpp80) cc_final: 0.7461 (ptt-90) REVERT: F 287 ARG cc_start: 0.6704 (mtt90) cc_final: 0.5808 (tmt170) REVERT: F 330 SER cc_start: 0.6053 (m) cc_final: 0.5399 (t) REVERT: F 344 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6547 (ttp80) REVERT: F 350 MET cc_start: 0.8073 (mtt) cc_final: 0.7402 (tmt) REVERT: F 356 ASP cc_start: 0.7731 (t0) cc_final: 0.7490 (t0) REVERT: F 587 MET cc_start: 0.8377 (mtp) cc_final: 0.8099 (mtp) REVERT: G 180 ASN cc_start: 0.8591 (t0) cc_final: 0.8183 (t0) REVERT: G 287 ARG cc_start: 0.6538 (mtt90) cc_final: 0.5527 (ttp-170) REVERT: G 344 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.7125 (ttp80) REVERT: G 403 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8638 (mt0) REVERT: G 500 LEU cc_start: 0.8929 (mm) cc_final: 0.8726 (mt) REVERT: G 563 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8661 (ttmm) REVERT: G 595 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7142 (ptt-90) outliers start: 74 outliers final: 46 residues processed: 307 average time/residue: 0.7366 time to fit residues: 254.2908 Evaluate side-chains 306 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL 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 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU 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 294 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN 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 413 SER Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 511 SER 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 371 THR Chi-restraints excluded: chain F residue 381 THR 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 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 563 LYS 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 99 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 476 ASN B 424 GLN B 476 ASN C 422 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN F 422 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102885 restraints weight = 32369.515| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.82 r_work: 0.3076 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23709 Z= 0.197 Angle : 0.573 8.062 32228 Z= 0.298 Chirality : 0.047 0.193 3696 Planarity : 0.004 0.037 4249 Dihedral : 4.780 40.917 3165 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.31 % Allowed : 19.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2947 helix: 0.63 (0.26), residues: 455 sheet: 1.20 (0.16), residues: 903 loop : -0.41 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 470 TYR 0.013 0.002 TYR F 410 PHE 0.013 0.001 PHE A 493 TRP 0.016 0.002 TRP E 226 HIS 0.004 0.001 HIS F 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (23709) covalent geometry : angle 0.57250 / 0.30 (32228) hydrogen bonds : bond 0.02967 / 1.99 ( 805) hydrogen bonds : angle 5.90348 / 4.15 ( 2184) =============================================================================== Job complete usr+sys time: 8974.68 seconds wall clock time: 153 minutes 52.72 seconds (9232.72 seconds total)