Starting phenix.real_space_refine on Thu Jun 19 19:58:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9c_6224/06_2025/3j9c_6224.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9c_6224/06_2025/3j9c_6224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j9c_6224/06_2025/3j9c_6224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9c_6224/06_2025/3j9c_6224.map" model { file = "/net/cci-nas-00/data/ceres_data/3j9c_6224/06_2025/3j9c_6224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9c_6224/06_2025/3j9c_6224.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 14504 2.51 5 N 4046 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23296 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3326 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 8.85, per 1000 atoms: 0.38 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: 5.88 Conformation dependent library (CDL) restraints added in 3.3 seconds 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 63 sheets defined 20.8% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 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: 9.39 Time building geometry restraints manager: 6.97 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 50.510 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:15.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23709 Z= 0.360 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2947 helix: -1.67 (0.20), residues: 497 sheet: -0.98 (0.15), residues: 1001 loop : 0.51 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 226 HIS 0.003 0.001 HIS D 263 PHE 0.011 0.001 PHE D 493 TYR 0.013 0.002 TYR B 456 ARG 0.003 0.001 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.10893 ( 805) hydrogen bonds : angle 10.38417 ( 2184) covalent geometry : bond 0.00537 (23709) covalent geometry : angle 1.11209 (32228) *********************** 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 : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6849 (mt0) cc_final: 0.6557 (mm110) REVERT: A 287 ARG cc_start: 0.6325 (mtt90) cc_final: 0.5455 (ttp-170) REVERT: A 291 LYS cc_start: 0.6378 (tptt) cc_final: 0.5327 (tmtt) REVERT: A 330 SER cc_start: 0.4698 (OUTLIER) cc_final: 0.4233 (p) REVERT: A 334 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6509 (mt) REVERT: A 343 GLU cc_start: 0.7844 (tt0) cc_final: 0.7613 (tt0) REVERT: A 344 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.6822 (ttp80) REVERT: A 348 GLU cc_start: 0.7973 (tt0) cc_final: 0.7746 (pt0) REVERT: A 350 MET cc_start: 0.8690 (mmm) cc_final: 0.7772 (ttp) REVERT: A 387 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: A 388 ASN cc_start: 0.8794 (p0) cc_final: 0.8302 (p0) REVERT: A 404 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 434 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8578 (ttp) REVERT: A 436 TYR cc_start: 0.8663 (t80) cc_final: 0.8337 (t80) REVERT: A 441 GLU cc_start: 0.8347 (tt0) cc_final: 0.7965 (mt-10) REVERT: A 447 GLN cc_start: 0.7028 (mt0) cc_final: 0.6791 (mp10) REVERT: A 465 GLU cc_start: 0.9131 (tt0) cc_final: 0.8657 (mm-30) REVERT: A 470 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8409 (ptp90) REVERT: A 486 GLU cc_start: 0.9036 (tp30) cc_final: 0.8790 (mm-30) REVERT: A 542 TYR cc_start: 0.8932 (t80) cc_final: 0.8319 (t80) REVERT: A 579 ASP cc_start: 0.8595 (p0) cc_final: 0.8303 (t0) REVERT: A 580 LYS cc_start: 0.8917 (mttp) cc_final: 0.8653 (mptt) REVERT: A 586 LYS cc_start: 0.8869 (mttm) cc_final: 0.8294 (mtpt) REVERT: A 595 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7417 (mtm180) REVERT: B 212 GLU cc_start: 0.8218 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 263 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8750 (p90) REVERT: B 285 GLN cc_start: 0.6923 (mt0) cc_final: 0.6677 (mm-40) REVERT: B 287 ARG cc_start: 0.6382 (mtt90) cc_final: 0.5504 (ttp-170) REVERT: B 291 LYS cc_start: 0.6358 (tptt) cc_final: 0.6106 (tmtm) REVERT: B 330 SER cc_start: 0.5150 (OUTLIER) cc_final: 0.4812 (p) REVERT: B 334 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6497 (mt) REVERT: B 344 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6430 (tmt170) REVERT: B 348 GLU cc_start: 0.8094 (tt0) cc_final: 0.7795 (pt0) REVERT: B 350 MET cc_start: 0.8513 (mmm) cc_final: 0.7413 (pp-130) REVERT: B 387 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8280 (tmmt) REVERT: B 403 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9079 (mt0) REVERT: B 404 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 414 LYS cc_start: 0.9060 (tptt) cc_final: 0.8793 (tppp) REVERT: B 434 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8726 (ttp) REVERT: B 436 TYR cc_start: 0.8613 (t80) cc_final: 0.8364 (t80) REVERT: B 441 GLU cc_start: 0.8208 (tt0) cc_final: 0.7619 (tp30) REVERT: B 446 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7124 (tptp) REVERT: B 447 GLN cc_start: 0.7238 (mt0) cc_final: 0.6675 (mp10) REVERT: B 462 TYR cc_start: 0.8981 (t80) cc_final: 0.8675 (t80) REVERT: B 465 GLU cc_start: 0.9093 (tt0) cc_final: 0.8583 (mm-30) REVERT: B 470 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8432 (mmm160) REVERT: B 500 LEU cc_start: 0.8730 (mt) cc_final: 0.8526 (mm) REVERT: B 545 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8032 (ttpp) REVERT: B 560 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8026 (tp40) REVERT: B 579 ASP cc_start: 0.8446 (p0) cc_final: 0.8124 (t0) REVERT: B 595 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7845 (mtm180) REVERT: C 285 GLN cc_start: 0.6860 (mt0) cc_final: 0.6548 (mm-40) REVERT: C 287 ARG cc_start: 0.6458 (mtt90) cc_final: 0.5597 (ttp-110) REVERT: C 291 LYS cc_start: 0.5830 (tptt) cc_final: 0.5430 (tttm) REVERT: C 330 SER cc_start: 0.4677 (OUTLIER) cc_final: 0.4134 (p) REVERT: C 344 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.6957 (ttp80) REVERT: C 350 MET cc_start: 0.8618 (mmm) cc_final: 0.7502 (tmt) REVERT: C 381 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8727 (p) REVERT: C 387 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (ttpp) REVERT: C 404 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8658 (tp) REVERT: C 434 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8743 (ttp) REVERT: C 436 TYR cc_start: 0.8803 (t80) cc_final: 0.8467 (t80) REVERT: C 441 GLU cc_start: 0.8416 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 447 GLN cc_start: 0.7330 (mt0) cc_final: 0.6789 (mp10) REVERT: C 465 GLU cc_start: 0.9147 (tt0) cc_final: 0.8642 (mm-30) REVERT: C 470 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8494 (ptm160) REVERT: C 521 MET cc_start: 0.8982 (tpp) cc_final: 0.8744 (tpp) REVERT: C 539 ASN cc_start: 0.7196 (m110) cc_final: 0.6955 (p0) REVERT: C 579 ASP cc_start: 0.8471 (p0) cc_final: 0.8186 (t0) REVERT: C 586 LYS cc_start: 0.8744 (mttm) cc_final: 0.8352 (mtpt) REVERT: C 587 MET cc_start: 0.8769 (mtt) cc_final: 0.8491 (mtp) REVERT: D 285 GLN cc_start: 0.7118 (mt0) cc_final: 0.6693 (mm-40) REVERT: D 287 ARG cc_start: 0.6525 (mtt90) cc_final: 0.5667 (ttp-110) REVERT: D 330 SER cc_start: 0.5099 (OUTLIER) cc_final: 0.4301 (p) REVERT: D 334 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6457 (mt) REVERT: D 340 LEU cc_start: 0.7542 (mt) cc_final: 0.7138 (mm) REVERT: D 344 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.6991 (ttp-170) REVERT: D 387 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: D 388 ASN cc_start: 0.8706 (p0) cc_final: 0.8490 (p0) REVERT: D 398 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8924 (pm20) REVERT: D 403 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.9108 (mt0) REVERT: D 404 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8829 (tp) REVERT: D 434 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: D 441 GLU cc_start: 0.8137 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 447 GLN cc_start: 0.6923 (mt0) cc_final: 0.6472 (mp10) REVERT: D 448 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8452 (tp) REVERT: D 465 GLU cc_start: 0.9117 (tt0) cc_final: 0.8670 (mm-30) REVERT: D 557 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (tp-100) REVERT: D 579 ASP cc_start: 0.8428 (p0) cc_final: 0.8206 (t0) REVERT: D 587 MET cc_start: 0.8855 (mtt) cc_final: 0.8415 (mtm) REVERT: E 209 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.6895 (p0) REVERT: E 285 GLN cc_start: 0.7089 (mt0) cc_final: 0.6840 (mm110) REVERT: E 287 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5446 (ttp-110) REVERT: E 291 LYS cc_start: 0.6195 (tptt) cc_final: 0.5264 (tttt) REVERT: E 294 SER cc_start: 0.6522 (OUTLIER) cc_final: 0.6026 (t) REVERT: E 330 SER cc_start: 0.5382 (OUTLIER) cc_final: 0.4531 (p) REVERT: E 344 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6388 (ttp80) REVERT: E 348 GLU cc_start: 0.8101 (tt0) cc_final: 0.7892 (pt0) REVERT: E 350 MET cc_start: 0.8752 (mmm) cc_final: 0.7947 (ttp) REVERT: E 404 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8768 (tp) REVERT: E 434 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8678 (ttp) REVERT: E 441 GLU cc_start: 0.8344 (tt0) cc_final: 0.8007 (mt-10) REVERT: E 447 GLN cc_start: 0.7191 (mt0) cc_final: 0.6753 (mp10) REVERT: E 465 GLU cc_start: 0.9114 (tt0) cc_final: 0.8728 (mm-30) REVERT: E 470 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8376 (mmm160) REVERT: E 542 TYR cc_start: 0.8790 (t80) cc_final: 0.8490 (t80) REVERT: E 545 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7437 (ttpt) REVERT: E 551 ASP cc_start: 0.8890 (p0) cc_final: 0.8519 (t0) REVERT: E 557 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7968 (tp-100) REVERT: E 560 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7409 (tm-30) REVERT: E 579 ASP cc_start: 0.8570 (p0) cc_final: 0.8214 (t0) REVERT: E 580 LYS cc_start: 0.8932 (mttp) cc_final: 0.8575 (mptt) REVERT: F 209 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7567 (p0) REVERT: F 212 GLU cc_start: 0.8409 (tt0) cc_final: 0.8184 (tm-30) REVERT: F 263 HIS cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (p90) REVERT: F 285 GLN cc_start: 0.6997 (mt0) cc_final: 0.6574 (mm-40) REVERT: F 287 ARG cc_start: 0.6452 (mtt90) cc_final: 0.5227 (tmt170) REVERT: F 294 SER cc_start: 0.6083 (OUTLIER) cc_final: 0.5649 (t) REVERT: F 330 SER cc_start: 0.4669 (OUTLIER) cc_final: 0.4152 (p) REVERT: F 344 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.6669 (ttp80) REVERT: F 350 MET cc_start: 0.8731 (mmm) cc_final: 0.7853 (ttp) REVERT: F 404 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8793 (tp) REVERT: F 434 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8637 (ttp) REVERT: F 441 GLU cc_start: 0.8511 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 444 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7643 (mtpp) REVERT: F 447 GLN cc_start: 0.7104 (mt0) cc_final: 0.6758 (mp10) REVERT: F 465 GLU cc_start: 0.9112 (tt0) cc_final: 0.8646 (mm-30) REVERT: F 486 GLU cc_start: 0.9079 (tp30) cc_final: 0.8857 (mm-30) REVERT: F 579 ASP cc_start: 0.8521 (p0) cc_final: 0.8216 (t0) REVERT: F 586 LYS cc_start: 0.8708 (mttm) cc_final: 0.8230 (mtpt) REVERT: G 285 GLN cc_start: 0.6917 (mt0) cc_final: 0.6674 (mm110) REVERT: G 287 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5357 (ttp-170) REVERT: G 291 LYS cc_start: 0.6560 (tptt) cc_final: 0.6271 (tmtp) REVERT: G 294 SER cc_start: 0.5545 (OUTLIER) cc_final: 0.4889 (t) REVERT: G 334 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6720 (mt) REVERT: G 344 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6743 (ttp80) REVERT: G 350 MET cc_start: 0.8716 (mmm) cc_final: 0.7857 (ttp) REVERT: G 387 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: G 404 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 434 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: G 441 GLU cc_start: 0.8407 (tt0) cc_final: 0.8039 (mt-10) REVERT: G 447 GLN cc_start: 0.6833 (mt0) cc_final: 0.6484 (mp10) REVERT: G 448 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 465 GLU cc_start: 0.9108 (tt0) cc_final: 0.8718 (mm-30) REVERT: G 500 LEU cc_start: 0.8851 (mt) cc_final: 0.8591 (mm) REVERT: G 579 ASP cc_start: 0.8757 (p0) cc_final: 0.8297 (t0) REVERT: G 580 LYS cc_start: 0.8985 (mttp) cc_final: 0.8773 (mmtm) REVERT: G 587 MET cc_start: 0.8768 (mtt) cc_final: 0.8526 (mtm) outliers start: 161 outliers final: 17 residues processed: 706 average time/residue: 1.4097 time to fit residues: 1130.1522 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 : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 557 GLN Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 1.9990 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 424 GLN A 483 GLN A 499 ASN A 541 GLN A 560 GLN B 198 ASN B 274 ASN B 483 GLN C 389 GLN C 483 GLN D 198 ASN D 274 ASN D 424 GLN D 499 ASN D 541 GLN E 263 HIS E 274 ASN E 389 GLN E 424 GLN E 483 GLN E 570 ASN F 274 ASN F 389 GLN F 483 GLN F 499 ASN G 198 ASN G 209 ASN G 274 ASN G 424 GLN G 483 GLN G 560 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103191 restraints weight = 32435.024| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.81 r_work: 0.3110 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23709 Z= 0.166 Angle : 0.568 5.077 32228 Z= 0.308 Chirality : 0.047 0.162 3696 Planarity : 0.004 0.034 4249 Dihedral : 7.808 57.439 3281 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.11 % Allowed : 14.93 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2947 helix: -0.29 (0.24), residues: 497 sheet: -0.17 (0.16), residues: 952 loop : 0.02 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 226 HIS 0.012 0.001 HIS E 263 PHE 0.014 0.002 PHE B 493 TYR 0.011 0.002 TYR D 575 ARG 0.004 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 805) hydrogen bonds : angle 7.05496 ( 2184) covalent geometry : bond 0.00387 (23709) covalent geometry : angle 0.56772 (32228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 347 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8094 (m-30) cc_final: 0.7782 (m-30) REVERT: A 287 ARG cc_start: 0.6372 (mtt90) cc_final: 0.5899 (tmt170) REVERT: A 294 SER cc_start: 0.7444 (OUTLIER) cc_final: 0.6596 (t) REVERT: A 343 GLU cc_start: 0.7806 (tt0) cc_final: 0.7510 (tt0) REVERT: A 344 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6716 (ttp80) REVERT: A 350 MET cc_start: 0.7842 (mmm) cc_final: 0.7338 (tmt) REVERT: A 388 ASN cc_start: 0.8589 (p0) cc_final: 0.8314 (p0) REVERT: A 542 TYR cc_start: 0.8664 (t80) cc_final: 0.8180 (t80) REVERT: A 545 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7982 (mtpt) REVERT: A 560 GLN cc_start: 0.8408 (tp40) cc_final: 0.8158 (tp40) REVERT: A 586 LYS cc_start: 0.8872 (mttm) cc_final: 0.8613 (mtpp) REVERT: B 287 ARG cc_start: 0.6444 (mtt90) cc_final: 0.5813 (ttp-170) REVERT: B 334 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6802 (pp) REVERT: B 344 ARG cc_start: 0.6955 (ttp-110) cc_final: 0.6646 (tmt170) REVERT: B 350 MET cc_start: 0.7853 (mmm) cc_final: 0.7578 (tmt) REVERT: B 356 ASP cc_start: 0.7864 (t0) cc_final: 0.7614 (t0) REVERT: B 447 GLN cc_start: 0.7527 (mt0) cc_final: 0.7256 (mp10) REVERT: B 545 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8212 (mtmt) REVERT: C 287 ARG cc_start: 0.6569 (mtt90) cc_final: 0.5920 (ttp-110) REVERT: C 291 LYS cc_start: 0.6278 (tptt) cc_final: 0.6061 (tttm) REVERT: C 344 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6924 (ttp80) REVERT: C 350 MET cc_start: 0.7745 (mmm) cc_final: 0.7252 (tmt) REVERT: C 356 ASP cc_start: 0.7920 (t0) cc_final: 0.7614 (t0) REVERT: C 426 ASP cc_start: 0.8344 (m-30) cc_final: 0.8092 (m-30) REVERT: C 441 GLU cc_start: 0.7922 (tt0) cc_final: 0.7586 (tm-30) REVERT: C 447 GLN cc_start: 0.7566 (mt0) cc_final: 0.7297 (mp10) REVERT: C 545 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7935 (mtpt) REVERT: C 587 MET cc_start: 0.8518 (mtt) cc_final: 0.8250 (mtp) REVERT: C 595 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7423 (ptt180) REVERT: D 180 ASN cc_start: 0.8648 (t0) cc_final: 0.8110 (t0) REVERT: D 287 ARG cc_start: 0.6331 (mtt90) cc_final: 0.5706 (ttp-110) REVERT: D 294 SER cc_start: 0.7086 (OUTLIER) cc_final: 0.6696 (t) REVERT: D 334 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6705 (pp) REVERT: D 344 ARG cc_start: 0.7033 (ttp-110) cc_final: 0.6813 (ttp-170) REVERT: D 356 ASP cc_start: 0.7959 (t0) cc_final: 0.7605 (t70) REVERT: D 557 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7649 (tp-100) REVERT: D 587 MET cc_start: 0.8365 (mtt) cc_final: 0.8162 (mtp) REVERT: E 209 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.6795 (p0) REVERT: E 271 LEU cc_start: 0.8501 (pt) cc_final: 0.8269 (pt) REVERT: E 287 ARG cc_start: 0.6594 (mtt90) cc_final: 0.5833 (ttp-110) REVERT: E 294 SER cc_start: 0.7543 (OUTLIER) cc_final: 0.7130 (t) REVERT: E 344 ARG cc_start: 0.6645 (ttp-110) cc_final: 0.6221 (ttp80) REVERT: E 348 GLU cc_start: 0.7900 (tt0) cc_final: 0.7094 (tm-30) REVERT: E 356 ASP cc_start: 0.7714 (t0) cc_final: 0.7445 (t0) REVERT: E 357 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8639 (t) REVERT: E 389 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: E 403 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8614 (mt0) REVERT: E 441 GLU cc_start: 0.7773 (tt0) cc_final: 0.7375 (tm-30) REVERT: E 486 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: E 542 TYR cc_start: 0.8578 (t80) cc_final: 0.8276 (t80) REVERT: E 545 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7651 (mtpt) REVERT: E 557 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7857 (tp-100) REVERT: E 560 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7991 (tp40) REVERT: E 595 ARG cc_start: 0.7836 (mpp80) cc_final: 0.7515 (ptt-90) REVERT: F 209 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.6831 (p0) REVERT: F 263 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8621 (p90) REVERT: F 287 ARG cc_start: 0.6651 (mtt90) cc_final: 0.5813 (tmt170) REVERT: F 294 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6656 (t) REVERT: F 330 SER cc_start: 0.6432 (m) cc_final: 0.5812 (t) REVERT: F 344 ARG cc_start: 0.6846 (ttp-110) cc_final: 0.6601 (ttp80) REVERT: F 350 MET cc_start: 0.7840 (mmm) cc_final: 0.7510 (tmt) REVERT: F 356 ASP cc_start: 0.7731 (t0) cc_final: 0.7503 (t0) REVERT: F 389 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8746 (tm-30) REVERT: F 441 GLU cc_start: 0.7784 (tt0) cc_final: 0.7522 (tm-30) REVERT: F 444 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7715 (mtpp) REVERT: F 545 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7811 (mtpm) REVERT: F 560 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7946 (tp-100) REVERT: F 595 ARG cc_start: 0.7488 (mtm180) cc_final: 0.7022 (ptt-90) REVERT: G 287 ARG cc_start: 0.6469 (mtt90) cc_final: 0.5552 (ttp-170) REVERT: G 294 SER cc_start: 0.7214 (OUTLIER) cc_final: 0.6387 (t) REVERT: G 334 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6995 (pp) REVERT: G 340 LEU cc_start: 0.7947 (mt) cc_final: 0.7636 (mm) REVERT: G 344 ARG cc_start: 0.7177 (ttp-110) cc_final: 0.6708 (ttp-170) REVERT: G 350 MET cc_start: 0.7989 (mmm) cc_final: 0.7653 (mmt) REVERT: G 357 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8423 (t) REVERT: G 403 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8777 (mt0) REVERT: G 448 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8399 (tt) REVERT: G 486 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: G 557 GLN cc_start: 0.8225 (tp-100) cc_final: 0.8007 (tp-100) REVERT: G 586 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8838 (mtpt) REVERT: G 595 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7243 (ptt-90) outliers start: 108 outliers final: 40 residues processed: 419 average time/residue: 1.6075 time to fit residues: 759.9042 Evaluate side-chains 352 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 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 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 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 294 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 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 78 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 217 optimal weight: 0.4980 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 E 285 GLN E 389 GLN E 424 GLN E 476 ASN E 570 ASN F 285 GLN F 476 ASN F 541 GLN G 285 GLN G 424 GLN G 541 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.103264 restraints weight = 32158.222| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.82 r_work: 0.3071 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23709 Z= 0.168 Angle : 0.540 5.213 32228 Z= 0.290 Chirality : 0.047 0.164 3696 Planarity : 0.004 0.034 4249 Dihedral : 5.964 51.629 3195 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.08 % Allowed : 16.80 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2947 helix: 0.06 (0.25), residues: 497 sheet: 0.60 (0.17), residues: 875 loop : -0.43 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 226 HIS 0.003 0.001 HIS G 263 PHE 0.013 0.001 PHE E 493 TYR 0.011 0.002 TYR C 411 ARG 0.004 0.000 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 805) hydrogen bonds : angle 6.56755 ( 2184) covalent geometry : bond 0.00400 (23709) covalent geometry : angle 0.53964 (32228) *********************** 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 399 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 292 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8145 (m-30) cc_final: 0.7927 (m-30) REVERT: A 287 ARG cc_start: 0.6294 (mtt90) cc_final: 0.5898 (tmt170) REVERT: A 294 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.6712 (t) REVERT: A 343 GLU cc_start: 0.7917 (tt0) cc_final: 0.7607 (tt0) REVERT: A 344 ARG cc_start: 0.7013 (ttp-110) cc_final: 0.6690 (ttp80) REVERT: A 350 MET cc_start: 0.7878 (mmm) cc_final: 0.7310 (tmt) REVERT: A 476 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8753 (p0) REVERT: A 545 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7779 (mtpt) REVERT: A 560 GLN cc_start: 0.8497 (tp40) cc_final: 0.8057 (tp40) REVERT: A 586 LYS cc_start: 0.8895 (mttm) cc_final: 0.8603 (mtpt) REVERT: A 595 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7394 (ptt180) REVERT: B 287 ARG cc_start: 0.6330 (mtt90) cc_final: 0.5769 (ttp-170) REVERT: B 294 SER cc_start: 0.7144 (OUTLIER) cc_final: 0.6465 (t) REVERT: B 334 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7059 (pp) REVERT: B 350 MET cc_start: 0.7898 (mmm) cc_final: 0.7581 (tmt) REVERT: B 447 GLN cc_start: 0.7575 (mt0) cc_final: 0.7281 (mp10) REVERT: B 465 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 545 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8227 (mtmt) REVERT: B 557 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8227 (mp10) REVERT: B 563 LYS cc_start: 0.8632 (tppp) cc_final: 0.8245 (mmtp) REVERT: B 580 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8655 (mptt) REVERT: C 287 ARG cc_start: 0.6523 (mtt90) cc_final: 0.5869 (ttp-110) REVERT: C 350 MET cc_start: 0.7683 (mmm) cc_final: 0.7212 (tmt) REVERT: C 404 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9056 (tp) REVERT: C 441 GLU cc_start: 0.7959 (tt0) cc_final: 0.7598 (tm-30) REVERT: C 447 GLN cc_start: 0.7649 (mt0) cc_final: 0.7406 (mp10) REVERT: C 521 MET cc_start: 0.8735 (tpp) cc_final: 0.8453 (tpp) REVERT: C 545 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7919 (mtpt) REVERT: C 587 MET cc_start: 0.8592 (mtt) cc_final: 0.8332 (mtp) REVERT: C 595 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7416 (ptt180) REVERT: D 180 ASN cc_start: 0.8651 (t0) cc_final: 0.8154 (t0) REVERT: D 287 ARG cc_start: 0.6322 (mtt90) cc_final: 0.5736 (ttp-110) REVERT: D 297 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5529 (mmt90) REVERT: D 340 LEU cc_start: 0.7890 (mt) cc_final: 0.7684 (mm) REVERT: D 356 ASP cc_start: 0.7835 (t0) cc_final: 0.7605 (t70) REVERT: D 403 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8879 (mt0) REVERT: D 545 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7751 (mtpt) REVERT: D 595 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7027 (ptt-90) REVERT: E 209 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6689 (p0) REVERT: E 287 ARG cc_start: 0.6514 (mtt90) cc_final: 0.5795 (ttp-110) REVERT: E 294 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (t) REVERT: E 344 ARG cc_start: 0.6687 (ttp-110) cc_final: 0.6323 (ttp80) REVERT: E 348 GLU cc_start: 0.7884 (tt0) cc_final: 0.7021 (tm-30) REVERT: E 389 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8656 (tp40) REVERT: E 403 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8773 (mt0) REVERT: E 441 GLU cc_start: 0.7706 (tt0) cc_final: 0.7310 (tm-30) REVERT: E 486 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: E 551 ASP cc_start: 0.7557 (p0) cc_final: 0.7356 (p0) REVERT: E 557 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7932 (tp-100) REVERT: F 209 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.6924 (p0) REVERT: F 287 ARG cc_start: 0.6475 (mtt90) cc_final: 0.5722 (tmt170) REVERT: F 330 SER cc_start: 0.6444 (m) cc_final: 0.5777 (t) REVERT: F 344 ARG cc_start: 0.6832 (ttp-110) cc_final: 0.6603 (ttp80) REVERT: F 350 MET cc_start: 0.7779 (mmm) cc_final: 0.7508 (tmt) REVERT: F 441 GLU cc_start: 0.7794 (tt0) cc_final: 0.7479 (tm-30) REVERT: F 444 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7808 (mtpp) REVERT: F 557 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8096 (mp10) REVERT: F 595 ARG cc_start: 0.7465 (mtm180) cc_final: 0.6890 (ptt-90) REVERT: G 287 ARG cc_start: 0.6568 (mtt90) cc_final: 0.5580 (ttp-170) REVERT: G 340 LEU cc_start: 0.7956 (mt) cc_final: 0.7654 (mm) REVERT: G 344 ARG cc_start: 0.6974 (ttp-110) cc_final: 0.6683 (ttp-170) REVERT: G 356 ASP cc_start: 0.7955 (t0) cc_final: 0.7711 (t0) REVERT: G 357 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8465 (t) REVERT: G 403 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8832 (mt0) REVERT: G 500 LEU cc_start: 0.8883 (mm) cc_final: 0.8665 (mt) REVERT: G 557 GLN cc_start: 0.8349 (tp-100) cc_final: 0.8070 (tp-100) REVERT: G 595 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7160 (ptt-90) outliers start: 107 outliers final: 59 residues processed: 368 average time/residue: 1.6390 time to fit residues: 682.0561 Evaluate side-chains 342 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 2.868 ------------------------------------------------------------------------------- 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 476 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain 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 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 387 LYS 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 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 104 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 424 GLN A 476 ASN B 424 GLN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 285 GLN D 476 ASN E 285 GLN E 424 GLN E 476 ASN F 389 GLN F 422 ASN F 476 ASN G 285 GLN G 424 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102563 restraints weight = 32627.229| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.82 r_work: 0.3064 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23709 Z= 0.180 Angle : 0.538 6.428 32228 Z= 0.284 Chirality : 0.047 0.161 3696 Planarity : 0.004 0.037 4249 Dihedral : 5.620 49.116 3183 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.42 % Allowed : 16.88 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 2947 helix: 0.08 (0.25), residues: 497 sheet: 0.59 (0.16), residues: 910 loop : -0.44 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 226 HIS 0.004 0.001 HIS C 263 PHE 0.013 0.001 PHE B 493 TYR 0.012 0.002 TYR C 411 ARG 0.005 0.000 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 805) hydrogen bonds : angle 6.36738 ( 2184) covalent geometry : bond 0.00430 (23709) covalent geometry : angle 0.53784 (32228) *********************** 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 392 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 276 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8171 (m-30) cc_final: 0.7946 (m-30) REVERT: A 287 ARG cc_start: 0.6336 (mtt90) cc_final: 0.5938 (tmt170) REVERT: A 335 ASP cc_start: 0.7855 (m-30) cc_final: 0.7579 (m-30) REVERT: A 343 GLU cc_start: 0.7847 (tt0) cc_final: 0.7514 (tt0) REVERT: A 344 ARG cc_start: 0.7154 (ttp-110) cc_final: 0.6745 (ttp80) REVERT: A 350 MET cc_start: 0.7914 (mmm) cc_final: 0.7314 (tmt) REVERT: A 387 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7855 (ttpp) REVERT: A 388 ASN cc_start: 0.8591 (p0) cc_final: 0.8366 (p0) REVERT: A 470 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8165 (mtp-110) REVERT: A 541 GLN cc_start: 0.7955 (mt0) cc_final: 0.7685 (mt0) REVERT: A 560 GLN cc_start: 0.8534 (tp40) cc_final: 0.8081 (tp40) REVERT: A 570 ASN cc_start: 0.8608 (m-40) cc_final: 0.8247 (p0) REVERT: A 586 LYS cc_start: 0.8904 (mttm) cc_final: 0.8667 (mtpt) REVERT: B 287 ARG cc_start: 0.6522 (mtt90) cc_final: 0.5894 (ttp-170) REVERT: B 294 SER cc_start: 0.7290 (OUTLIER) cc_final: 0.6559 (t) REVERT: B 334 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7097 (pp) REVERT: B 350 MET cc_start: 0.7896 (mmm) cc_final: 0.7579 (tmt) REVERT: B 403 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8835 (mt0) REVERT: B 447 GLN cc_start: 0.7545 (mt0) cc_final: 0.7227 (mp10) REVERT: B 465 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 541 GLN cc_start: 0.7919 (mt0) cc_final: 0.7455 (mt0) REVERT: B 557 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8278 (mp10) REVERT: B 563 LYS cc_start: 0.8642 (tppp) cc_final: 0.8379 (ttmm) REVERT: C 287 ARG cc_start: 0.6424 (mtt90) cc_final: 0.5863 (ttp-110) REVERT: C 350 MET cc_start: 0.7707 (mmm) cc_final: 0.7229 (tmt) REVERT: C 404 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9054 (tp) REVERT: C 447 GLN cc_start: 0.7688 (mt0) cc_final: 0.7415 (mp10) REVERT: C 541 GLN cc_start: 0.8174 (mt0) cc_final: 0.7804 (mt0) REVERT: C 587 MET cc_start: 0.8658 (mtt) cc_final: 0.8401 (mtp) REVERT: D 180 ASN cc_start: 0.8617 (t0) cc_final: 0.8121 (t0) REVERT: D 287 ARG cc_start: 0.6393 (mtt90) cc_final: 0.5762 (ttp-110) REVERT: D 356 ASP cc_start: 0.7799 (t0) cc_final: 0.7594 (t70) REVERT: D 403 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8895 (mt0) REVERT: E 287 ARG cc_start: 0.6485 (mtt90) cc_final: 0.5851 (ttp-110) REVERT: E 344 ARG cc_start: 0.6752 (ttp-110) cc_final: 0.6363 (ttp80) REVERT: E 348 GLU cc_start: 0.7842 (tt0) cc_final: 0.6974 (tm-30) REVERT: E 403 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8798 (mt0) REVERT: E 441 GLU cc_start: 0.7727 (tt0) cc_final: 0.7322 (tm-30) REVERT: E 486 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: E 541 GLN cc_start: 0.8026 (mt0) cc_final: 0.7652 (mt0) REVERT: E 551 ASP cc_start: 0.7500 (p0) cc_final: 0.7263 (p0) REVERT: E 557 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8112 (mp10) REVERT: F 287 ARG cc_start: 0.6544 (mtt90) cc_final: 0.5799 (tmt170) REVERT: F 330 SER cc_start: 0.6430 (m) cc_final: 0.5732 (t) REVERT: F 344 ARG cc_start: 0.6868 (ttp-110) cc_final: 0.6596 (ttp80) REVERT: F 350 MET cc_start: 0.7873 (mmm) cc_final: 0.7534 (tmt) REVERT: F 387 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8059 (tmmt) REVERT: F 441 GLU cc_start: 0.7833 (tt0) cc_final: 0.7628 (tm-30) REVERT: F 444 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7839 (mtpp) REVERT: F 486 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: F 541 GLN cc_start: 0.7886 (mt0) cc_final: 0.7461 (mt0) REVERT: F 557 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8033 (mp10) REVERT: F 580 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8697 (mptt) REVERT: F 595 ARG cc_start: 0.7482 (mtm180) cc_final: 0.6875 (ptt-90) REVERT: G 212 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: G 287 ARG cc_start: 0.6579 (mtt90) cc_final: 0.5631 (ttp-170) REVERT: G 334 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7100 (pp) REVERT: G 340 LEU cc_start: 0.7930 (mt) cc_final: 0.7623 (mm) REVERT: G 344 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6809 (ttp-170) REVERT: G 357 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8417 (t) REVERT: G 403 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8801 (mt0) REVERT: G 414 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8929 (mmtt) REVERT: G 541 GLN cc_start: 0.7957 (mt0) cc_final: 0.7596 (mt0) outliers start: 116 outliers final: 63 residues processed: 351 average time/residue: 1.5918 time to fit residues: 628.9610 Evaluate side-chains 337 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 259 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 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 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 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR 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 387 LYS Chi-restraints excluded: chain D residue 403 GLN 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 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN 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 500 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 580 LYS Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 35 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 134 optimal weight: 0.0010 chunk 252 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 424 GLN E 476 ASN F 422 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105054 restraints weight = 32339.324| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.82 r_work: 0.3110 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23709 Z= 0.112 Angle : 0.494 6.563 32228 Z= 0.262 Chirality : 0.045 0.160 3696 Planarity : 0.004 0.033 4249 Dihedral : 5.024 45.599 3177 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.47 % Allowed : 18.06 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2947 helix: 0.32 (0.26), residues: 497 sheet: 0.69 (0.16), residues: 910 loop : -0.36 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 226 HIS 0.002 0.001 HIS A 263 PHE 0.012 0.001 PHE E 493 TYR 0.012 0.001 TYR C 411 ARG 0.006 0.000 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 805) hydrogen bonds : angle 5.97684 ( 2184) covalent geometry : bond 0.00261 (23709) covalent geometry : angle 0.49438 (32228) *********************** 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 378 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 287 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6363 (mtt90) cc_final: 0.5929 (tmt170) REVERT: A 343 GLU cc_start: 0.7792 (tt0) cc_final: 0.7461 (tt0) REVERT: A 344 ARG cc_start: 0.7039 (ttp-110) cc_final: 0.6653 (ttp80) REVERT: A 350 MET cc_start: 0.7926 (mmm) cc_final: 0.7231 (tmt) REVERT: A 387 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7759 (ttpp) REVERT: A 388 ASN cc_start: 0.8617 (p0) cc_final: 0.8399 (p0) REVERT: A 541 GLN cc_start: 0.7855 (mt0) cc_final: 0.7523 (mt0) REVERT: A 545 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8012 (mtpt) REVERT: A 560 GLN cc_start: 0.8399 (tp40) cc_final: 0.7983 (tp40) REVERT: A 570 ASN cc_start: 0.8620 (m-40) cc_final: 0.8087 (p0) REVERT: A 586 LYS cc_start: 0.8891 (mttm) cc_final: 0.8654 (mtpt) REVERT: A 595 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7224 (ptt-90) REVERT: B 180 ASN cc_start: 0.8596 (t0) cc_final: 0.8079 (t0) REVERT: B 287 ARG cc_start: 0.6391 (mtt90) cc_final: 0.5849 (ttp-170) REVERT: B 334 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.7016 (pp) REVERT: B 344 ARG cc_start: 0.7380 (ttp80) cc_final: 0.7165 (tmt170) REVERT: B 350 MET cc_start: 0.7824 (mmm) cc_final: 0.7505 (tmt) REVERT: B 447 GLN cc_start: 0.7598 (mt0) cc_final: 0.7229 (mp10) REVERT: B 465 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 541 GLN cc_start: 0.7914 (mt0) cc_final: 0.7480 (mt0) REVERT: B 557 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8288 (mp10) REVERT: B 563 LYS cc_start: 0.8621 (tppp) cc_final: 0.8360 (ttmm) REVERT: B 595 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7481 (ptt180) REVERT: C 287 ARG cc_start: 0.6461 (mtt90) cc_final: 0.5874 (ttp-110) REVERT: C 344 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7212 (tmt170) REVERT: C 350 MET cc_start: 0.7580 (mmm) cc_final: 0.7075 (tmt) REVERT: C 356 ASP cc_start: 0.7650 (t0) cc_final: 0.7300 (t0) REVERT: C 447 GLN cc_start: 0.7665 (mt0) cc_final: 0.7410 (mp10) REVERT: C 541 GLN cc_start: 0.8075 (mt0) cc_final: 0.7758 (mt0) REVERT: C 587 MET cc_start: 0.8612 (mtt) cc_final: 0.8317 (mtp) REVERT: C 595 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7337 (ptt180) REVERT: D 180 ASN cc_start: 0.8562 (t0) cc_final: 0.8115 (t0) REVERT: D 287 ARG cc_start: 0.6445 (mtt90) cc_final: 0.5770 (ttp-110) REVERT: D 297 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.5583 (mmt90) REVERT: D 586 LYS cc_start: 0.9002 (mtpp) cc_final: 0.8784 (mtpp) REVERT: E 287 ARG cc_start: 0.6463 (mtt90) cc_final: 0.5798 (ttp-110) REVERT: E 344 ARG cc_start: 0.6684 (ttp-110) cc_final: 0.6341 (ttp80) REVERT: E 348 GLU cc_start: 0.7867 (tt0) cc_final: 0.6997 (tm-30) REVERT: E 356 ASP cc_start: 0.7826 (t0) cc_final: 0.7626 (t0) REVERT: E 541 GLN cc_start: 0.7997 (mt0) cc_final: 0.7634 (mt0) REVERT: E 557 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8052 (mp10) REVERT: E 595 ARG cc_start: 0.7885 (mpp80) cc_final: 0.7449 (ptt180) REVERT: F 271 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8009 (pp) REVERT: F 287 ARG cc_start: 0.6578 (mtt90) cc_final: 0.5775 (tmt170) REVERT: F 330 SER cc_start: 0.6289 (m) cc_final: 0.5601 (t) REVERT: F 344 ARG cc_start: 0.6788 (ttp-110) cc_final: 0.6548 (ttp80) REVERT: F 350 MET cc_start: 0.7831 (mmm) cc_final: 0.7495 (tmt) REVERT: F 444 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7880 (mtpp) REVERT: F 541 GLN cc_start: 0.7902 (mt0) cc_final: 0.7572 (mt0) REVERT: F 555 ASP cc_start: 0.7015 (p0) cc_final: 0.6702 (p0) REVERT: F 557 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8166 (mp10) REVERT: F 570 ASN cc_start: 0.8514 (m-40) cc_final: 0.8149 (p0) REVERT: F 595 ARG cc_start: 0.7568 (mtm180) cc_final: 0.6972 (ptt-90) REVERT: G 180 ASN cc_start: 0.8629 (t0) cc_final: 0.8224 (t0) REVERT: G 212 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: G 287 ARG cc_start: 0.6592 (mtt90) cc_final: 0.5613 (ttp-170) REVERT: G 340 LEU cc_start: 0.7881 (mt) cc_final: 0.7579 (mm) REVERT: G 356 ASP cc_start: 0.7823 (t0) cc_final: 0.7602 (t0) REVERT: G 357 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8377 (t) REVERT: G 403 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8767 (mt0) REVERT: G 465 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7588 (mm-30) REVERT: G 500 LEU cc_start: 0.8875 (mm) cc_final: 0.8667 (mt) REVERT: G 541 GLN cc_start: 0.7996 (mt0) cc_final: 0.7704 (mt0) REVERT: G 562 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8687 (tp) REVERT: G 595 ARG cc_start: 0.7779 (mtp180) cc_final: 0.6936 (ptt180) outliers start: 91 outliers final: 43 residues processed: 348 average time/residue: 1.6227 time to fit residues: 634.8396 Evaluate side-chains 315 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 THR 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 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 286 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 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 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 577 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 19 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN B 476 ASN C 476 ASN D 476 ASN E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100710 restraints weight = 32447.522| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.82 r_work: 0.3032 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 23709 Z= 0.273 Angle : 0.595 8.099 32228 Z= 0.313 Chirality : 0.049 0.185 3696 Planarity : 0.005 0.042 4249 Dihedral : 5.456 45.842 3173 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.99 % Allowed : 17.30 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2947 helix: -0.04 (0.24), residues: 497 sheet: 0.63 (0.15), residues: 931 loop : -0.64 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 226 HIS 0.005 0.001 HIS A 299 PHE 0.014 0.002 PHE B 493 TYR 0.015 0.002 TYR G 462 ARG 0.006 0.001 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 805) hydrogen bonds : angle 6.36178 ( 2184) covalent geometry : bond 0.00656 (23709) covalent geometry : angle 0.59518 (32228) *********************** 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 388 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 257 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7933 (m-30) cc_final: 0.7417 (t70) REVERT: A 287 ARG cc_start: 0.6353 (mtt90) cc_final: 0.5983 (tmt170) REVERT: A 297 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.4999 (mmt90) REVERT: A 299 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5994 (p90) REVERT: A 343 GLU cc_start: 0.7879 (tt0) cc_final: 0.7600 (tt0) REVERT: A 344 ARG cc_start: 0.7196 (ttp-110) cc_final: 0.6903 (ttp-170) REVERT: A 350 MET cc_start: 0.8040 (mmm) cc_final: 0.7376 (tmt) REVERT: A 387 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7801 (ttpp) REVERT: A 388 ASN cc_start: 0.8618 (p0) cc_final: 0.8406 (p0) REVERT: A 541 GLN cc_start: 0.8085 (mt0) cc_final: 0.7792 (mt0) REVERT: A 560 GLN cc_start: 0.8465 (tp40) cc_final: 0.8020 (tp40) REVERT: A 570 ASN cc_start: 0.8434 (m-40) cc_final: 0.8094 (p0) REVERT: B 287 ARG cc_start: 0.6506 (mtt90) cc_final: 0.5922 (ttp-170) REVERT: B 297 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5839 (mmt90) REVERT: B 344 ARG cc_start: 0.7320 (ttp80) cc_final: 0.7115 (tmt170) REVERT: B 350 MET cc_start: 0.7983 (mmm) cc_final: 0.7399 (tmt) REVERT: B 403 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8891 (mt0) REVERT: B 447 GLN cc_start: 0.7693 (mt0) cc_final: 0.7292 (mp10) REVERT: B 465 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7518 (mm-30) REVERT: B 541 GLN cc_start: 0.8066 (mt0) cc_final: 0.7658 (mt0) REVERT: B 557 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8257 (mp10) REVERT: B 563 LYS cc_start: 0.8694 (tppp) cc_final: 0.8455 (ttmm) REVERT: B 580 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8594 (mptt) REVERT: C 287 ARG cc_start: 0.6558 (mtt90) cc_final: 0.6023 (ttp-110) REVERT: C 350 MET cc_start: 0.7770 (mmm) cc_final: 0.7302 (tmt) REVERT: C 356 ASP cc_start: 0.7862 (t0) cc_final: 0.7503 (t0) REVERT: C 389 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: C 404 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9051 (tp) REVERT: C 447 GLN cc_start: 0.7799 (mt0) cc_final: 0.7456 (mp10) REVERT: C 587 MET cc_start: 0.8788 (mtt) cc_final: 0.8541 (mtp) REVERT: D 180 ASN cc_start: 0.8659 (t0) cc_final: 0.8165 (t0) REVERT: D 221 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.9024 (p) REVERT: D 287 ARG cc_start: 0.6355 (mtt90) cc_final: 0.5762 (ttp-110) REVERT: D 297 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5682 (mmt90) REVERT: E 287 ARG cc_start: 0.6552 (mtt90) cc_final: 0.5920 (ttp-110) REVERT: E 294 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7161 (t) REVERT: E 344 ARG cc_start: 0.6860 (ttp-110) cc_final: 0.6482 (ttp80) REVERT: E 348 GLU cc_start: 0.8073 (tt0) cc_final: 0.7715 (pt0) REVERT: E 356 ASP cc_start: 0.8030 (t0) cc_final: 0.7821 (t0) REVERT: E 403 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8996 (mt0) REVERT: E 486 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: E 541 GLN cc_start: 0.8140 (mt0) cc_final: 0.7843 (tt0) REVERT: E 557 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7981 (mp10) REVERT: E 595 ARG cc_start: 0.7875 (mpp80) cc_final: 0.7473 (ptt-90) REVERT: F 287 ARG cc_start: 0.6572 (mtt90) cc_final: 0.5708 (tmt170) REVERT: F 297 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5071 (mmt90) REVERT: F 330 SER cc_start: 0.6197 (m) cc_final: 0.5346 (p) REVERT: F 344 ARG cc_start: 0.6965 (ttp-110) cc_final: 0.6695 (ttp80) REVERT: F 350 MET cc_start: 0.7986 (mmm) cc_final: 0.7483 (tmt) REVERT: F 356 ASP cc_start: 0.7934 (t0) cc_final: 0.7628 (t0) REVERT: F 389 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: F 444 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7922 (mtpp) REVERT: F 486 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8352 (mm-30) REVERT: F 541 GLN cc_start: 0.8074 (mt0) cc_final: 0.7298 (mm-40) REVERT: F 555 ASP cc_start: 0.7055 (p0) cc_final: 0.6637 (p0) REVERT: F 557 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8170 (mp10) REVERT: F 580 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8632 (mptt) REVERT: G 212 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: G 287 ARG cc_start: 0.6604 (mtt90) cc_final: 0.5666 (ttp-170) REVERT: G 340 LEU cc_start: 0.8008 (mt) cc_final: 0.7750 (mp) REVERT: G 356 ASP cc_start: 0.8204 (t0) cc_final: 0.7979 (t0) REVERT: G 357 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8451 (t) REVERT: G 403 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8822 (mt0) REVERT: G 465 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7575 (mm-30) REVERT: G 541 GLN cc_start: 0.8184 (mt0) cc_final: 0.7855 (mt0) outliers start: 131 outliers final: 73 residues processed: 346 average time/residue: 1.8436 time to fit residues: 721.4114 Evaluate side-chains 336 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 245 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 299 HIS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 GLN 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 297 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 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 389 GLN Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 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 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN 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 500 LEU 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 212 GLU Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 225 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 133 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN B 476 ASN ** 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 476 ASN E 499 ASN F 422 ASN ** F 476 ASN ** 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 = 0.3678 r_free = 0.3678 target = 0.136960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103108 restraints weight = 32314.584| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.81 r_work: 0.3069 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23709 Z= 0.155 Angle : 0.526 8.075 32228 Z= 0.277 Chirality : 0.046 0.163 3696 Planarity : 0.004 0.037 4249 Dihedral : 5.051 44.567 3171 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.04 % Allowed : 18.25 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2947 helix: 0.45 (0.26), residues: 455 sheet: 0.99 (0.16), residues: 903 loop : -0.43 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 226 HIS 0.004 0.001 HIS C 263 PHE 0.013 0.001 PHE A 493 TYR 0.012 0.001 TYR C 411 ARG 0.006 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 805) hydrogen bonds : angle 6.08223 ( 2184) covalent geometry : bond 0.00369 (23709) covalent geometry : angle 0.52633 (32228) *********************** 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: 106 poor density : 258 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7899 (m-30) cc_final: 0.7399 (t0) REVERT: A 287 ARG cc_start: 0.6327 (mtt90) cc_final: 0.5870 (tmt170) REVERT: A 343 GLU cc_start: 0.7833 (tt0) cc_final: 0.7492 (tt0) REVERT: A 344 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6852 (ttp-170) REVERT: A 350 MET cc_start: 0.7987 (mmm) cc_final: 0.7268 (tmt) REVERT: A 541 GLN cc_start: 0.7978 (mt0) cc_final: 0.7740 (mt0) REVERT: A 560 GLN cc_start: 0.8393 (tp40) cc_final: 0.7955 (tp40) REVERT: A 570 ASN cc_start: 0.8422 (m-40) cc_final: 0.8020 (p0) REVERT: B 180 ASN cc_start: 0.8618 (t0) cc_final: 0.8144 (t0) REVERT: B 287 ARG cc_start: 0.6502 (mtt90) cc_final: 0.5895 (ttp-170) REVERT: B 350 MET cc_start: 0.7919 (mmm) cc_final: 0.7340 (tmt) REVERT: B 403 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8831 (mt0) REVERT: B 447 GLN cc_start: 0.7671 (mt0) cc_final: 0.7302 (mp10) REVERT: B 465 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 541 GLN cc_start: 0.8065 (mt0) cc_final: 0.7671 (mt0) REVERT: B 557 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8275 (mp10) REVERT: B 563 LYS cc_start: 0.8668 (tppp) cc_final: 0.8315 (mmtp) REVERT: B 580 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8650 (mptt) REVERT: C 287 ARG cc_start: 0.6597 (mtt90) cc_final: 0.6036 (ttp-110) REVERT: C 344 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7299 (tmt170) REVERT: C 350 MET cc_start: 0.7718 (mmm) cc_final: 0.7141 (tmt) REVERT: C 404 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9007 (tp) REVERT: C 441 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7738 (pt0) REVERT: C 447 GLN cc_start: 0.7718 (mt0) cc_final: 0.7438 (mp10) REVERT: C 587 MET cc_start: 0.8701 (mtt) cc_final: 0.8404 (mtp) REVERT: D 180 ASN cc_start: 0.8614 (t0) cc_final: 0.8147 (t0) REVERT: D 221 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8985 (p) REVERT: D 287 ARG cc_start: 0.6415 (mtt90) cc_final: 0.5898 (ttp-110) REVERT: D 297 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.5583 (mmt90) REVERT: E 287 ARG cc_start: 0.6547 (mtt90) cc_final: 0.5891 (ttp-110) REVERT: E 344 ARG cc_start: 0.6709 (ttp-110) cc_final: 0.6364 (ttp80) REVERT: E 348 GLU cc_start: 0.8079 (tt0) cc_final: 0.7240 (tm-30) REVERT: E 541 GLN cc_start: 0.8104 (mt0) cc_final: 0.7842 (tt0) REVERT: E 557 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8015 (mp10) REVERT: E 595 ARG cc_start: 0.7854 (mpp80) cc_final: 0.7453 (ptt-90) REVERT: F 287 ARG cc_start: 0.6560 (mtt90) cc_final: 0.5697 (tmt170) REVERT: F 344 ARG cc_start: 0.6898 (ttp-110) cc_final: 0.6652 (ttp80) REVERT: F 350 MET cc_start: 0.7897 (mmm) cc_final: 0.7495 (tmt) REVERT: F 356 ASP cc_start: 0.7775 (t0) cc_final: 0.7466 (t0) REVERT: F 389 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: F 486 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8317 (mm-30) REVERT: F 541 GLN cc_start: 0.7994 (mt0) cc_final: 0.7313 (mm-40) REVERT: F 555 ASP cc_start: 0.6997 (p0) cc_final: 0.6770 (p0) REVERT: F 580 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8639 (mptt) REVERT: F 595 ARG cc_start: 0.7753 (mpp80) cc_final: 0.7422 (ptt-90) REVERT: G 287 ARG cc_start: 0.6574 (mtt90) cc_final: 0.5543 (ttp-170) REVERT: G 299 HIS cc_start: 0.6260 (OUTLIER) cc_final: 0.5942 (p-80) REVERT: G 340 LEU cc_start: 0.7943 (mt) cc_final: 0.7729 (mp) REVERT: G 356 ASP cc_start: 0.8041 (t0) cc_final: 0.7765 (t0) REVERT: G 357 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8444 (t) REVERT: G 403 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8689 (mt0) REVERT: G 465 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7649 (mm-30) REVERT: G 500 LEU cc_start: 0.8992 (mm) cc_final: 0.8771 (mt) outliers start: 106 outliers final: 65 residues processed: 326 average time/residue: 1.6351 time to fit residues: 597.7359 Evaluate side-chains 317 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 242 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR 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 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 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 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 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL 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 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 299 HIS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 394 ILE 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 577 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 151 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN ** 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 403 GLN E 422 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.138681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105155 restraints weight = 32233.898| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.81 r_work: 0.3098 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23709 Z= 0.114 Angle : 0.513 8.033 32228 Z= 0.269 Chirality : 0.045 0.160 3696 Planarity : 0.004 0.034 4249 Dihedral : 4.745 40.125 3171 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.01 % Allowed : 19.20 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2947 helix: 0.66 (0.27), residues: 455 sheet: 1.17 (0.16), residues: 903 loop : -0.35 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 226 HIS 0.002 0.001 HIS A 299 PHE 0.012 0.001 PHE A 493 TYR 0.011 0.001 TYR C 411 ARG 0.007 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 805) hydrogen bonds : angle 5.83459 ( 2184) covalent geometry : bond 0.00267 (23709) covalent geometry : angle 0.51348 (32228) *********************** 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 349 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 270 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7755 (m-30) cc_final: 0.7289 (t0) REVERT: A 287 ARG cc_start: 0.6316 (mtt90) cc_final: 0.5841 (tmt170) REVERT: A 299 HIS cc_start: 0.6463 (OUTLIER) cc_final: 0.6085 (p90) REVERT: A 343 GLU cc_start: 0.7823 (tt0) cc_final: 0.7463 (tt0) REVERT: A 344 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6791 (ttp-170) REVERT: A 350 MET cc_start: 0.7919 (mmm) cc_final: 0.7150 (tmt) REVERT: A 388 ASN cc_start: 0.8583 (p0) cc_final: 0.8378 (p0) REVERT: A 541 GLN cc_start: 0.7991 (mt0) cc_final: 0.7775 (mt0) REVERT: A 560 GLN cc_start: 0.8272 (tp40) cc_final: 0.7824 (tp40) REVERT: A 570 ASN cc_start: 0.8490 (m-40) cc_final: 0.8001 (p0) REVERT: A 595 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7069 (ptt180) REVERT: B 180 ASN cc_start: 0.8614 (t0) cc_final: 0.8120 (t0) REVERT: B 287 ARG cc_start: 0.6363 (mtt90) cc_final: 0.5890 (ttp-170) REVERT: B 335 ASP cc_start: 0.7568 (m-30) cc_final: 0.7228 (t0) REVERT: B 350 MET cc_start: 0.7849 (mmm) cc_final: 0.7280 (tmt) REVERT: B 447 GLN cc_start: 0.7613 (mt0) cc_final: 0.7266 (mp10) REVERT: B 465 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 541 GLN cc_start: 0.8043 (mt0) cc_final: 0.7685 (mt0) REVERT: B 557 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8342 (mp10) REVERT: B 563 LYS cc_start: 0.8647 (tppp) cc_final: 0.8345 (mmtp) REVERT: B 580 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8702 (mptt) REVERT: B 595 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7361 (ptt180) REVERT: C 287 ARG cc_start: 0.6587 (mtt90) cc_final: 0.6004 (ttp-110) REVERT: C 344 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7233 (tmt170) REVERT: C 350 MET cc_start: 0.7620 (mmm) cc_final: 0.7059 (tmt) REVERT: C 441 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7748 (pt0) REVERT: C 447 GLN cc_start: 0.7656 (mt0) cc_final: 0.7447 (mp10) REVERT: C 496 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7190 (tptm) REVERT: C 587 MET cc_start: 0.8694 (mtt) cc_final: 0.8303 (mtp) REVERT: C 595 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7240 (ptt180) REVERT: D 180 ASN cc_start: 0.8508 (t0) cc_final: 0.8089 (t0) REVERT: D 221 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8951 (p) REVERT: D 287 ARG cc_start: 0.6432 (mtt90) cc_final: 0.5886 (ttp-110) REVERT: D 297 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5593 (mmt90) REVERT: D 387 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7840 (tmmm) REVERT: D 563 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8351 (mmtp) REVERT: E 180 ASN cc_start: 0.8466 (t0) cc_final: 0.8054 (t0) REVERT: E 287 ARG cc_start: 0.6541 (mtt90) cc_final: 0.5895 (ttp-110) REVERT: E 344 ARG cc_start: 0.6697 (ttp-110) cc_final: 0.6325 (ttp80) REVERT: E 348 GLU cc_start: 0.7987 (tt0) cc_final: 0.7154 (tm-30) REVERT: E 541 GLN cc_start: 0.8072 (mt0) cc_final: 0.7793 (tt0) REVERT: E 557 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8080 (mp10) REVERT: E 570 ASN cc_start: 0.8263 (m-40) cc_final: 0.7909 (p0) REVERT: E 595 ARG cc_start: 0.7822 (mpp80) cc_final: 0.7439 (ptt-90) REVERT: F 287 ARG cc_start: 0.6558 (mtt90) cc_final: 0.5697 (tmt170) REVERT: F 344 ARG cc_start: 0.6814 (ttp-110) cc_final: 0.6548 (ttp80) REVERT: F 350 MET cc_start: 0.7896 (mmm) cc_final: 0.7450 (tmt) REVERT: F 356 ASP cc_start: 0.7761 (t0) cc_final: 0.7474 (t0) REVERT: F 486 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8278 (mm-30) REVERT: F 541 GLN cc_start: 0.7969 (mt0) cc_final: 0.7333 (mm-40) REVERT: F 569 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8117 (mt) REVERT: F 587 MET cc_start: 0.8503 (mtp) cc_final: 0.8301 (mtp) REVERT: G 180 ASN cc_start: 0.8667 (t0) cc_final: 0.8280 (t0) REVERT: G 287 ARG cc_start: 0.6563 (mtt90) cc_final: 0.5529 (ttp-170) REVERT: G 344 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.7162 (ttp80) REVERT: G 356 ASP cc_start: 0.7893 (t0) cc_final: 0.7669 (t0) REVERT: G 403 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8687 (mt0) REVERT: G 465 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7618 (mm-30) REVERT: G 563 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8623 (ttmm) REVERT: G 595 ARG cc_start: 0.7741 (mtp180) cc_final: 0.6978 (ptt-90) outliers start: 79 outliers final: 46 residues processed: 319 average time/residue: 1.6083 time to fit residues: 575.5484 Evaluate side-chains 309 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 293 THR 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 B residue 210 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 B residue 580 LYS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 433 THR 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 221 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 433 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 338 LEU 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 562 ILE Chi-restraints excluded: chain E residue 577 VAL 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 381 THR Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 569 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 7 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 256 optimal weight: 0.0000 chunk 50 optimal weight: 0.9980 chunk 273 optimal weight: 0.0570 chunk 113 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 403 GLN E 422 ASN F 422 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.106191 restraints weight = 32244.668| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.80 r_work: 0.3114 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23709 Z= 0.107 Angle : 0.511 8.075 32228 Z= 0.267 Chirality : 0.044 0.158 3696 Planarity : 0.004 0.033 4249 Dihedral : 4.515 34.848 3165 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.63 % Allowed : 20.08 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2947 helix: 0.76 (0.27), residues: 462 sheet: 1.20 (0.16), residues: 931 loop : -0.08 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 226 HIS 0.002 0.000 HIS A 299 PHE 0.012 0.001 PHE A 493 TYR 0.014 0.001 TYR F 410 ARG 0.008 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.02600 ( 805) hydrogen bonds : angle 5.65665 ( 2184) covalent geometry : bond 0.00251 (23709) covalent geometry : angle 0.51083 (32228) *********************** 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: 69 poor density : 273 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8662 (t0) cc_final: 0.8185 (t0) REVERT: A 283 ASP cc_start: 0.7807 (m-30) cc_final: 0.7328 (t0) REVERT: A 287 ARG cc_start: 0.6300 (mtt90) cc_final: 0.5851 (tmt170) REVERT: A 299 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.6062 (p90) REVERT: A 343 GLU cc_start: 0.7820 (tt0) cc_final: 0.7459 (tt0) REVERT: A 344 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6795 (ttp-170) REVERT: A 350 MET cc_start: 0.7939 (mmm) cc_final: 0.7094 (tmt) REVERT: A 388 ASN cc_start: 0.8575 (p0) cc_final: 0.8362 (p0) REVERT: A 541 GLN cc_start: 0.7981 (mt0) cc_final: 0.7773 (mt0) REVERT: A 560 GLN cc_start: 0.8227 (tp40) cc_final: 0.7786 (tp40) REVERT: A 570 ASN cc_start: 0.8474 (m-40) cc_final: 0.7998 (p0) REVERT: A 595 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7119 (ptt180) REVERT: B 180 ASN cc_start: 0.8586 (t0) cc_final: 0.8134 (t0) REVERT: B 287 ARG cc_start: 0.6367 (mtt90) cc_final: 0.5782 (ttp-170) REVERT: B 335 ASP cc_start: 0.7571 (m-30) cc_final: 0.7217 (t0) REVERT: B 344 ARG cc_start: 0.7270 (ttp80) cc_final: 0.7047 (tmt170) REVERT: B 350 MET cc_start: 0.7865 (mmm) cc_final: 0.7181 (tmt) REVERT: B 447 GLN cc_start: 0.7681 (mt0) cc_final: 0.7319 (mp10) REVERT: B 465 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 541 GLN cc_start: 0.8062 (mt0) cc_final: 0.7703 (mt0) REVERT: B 563 LYS cc_start: 0.8649 (tppp) cc_final: 0.8379 (mmtp) REVERT: B 580 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8702 (mptt) REVERT: B 595 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7501 (ptt180) REVERT: C 287 ARG cc_start: 0.6587 (mtt90) cc_final: 0.6000 (ttp-110) REVERT: C 344 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7240 (tmt170) REVERT: C 350 MET cc_start: 0.7568 (mmm) cc_final: 0.6994 (tmt) REVERT: C 441 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7729 (pt0) REVERT: C 496 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7163 (tptm) REVERT: C 587 MET cc_start: 0.8702 (mtt) cc_final: 0.8427 (mtp) REVERT: C 595 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7266 (ptt180) REVERT: D 180 ASN cc_start: 0.8456 (t0) cc_final: 0.8065 (t0) REVERT: D 287 ARG cc_start: 0.6434 (mtt90) cc_final: 0.5907 (ttp-110) REVERT: D 297 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5601 (mmt90) REVERT: D 350 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7449 (tmt) REVERT: D 388 ASN cc_start: 0.8243 (p0) cc_final: 0.7371 (m-40) REVERT: D 563 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8487 (ttmm) REVERT: D 595 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7242 (ptt-90) REVERT: E 180 ASN cc_start: 0.8422 (t0) cc_final: 0.8029 (t0) REVERT: E 287 ARG cc_start: 0.6482 (mtt90) cc_final: 0.5857 (ttp-110) REVERT: E 344 ARG cc_start: 0.6609 (ttp-110) cc_final: 0.6262 (ttp80) REVERT: E 348 GLU cc_start: 0.8038 (tt0) cc_final: 0.7197 (tm-30) REVERT: E 541 GLN cc_start: 0.8053 (mt0) cc_final: 0.7771 (tt0) REVERT: E 557 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8085 (mp10) REVERT: F 287 ARG cc_start: 0.6524 (mtt90) cc_final: 0.5691 (tmt170) REVERT: F 344 ARG cc_start: 0.6771 (ttp-110) cc_final: 0.6528 (ttp80) REVERT: F 350 MET cc_start: 0.7867 (mmm) cc_final: 0.7412 (tmt) REVERT: F 356 ASP cc_start: 0.7729 (t0) cc_final: 0.7467 (t0) REVERT: F 486 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8040 (mm-30) REVERT: F 586 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8631 (mtpt) REVERT: F 587 MET cc_start: 0.8509 (mtp) cc_final: 0.8290 (mtp) REVERT: G 180 ASN cc_start: 0.8605 (t0) cc_final: 0.8204 (t0) REVERT: G 287 ARG cc_start: 0.6553 (mtt90) cc_final: 0.5522 (ttp-170) REVERT: G 299 HIS cc_start: 0.6266 (OUTLIER) cc_final: 0.5981 (p-80) REVERT: G 344 ARG cc_start: 0.7414 (ttp-170) cc_final: 0.7113 (ttp80) REVERT: G 356 ASP cc_start: 0.7853 (t0) cc_final: 0.7648 (t0) REVERT: G 403 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8659 (mt0) REVERT: G 465 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7611 (mm-30) REVERT: G 563 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8569 (ttmm) REVERT: G 595 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7101 (ptt-90) outliers start: 69 outliers final: 46 residues processed: 315 average time/residue: 1.6780 time to fit residues: 594.0814 Evaluate side-chains 311 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 293 THR 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 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 B residue 580 LYS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 433 THR 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 297 ARG 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 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 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 381 THR Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE 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 562 ILE Chi-restraints excluded: chain G residue 563 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 127 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 476 ASN B 499 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 541 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102725 restraints weight = 32448.883| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.83 r_work: 0.3075 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23709 Z= 0.200 Angle : 0.578 13.004 32228 Z= 0.301 Chirality : 0.047 0.173 3696 Planarity : 0.004 0.039 4249 Dihedral : 4.845 33.880 3165 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.70 % Allowed : 19.81 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2947 helix: 0.57 (0.26), residues: 455 sheet: 1.23 (0.16), residues: 903 loop : -0.40 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 226 HIS 0.004 0.001 HIS C 263 PHE 0.013 0.001 PHE A 493 TYR 0.013 0.002 TYR F 410 ARG 0.008 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 805) hydrogen bonds : angle 5.91529 ( 2184) covalent geometry : bond 0.00482 (23709) covalent geometry : angle 0.57836 (32228) ********************** 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 320 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7857 (m-30) cc_final: 0.7389 (t0) REVERT: A 287 ARG cc_start: 0.6282 (mtt90) cc_final: 0.6000 (tmt170) REVERT: A 299 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.6083 (p90) REVERT: A 343 GLU cc_start: 0.7874 (tt0) cc_final: 0.7534 (tt0) REVERT: A 344 ARG cc_start: 0.7164 (ttp-110) cc_final: 0.6847 (ttp-170) REVERT: A 350 MET cc_start: 0.8001 (mmm) cc_final: 0.7297 (tmt) REVERT: A 388 ASN cc_start: 0.8598 (p0) cc_final: 0.8392 (p0) REVERT: A 541 GLN cc_start: 0.8068 (mt0) cc_final: 0.7842 (mt0) REVERT: A 560 GLN cc_start: 0.8336 (tp40) cc_final: 0.7940 (tp40) REVERT: A 570 ASN cc_start: 0.8318 (m-40) cc_final: 0.8012 (p0) REVERT: A 595 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7016 (ptt180) REVERT: B 180 ASN cc_start: 0.8575 (t0) cc_final: 0.8123 (t0) REVERT: B 287 ARG cc_start: 0.6535 (mtt90) cc_final: 0.5958 (ttp-170) REVERT: B 335 ASP cc_start: 0.7646 (m-30) cc_final: 0.7258 (t0) REVERT: B 344 ARG cc_start: 0.7360 (ttp80) cc_final: 0.7139 (tmt170) REVERT: B 350 MET cc_start: 0.7975 (mmm) cc_final: 0.7320 (tmt) REVERT: B 403 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8855 (mt0) REVERT: B 447 GLN cc_start: 0.7641 (mt0) cc_final: 0.7289 (mp10) REVERT: B 465 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 541 GLN cc_start: 0.8097 (mt0) cc_final: 0.7757 (mt0) REVERT: B 563 LYS cc_start: 0.8660 (tppp) cc_final: 0.8414 (ttmm) REVERT: B 580 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8713 (mptt) REVERT: C 287 ARG cc_start: 0.6646 (mtt90) cc_final: 0.5962 (tmt170) REVERT: C 344 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7159 (tmt170) REVERT: C 350 MET cc_start: 0.7691 (mmm) cc_final: 0.7105 (tmt) REVERT: C 389 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: C 496 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7166 (tptm) REVERT: C 587 MET cc_start: 0.8780 (mtt) cc_final: 0.8502 (mtp) REVERT: C 595 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7311 (ptt180) REVERT: D 180 ASN cc_start: 0.8572 (t0) cc_final: 0.8123 (t0) REVERT: D 287 ARG cc_start: 0.6493 (mtt90) cc_final: 0.5995 (ttp-110) REVERT: D 297 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5642 (mmt90) REVERT: D 465 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7033 (mm-30) REVERT: D 521 MET cc_start: 0.8736 (tpt) cc_final: 0.8522 (tpt) REVERT: D 563 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8382 (mmtp) REVERT: E 287 ARG cc_start: 0.6545 (mtt90) cc_final: 0.5961 (ttp-110) REVERT: E 344 ARG cc_start: 0.6775 (ttp-110) cc_final: 0.6387 (ttp80) REVERT: E 348 GLU cc_start: 0.7997 (tt0) cc_final: 0.7195 (tm-30) REVERT: E 541 GLN cc_start: 0.8178 (mt0) cc_final: 0.7918 (tt0) REVERT: E 557 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8089 (mp10) REVERT: F 209 ASN cc_start: 0.7702 (m-40) cc_final: 0.7191 (p0) REVERT: F 287 ARG cc_start: 0.6827 (mtt90) cc_final: 0.5877 (tmt170) REVERT: F 344 ARG cc_start: 0.6684 (ttp-110) cc_final: 0.6448 (ttp80) REVERT: F 350 MET cc_start: 0.7935 (mmm) cc_final: 0.7475 (tmt) REVERT: F 356 ASP cc_start: 0.7876 (t0) cc_final: 0.7623 (t0) REVERT: F 389 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: F 486 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8355 (mm-30) REVERT: F 580 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8651 (mptt) REVERT: G 287 ARG cc_start: 0.6588 (mtt90) cc_final: 0.5578 (ttp-170) REVERT: G 299 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.5977 (p-80) REVERT: G 344 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.7146 (ttp80) REVERT: G 403 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8715 (mt0) REVERT: G 465 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7518 (mm-30) REVERT: G 563 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8568 (ttmm) outliers start: 71 outliers final: 48 residues processed: 295 average time/residue: 1.8319 time to fit residues: 606.6664 Evaluate side-chains 304 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 293 THR 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 338 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 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 293 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 297 ARG 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 338 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 338 LEU 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 580 LYS Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 232 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 422 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106022 restraints weight = 32328.900| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.82 r_work: 0.3111 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23709 Z= 0.109 Angle : 0.529 10.166 32228 Z= 0.277 Chirality : 0.045 0.160 3696 Planarity : 0.004 0.033 4249 Dihedral : 4.521 24.100 3165 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.44 % Allowed : 20.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2947 helix: 0.72 (0.27), residues: 462 sheet: 1.42 (0.16), residues: 889 loop : -0.26 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 226 HIS 0.002 0.000 HIS F 263 PHE 0.011 0.001 PHE A 493 TYR 0.012 0.001 TYR F 410 ARG 0.008 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.02589 ( 805) hydrogen bonds : angle 5.63533 ( 2184) covalent geometry : bond 0.00255 (23709) covalent geometry : angle 0.52876 (32228) =============================================================================== Job complete usr+sys time: 21021.54 seconds wall clock time: 365 minutes 29.50 seconds (21929.50 seconds total)