Starting phenix.real_space_refine on Fri Sep 19 03:50:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9c_6224/09_2025/3j9c_6224.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9c_6224/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2025/3j9c_6224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2025/3j9c_6224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2025/3j9c_6224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9c_6224/09_2025/3j9c_6224.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 14504 2.51 5 N 4046 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23296 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3326 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.64, per 1000 atoms: 0.16 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: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 63 sheets defined 20.8% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 578 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.610A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 578 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 578 " --> pdb=" O TYR D 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Proline residue: E 482 - end of helix Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU E 578 " --> pdb=" O TYR E 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 Processing helix chain 'F' and resid 555 through 569 Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 578 " --> pdb=" O TYR F 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 578 " --> pdb=" O TYR G 575 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=2, first strand: chain 'A' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL A 264 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 367 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET A 266 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A 365 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 268 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 276 through 299 Processing sheet with id=5, first strand: chain 'A' and resid 302 through 311 Processing sheet with id=6, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN A 376 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN A 458 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 454 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER A 382 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR A 452 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 384 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 450 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=8, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=10, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=11, first strand: chain 'B' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL B 264 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 367 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET B 266 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 365 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 268 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 276 through 299 Processing sheet with id=14, first strand: chain 'B' and resid 302 through 311 Processing sheet with id=15, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN B 376 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN B 458 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 454 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER B 382 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR B 452 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 384 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 450 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=17, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=19, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=20, first strand: chain 'C' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL C 264 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 367 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET C 266 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 365 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 268 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 276 through 299 Processing sheet with id=23, first strand: chain 'C' and resid 302 through 311 Processing sheet with id=24, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN C 376 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN C 458 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 454 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER C 382 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C 452 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 384 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 450 " --> pdb=" O VAL C 384 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=26, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=28, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=29, first strand: chain 'D' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL D 264 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 367 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET D 266 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG D 365 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 268 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'D' and resid 276 through 299 Processing sheet with id=32, first strand: chain 'D' and resid 302 through 311 Processing sheet with id=33, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN D 376 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN D 458 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 454 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER D 382 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR D 452 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 384 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 450 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'D' and resid 460 through 462 Processing sheet with id=35, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=37, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=38, first strand: chain 'E' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL E 264 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E 367 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET E 266 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG E 365 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 268 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'E' and resid 276 through 299 Processing sheet with id=41, first strand: chain 'E' and resid 302 through 311 Processing sheet with id=42, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN E 376 " --> pdb=" O ASN E 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN E 458 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN E 454 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER E 382 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR E 452 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL E 384 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU E 450 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=44, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=46, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=47, first strand: chain 'F' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL F 264 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 367 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET F 266 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG F 365 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 268 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'F' and resid 276 through 299 Processing sheet with id=50, first strand: chain 'F' and resid 302 through 311 Processing sheet with id=51, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN F 376 " --> pdb=" O ASN F 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN F 458 " --> pdb=" O ASN F 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN F 454 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER F 382 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR F 452 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 384 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU F 450 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'F' and resid 460 through 462 Processing sheet with id=53, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=55, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=56, first strand: chain 'G' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'G' and resid 276 through 299 Processing sheet with id=59, first strand: chain 'G' and resid 302 through 311 Processing sheet with id=60, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN G 376 " --> pdb=" O ASN G 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN G 458 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN G 454 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER G 382 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR G 452 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL G 384 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU G 450 " --> pdb=" O VAL G 384 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'G' and resid 460 through 462 Processing sheet with id=62, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'G' and resid 541 through 542 805 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7766 1.34 - 1.45: 2866 1.45 - 1.57: 13000 1.57 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 23709 Sorted by residual: bond pdb=" CA LYS F 444 " pdb=" C LYS F 444 " ideal model delta sigma weight residual 1.523 1.606 -0.082 1.34e-02 5.57e+03 3.78e+01 bond pdb=" CA LYS D 444 " pdb=" C LYS D 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.75e+01 bond pdb=" CA LYS E 444 " pdb=" C LYS E 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS G 444 " pdb=" C LYS G 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS A 444 " pdb=" C LYS A 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.72e+01 ... (remaining 23704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 30274 2.17 - 4.33: 1721 4.33 - 6.50: 212 6.50 - 8.67: 14 8.67 - 10.83: 7 Bond angle restraints: 32228 Sorted by residual: angle pdb=" C ALA G 417 " pdb=" N PRO G 418 " pdb=" CA PRO G 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA B 417 " pdb=" N PRO B 418 " pdb=" CA PRO B 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA C 417 " pdb=" N PRO C 418 " pdb=" CA PRO C 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.96e+01 angle pdb=" C ALA A 417 " pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C ALA E 417 " pdb=" N PRO E 418 " pdb=" CA PRO E 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.94e+01 ... (remaining 32223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 12749 13.72 - 27.44: 1069 27.44 - 41.16: 378 41.16 - 54.88: 189 54.88 - 68.60: 84 Dihedral angle restraints: 14469 sinusoidal: 5768 harmonic: 8701 Sorted by residual: dihedral pdb=" CA SER D 413 " pdb=" C SER D 413 " pdb=" N LYS D 414 " pdb=" CA LYS D 414 " ideal model delta harmonic sigma weight residual 180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 413 " pdb=" C SER G 413 " pdb=" N LYS G 414 " pdb=" CA LYS G 414 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER B 413 " pdb=" C SER B 413 " pdb=" N LYS B 414 " pdb=" CA LYS B 414 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 14466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2893 0.050 - 0.100: 610 0.100 - 0.150: 172 0.150 - 0.200: 7 0.200 - 0.249: 14 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CA LYS E 444 " pdb=" N LYS E 444 " pdb=" C LYS E 444 " pdb=" CB LYS E 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS D 444 " pdb=" N LYS D 444 " pdb=" C LYS D 444 " pdb=" CB LYS D 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLN D 543 " pdb=" N GLN D 543 " pdb=" C GLN D 543 " pdb=" CB GLN D 543 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3693 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 378 " 0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO F 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 379 " 0.024 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6067 2.80 - 3.33: 21651 3.33 - 3.85: 40623 3.85 - 4.38: 48842 4.38 - 4.90: 82490 Nonbonded interactions: 199673 Sorted by model distance: nonbonded pdb=" O ILE C 183 " pdb="CA CA C 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE F 183 " pdb="CA CA F 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE E 183 " pdb="CA CA E 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE D 183 " pdb="CA CA D 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE A 183 " pdb="CA CA A 801 " model vdw 2.277 2.510 ... (remaining 199668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.16), residues: 2947 helix: -1.67 (0.20), residues: 497 sheet: -0.98 (0.15), residues: 1001 loop : 0.51 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 359 TYR 0.013 0.002 TYR B 456 PHE 0.011 0.001 PHE D 493 TRP 0.012 0.002 TRP G 226 HIS 0.003 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00537 (23709) covalent geometry : angle 1.11209 (32228) hydrogen bonds : bond 0.10893 ( 805) hydrogen bonds : angle 10.38417 ( 2184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 600 time to evaluate : 0.927 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 560 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7800 (tp40) REVERT: E 579 ASP cc_start: 0.8570 (p0) cc_final: 0.8214 (t0) REVERT: E 580 LYS cc_start: 0.8932 (mttp) cc_final: 0.8575 (mptt) REVERT: F 209 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7567 (p0) REVERT: F 212 GLU cc_start: 0.8409 (tt0) cc_final: 0.8184 (tm-30) REVERT: F 263 HIS cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (p90) REVERT: F 285 GLN cc_start: 0.6997 (mt0) cc_final: 0.6574 (mm-40) REVERT: F 287 ARG cc_start: 0.6452 (mtt90) cc_final: 0.5227 (tmt170) REVERT: F 294 SER cc_start: 0.6083 (OUTLIER) cc_final: 0.5649 (t) REVERT: F 330 SER cc_start: 0.4669 (OUTLIER) cc_final: 0.4152 (p) REVERT: F 344 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.6669 (ttp80) REVERT: F 350 MET cc_start: 0.8731 (mmm) cc_final: 0.7853 (ttp) REVERT: F 404 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8793 (tp) REVERT: F 434 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8637 (ttp) REVERT: F 441 GLU cc_start: 0.8511 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 444 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7643 (mtpp) REVERT: F 447 GLN cc_start: 0.7104 (mt0) cc_final: 0.6758 (mp10) REVERT: F 465 GLU cc_start: 0.9112 (tt0) cc_final: 0.8646 (mm-30) REVERT: F 486 GLU cc_start: 0.9079 (tp30) cc_final: 0.8857 (mm-30) REVERT: F 579 ASP cc_start: 0.8521 (p0) cc_final: 0.8216 (t0) REVERT: F 586 LYS cc_start: 0.8708 (mttm) cc_final: 0.8230 (mtpt) REVERT: G 285 GLN cc_start: 0.6917 (mt0) cc_final: 0.6674 (mm110) REVERT: G 287 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5357 (ttp-170) REVERT: G 291 LYS cc_start: 0.6560 (tptt) cc_final: 0.6271 (tmtp) REVERT: G 294 SER cc_start: 0.5545 (OUTLIER) cc_final: 0.4889 (t) REVERT: G 334 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6720 (mt) REVERT: G 344 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6743 (ttp80) REVERT: G 350 MET cc_start: 0.8716 (mmm) cc_final: 0.7857 (ttp) REVERT: G 387 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: G 404 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 434 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: G 441 GLU cc_start: 0.8407 (tt0) cc_final: 0.8039 (mt-10) REVERT: G 447 GLN cc_start: 0.6833 (mt0) cc_final: 0.6484 (mp10) REVERT: G 448 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 465 GLU cc_start: 0.9108 (tt0) cc_final: 0.8718 (mm-30) REVERT: G 500 LEU cc_start: 0.8851 (mt) cc_final: 0.8591 (mm) REVERT: G 579 ASP cc_start: 0.8757 (p0) cc_final: 0.8297 (t0) REVERT: G 580 LYS cc_start: 0.8985 (mttp) cc_final: 0.8773 (mmtm) REVERT: G 587 MET cc_start: 0.8768 (mtt) cc_final: 0.8526 (mtm) outliers start: 161 outliers final: 17 residues processed: 706 average time/residue: 0.7140 time to fit residues: 569.7485 Evaluate side-chains 414 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 355 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 F residue 209 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 389 GLN A 424 GLN A 483 GLN A 499 ASN A 541 GLN A 560 GLN B 198 ASN B 268 ASN B 274 ASN B 483 GLN B 557 GLN C 263 HIS C 268 ASN C 389 GLN C 483 GLN D 198 ASN D 268 ASN D 274 ASN D 424 GLN D 499 ASN D 541 GLN E 263 HIS E 268 ASN E 274 ASN E 389 GLN E 424 GLN E 483 GLN E 557 GLN E 570 ASN F 268 ASN F 274 ASN F 389 GLN F 483 GLN F 499 ASN G 198 ASN G 209 ASN G 268 ASN G 274 ASN G 424 GLN G 483 GLN G 560 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105726 restraints weight = 32412.418| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.81 r_work: 0.3150 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23709 Z= 0.119 Angle : 0.542 5.496 32228 Z= 0.294 Chirality : 0.046 0.160 3696 Planarity : 0.004 0.032 4249 Dihedral : 7.463 56.824 3278 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.16 % Allowed : 16.23 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2947 helix: -0.28 (0.25), residues: 497 sheet: -0.19 (0.15), residues: 980 loop : 0.08 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 449 TYR 0.011 0.001 TYR C 410 PHE 0.012 0.001 PHE B 493 TRP 0.018 0.002 TRP A 226 HIS 0.011 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00263 (23709) covalent geometry : angle 0.54240 (32228) hydrogen bonds : bond 0.02997 ( 805) hydrogen bonds : angle 7.00486 ( 2184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 365 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6410 (mtt90) cc_final: 0.5816 (tmt170) REVERT: A 291 LYS cc_start: 0.6652 (tptt) cc_final: 0.6186 (tptt) REVERT: A 294 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.6714 (t) REVERT: A 343 GLU cc_start: 0.7766 (tt0) cc_final: 0.7477 (tt0) REVERT: A 344 ARG cc_start: 0.7076 (ttp-110) cc_final: 0.6737 (ttp80) REVERT: A 350 MET cc_start: 0.7873 (mmm) cc_final: 0.7305 (tmt) REVERT: A 542 TYR cc_start: 0.8569 (t80) cc_final: 0.8127 (t80) REVERT: A 560 GLN cc_start: 0.8421 (tp40) cc_final: 0.8174 (tp40) REVERT: A 586 LYS cc_start: 0.8773 (mttm) cc_final: 0.8541 (mtpp) REVERT: B 287 ARG cc_start: 0.6312 (mtt90) cc_final: 0.5798 (ttp-170) REVERT: B 294 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6409 (t) REVERT: B 334 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6981 (mt) REVERT: B 350 MET cc_start: 0.7775 (mmm) cc_final: 0.7522 (tmt) REVERT: B 356 ASP cc_start: 0.7956 (t0) cc_final: 0.7653 (t0) REVERT: B 447 GLN cc_start: 0.7483 (mt0) cc_final: 0.7226 (mp10) REVERT: C 287 ARG cc_start: 0.6543 (mtt90) cc_final: 0.5902 (ttp-110) REVERT: C 291 LYS cc_start: 0.6235 (tptt) cc_final: 0.6035 (tttm) REVERT: C 344 ARG cc_start: 0.7089 (ttp-110) cc_final: 0.6856 (ttp80) REVERT: C 350 MET cc_start: 0.7744 (mmm) cc_final: 0.7163 (tmt) REVERT: C 356 ASP cc_start: 0.7902 (t0) cc_final: 0.7556 (t0) REVERT: C 426 ASP cc_start: 0.8413 (m-30) cc_final: 0.8171 (m-30) REVERT: C 447 GLN cc_start: 0.7586 (mt0) cc_final: 0.7301 (mp10) REVERT: C 545 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7697 (mtpt) REVERT: C 587 MET cc_start: 0.8297 (mtt) cc_final: 0.8038 (mtp) REVERT: C 595 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7421 (ptt180) REVERT: D 180 ASN cc_start: 0.8621 (t0) cc_final: 0.8079 (t0) REVERT: D 287 ARG cc_start: 0.6539 (mtt90) cc_final: 0.6017 (ttp-110) REVERT: D 334 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6631 (pp) REVERT: D 344 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6825 (ttp-170) REVERT: D 350 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7531 (OUTLIER) REVERT: D 356 ASP cc_start: 0.8005 (t0) cc_final: 0.7653 (t0) REVERT: D 557 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7654 (tp-100) REVERT: D 587 MET cc_start: 0.8180 (mtt) cc_final: 0.7963 (mtp) REVERT: D 595 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7173 (ptt-90) REVERT: E 209 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.6809 (p0) REVERT: E 271 LEU cc_start: 0.8471 (pt) cc_final: 0.8256 (pt) REVERT: E 287 ARG cc_start: 0.6571 (mtt90) cc_final: 0.5818 (ttp-110) REVERT: E 294 SER cc_start: 0.7488 (OUTLIER) cc_final: 0.7101 (t) REVERT: E 344 ARG cc_start: 0.6608 (ttp-110) cc_final: 0.6275 (ttp80) REVERT: E 348 GLU cc_start: 0.7888 (tt0) cc_final: 0.7086 (tm-30) REVERT: E 356 ASP cc_start: 0.7640 (t0) cc_final: 0.7338 (t0) REVERT: E 357 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8590 (t) REVERT: E 542 TYR cc_start: 0.8327 (t80) cc_final: 0.8066 (t80) REVERT: E 545 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7723 (mtpp) REVERT: E 560 GLN cc_start: 0.8219 (tp-100) cc_final: 0.8004 (tp40) REVERT: E 595 ARG cc_start: 0.7830 (mpp80) cc_final: 0.7538 (ptt-90) REVERT: F 209 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.6796 (p0) REVERT: F 263 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8580 (p90) REVERT: F 287 ARG cc_start: 0.6559 (mtt90) cc_final: 0.5698 (tmt170) REVERT: F 330 SER cc_start: 0.6409 (m) cc_final: 0.5794 (t) REVERT: F 344 ARG cc_start: 0.6834 (ttp-110) cc_final: 0.6600 (ttp80) REVERT: F 350 MET cc_start: 0.7802 (mmm) cc_final: 0.7395 (tmt) REVERT: F 389 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8768 (tm-30) REVERT: F 441 GLU cc_start: 0.7943 (tt0) cc_final: 0.7710 (tm-30) REVERT: F 444 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7687 (mtpp) REVERT: F 545 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7586 (mtpt) REVERT: F 560 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7945 (tp-100) REVERT: F 587 MET cc_start: 0.8381 (mtp) cc_final: 0.8176 (ttp) REVERT: F 595 ARG cc_start: 0.7472 (mtm180) cc_final: 0.7042 (ptt-90) REVERT: G 287 ARG cc_start: 0.6501 (mtt90) cc_final: 0.5630 (ttp-170) REVERT: G 334 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7050 (mt) REVERT: G 344 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.6697 (ttp-170) REVERT: G 350 MET cc_start: 0.7953 (mmm) cc_final: 0.7623 (ttp) REVERT: G 357 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8467 (t) REVERT: G 448 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8352 (tt) REVERT: G 486 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: G 557 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7948 (tp-100) REVERT: G 586 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8737 (mtpt) REVERT: G 595 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7093 (ptt180) outliers start: 83 outliers final: 27 residues processed: 420 average time/residue: 0.8064 time to fit residues: 379.1968 Evaluate side-chains 338 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 251 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 B 424 GLN B 476 ASN B 557 GLN C 389 GLN C 476 ASN C 541 GLN D 285 GLN D 476 ASN E 285 GLN E 389 GLN E 422 ASN E 476 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102457 restraints weight = 32491.985| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.80 r_work: 0.3057 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3029 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= 0.210 Angle : 0.571 6.551 32228 Z= 0.305 Chirality : 0.048 0.165 3696 Planarity : 0.004 0.034 4249 Dihedral : 6.028 51.174 3192 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.46 % Allowed : 16.76 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2947 helix: 0.00 (0.25), residues: 497 sheet: 0.62 (0.17), residues: 875 loop : -0.42 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 470 TYR 0.011 0.002 TYR F 410 PHE 0.013 0.002 PHE B 493 TRP 0.016 0.002 TRP A 226 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00505 (23709) covalent geometry : angle 0.57141 (32228) hydrogen bonds : bond 0.03233 ( 805) hydrogen bonds : angle 6.62985 ( 2184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 285 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6428 (mtt90) cc_final: 0.5950 (tmt170) REVERT: A 335 ASP cc_start: 0.7808 (m-30) cc_final: 0.7554 (m-30) REVERT: A 343 GLU cc_start: 0.7895 (tt0) cc_final: 0.7591 (tt0) REVERT: A 344 ARG cc_start: 0.7061 (ttp-110) cc_final: 0.6708 (ttp80) REVERT: A 350 MET cc_start: 0.7877 (mmm) cc_final: 0.7344 (tmt) REVERT: A 545 LYS cc_start: 0.8299 (mtpp) cc_final: 0.8008 (mtpt) REVERT: A 560 GLN cc_start: 0.8414 (tp40) cc_final: 0.8058 (tp40) REVERT: A 586 LYS cc_start: 0.8939 (mttm) cc_final: 0.8679 (mtpt) REVERT: B 287 ARG cc_start: 0.6308 (mtt90) cc_final: 0.5759 (ttp-170) REVERT: B 294 SER cc_start: 0.7199 (OUTLIER) cc_final: 0.6482 (t) REVERT: B 334 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7004 (pp) REVERT: B 350 MET cc_start: 0.7932 (mmm) cc_final: 0.7615 (tmt) REVERT: B 447 GLN cc_start: 0.7613 (mt0) cc_final: 0.7264 (mp10) REVERT: B 557 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8251 (mp10) REVERT: B 563 LYS cc_start: 0.8676 (tppp) cc_final: 0.8290 (mmtp) REVERT: C 287 ARG cc_start: 0.6620 (mtt90) cc_final: 0.5977 (ttp-110) REVERT: C 350 MET cc_start: 0.7690 (mmm) cc_final: 0.7238 (tmt) REVERT: C 394 ILE cc_start: 0.9303 (mp) cc_final: 0.9097 (mm) REVERT: C 404 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9089 (tp) REVERT: C 447 GLN cc_start: 0.7684 (mt0) cc_final: 0.7395 (mp10) REVERT: C 486 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: C 521 MET cc_start: 0.8728 (tpp) cc_final: 0.8463 (tpp) REVERT: C 587 MET cc_start: 0.8625 (mtt) cc_final: 0.8373 (mtp) REVERT: D 180 ASN cc_start: 0.8629 (t0) cc_final: 0.8125 (t0) REVERT: D 287 ARG cc_start: 0.6314 (mtt90) cc_final: 0.5736 (ttp-110) REVERT: D 294 SER cc_start: 0.7144 (OUTLIER) cc_final: 0.6800 (t) REVERT: D 297 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5516 (mmt90) REVERT: D 340 LEU cc_start: 0.7910 (mt) cc_final: 0.7700 (mm) REVERT: D 356 ASP cc_start: 0.7762 (t0) cc_final: 0.7551 (t70) REVERT: D 545 LYS cc_start: 0.8254 (mtpp) cc_final: 0.8018 (mtpt) REVERT: E 209 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6703 (p0) REVERT: E 287 ARG cc_start: 0.6622 (mtt90) cc_final: 0.5928 (ttp-110) REVERT: E 294 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7205 (t) REVERT: E 335 ASP cc_start: 0.7711 (m-30) cc_final: 0.7478 (m-30) REVERT: E 344 ARG cc_start: 0.6732 (ttp-110) cc_final: 0.6333 (ttp80) REVERT: E 348 GLU cc_start: 0.7866 (tt0) cc_final: 0.7034 (tm-30) REVERT: E 389 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: E 486 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: E 551 ASP cc_start: 0.7554 (p0) cc_final: 0.7350 (p0) REVERT: F 287 ARG cc_start: 0.6478 (mtt90) cc_final: 0.5732 (tmt170) REVERT: F 294 SER cc_start: 0.7034 (OUTLIER) cc_final: 0.6804 (t) REVERT: F 330 SER cc_start: 0.6434 (m) cc_final: 0.5752 (t) REVERT: F 344 ARG cc_start: 0.6849 (ttp-110) cc_final: 0.6603 (ttp80) REVERT: F 350 MET cc_start: 0.7787 (mmm) cc_final: 0.7536 (tmt) REVERT: F 441 GLU cc_start: 0.7843 (tt0) cc_final: 0.7568 (tm-30) REVERT: F 444 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7793 (mtpp) REVERT: F 560 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7968 (tp-100) REVERT: F 595 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7057 (ptt-90) REVERT: G 212 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: G 287 ARG cc_start: 0.6517 (mtt90) cc_final: 0.5583 (ttp-170) REVERT: G 334 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7113 (pp) REVERT: G 344 ARG cc_start: 0.6993 (ttp-110) cc_final: 0.6698 (ttp-170) REVERT: G 356 ASP cc_start: 0.8032 (t0) cc_final: 0.7831 (t0) REVERT: G 357 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8420 (t) REVERT: G 403 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8838 (mt0) REVERT: G 436 TYR cc_start: 0.8585 (t80) cc_final: 0.8383 (t80) REVERT: G 448 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8388 (tt) outliers start: 117 outliers final: 58 residues processed: 368 average time/residue: 0.8097 time to fit residues: 333.6444 Evaluate side-chains 336 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 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 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 413 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 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 486 GLU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 387 LYS 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 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 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 511 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 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 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 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 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 136 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 268 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 285 GLN B 424 GLN B 476 ASN C 389 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN D 476 ASN E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN F 389 GLN F 476 ASN G 285 GLN G 424 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102963 restraints weight = 32352.217| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.81 r_work: 0.3071 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3345 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= 0.166 Angle : 0.528 4.981 32228 Z= 0.281 Chirality : 0.046 0.163 3696 Planarity : 0.004 0.036 4249 Dihedral : 5.553 49.319 3184 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.15 % Allowed : 17.60 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 2947 helix: 0.13 (0.25), residues: 497 sheet: 0.61 (0.16), residues: 910 loop : -0.42 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 470 TYR 0.012 0.001 TYR C 411 PHE 0.013 0.001 PHE B 493 TRP 0.015 0.002 TRP D 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00397 (23709) covalent geometry : angle 0.52835 (32228) hydrogen bonds : bond 0.03008 ( 805) hydrogen bonds : angle 6.33343 ( 2184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 271 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6295 (mtt90) cc_final: 0.5931 (tmt170) REVERT: A 343 GLU cc_start: 0.7855 (tt0) cc_final: 0.7529 (tt0) REVERT: A 344 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6700 (ttp80) REVERT: A 350 MET cc_start: 0.7859 (mmm) cc_final: 0.7267 (tmt) REVERT: A 388 ASN cc_start: 0.8589 (p0) cc_final: 0.8367 (p0) REVERT: A 560 GLN cc_start: 0.8508 (tp40) cc_final: 0.8040 (tp40) REVERT: A 586 LYS cc_start: 0.8903 (mttm) cc_final: 0.8651 (mtpt) REVERT: B 287 ARG cc_start: 0.6491 (mtt90) cc_final: 0.5872 (ttp-170) REVERT: B 334 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7044 (pp) REVERT: B 344 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7197 (tmt170) REVERT: B 350 MET cc_start: 0.7894 (mmm) cc_final: 0.7598 (tmt) REVERT: B 447 GLN cc_start: 0.7584 (mt0) cc_final: 0.7233 (mp10) REVERT: B 557 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8272 (mp10) REVERT: B 563 LYS cc_start: 0.8647 (tppp) cc_final: 0.8387 (ttmm) REVERT: B 595 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7477 (ptt180) REVERT: C 287 ARG cc_start: 0.6492 (mtt90) cc_final: 0.5907 (ttp-110) REVERT: C 350 MET cc_start: 0.7675 (mmm) cc_final: 0.7216 (tmt) REVERT: C 404 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9040 (tp) REVERT: C 447 GLN cc_start: 0.7703 (mt0) cc_final: 0.7420 (mp10) REVERT: C 587 MET cc_start: 0.8647 (mtt) cc_final: 0.8379 (mtp) REVERT: C 595 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7315 (ptt180) REVERT: D 180 ASN cc_start: 0.8591 (t0) cc_final: 0.8104 (t0) REVERT: D 287 ARG cc_start: 0.6397 (mtt90) cc_final: 0.5755 (ttp-110) REVERT: D 294 SER cc_start: 0.7128 (OUTLIER) cc_final: 0.6851 (t) REVERT: D 545 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7936 (mtpt) REVERT: E 287 ARG cc_start: 0.6487 (mtt90) cc_final: 0.5858 (ttp-110) REVERT: E 335 ASP cc_start: 0.7873 (m-30) cc_final: 0.7671 (m-30) REVERT: E 344 ARG cc_start: 0.6689 (ttp-110) cc_final: 0.6336 (ttp80) REVERT: E 348 GLU cc_start: 0.7877 (tt0) cc_final: 0.7010 (tm-30) REVERT: E 551 ASP cc_start: 0.7498 (p0) cc_final: 0.7263 (p0) REVERT: F 287 ARG cc_start: 0.6520 (mtt90) cc_final: 0.5788 (tmt170) REVERT: F 294 SER cc_start: 0.7056 (OUTLIER) cc_final: 0.6824 (t) REVERT: F 330 SER cc_start: 0.6350 (m) cc_final: 0.5660 (t) REVERT: F 344 ARG cc_start: 0.6819 (ttp-110) cc_final: 0.6599 (ttp80) REVERT: F 350 MET cc_start: 0.7803 (mmm) cc_final: 0.7540 (tmt) REVERT: F 441 GLU cc_start: 0.7899 (tt0) cc_final: 0.7643 (tm-30) REVERT: F 444 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7853 (mtpp) REVERT: F 541 GLN cc_start: 0.7893 (mt0) cc_final: 0.7475 (mt0) REVERT: F 557 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8146 (mp10) REVERT: F 595 ARG cc_start: 0.7534 (mtm180) cc_final: 0.7057 (ptt-90) REVERT: G 287 ARG cc_start: 0.6579 (mtt90) cc_final: 0.5654 (ttp-170) REVERT: G 294 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6559 (t) REVERT: G 344 ARG cc_start: 0.7029 (ttp-110) cc_final: 0.6809 (ttp-170) REVERT: G 357 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8402 (t) REVERT: G 403 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8755 (mt0) REVERT: G 414 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8926 (mmtt) REVERT: G 436 TYR cc_start: 0.8585 (t80) cc_final: 0.8325 (t80) REVERT: G 500 LEU cc_start: 0.8986 (mm) cc_final: 0.8719 (mt) outliers start: 109 outliers final: 63 residues processed: 345 average time/residue: 0.8051 time to fit residues: 311.6506 Evaluate side-chains 330 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 259 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 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 413 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain 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 433 THR Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 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 293 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 394 ILE 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 283 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN B 476 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 422 ASN E 476 ASN F 422 ASN ** F 476 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.137357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103414 restraints weight = 31997.289| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.80 r_work: 0.3087 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23709 Z= 0.154 Angle : 0.522 6.953 32228 Z= 0.276 Chirality : 0.046 0.166 3696 Planarity : 0.004 0.036 4249 Dihedral : 5.207 43.417 3176 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.19 % Allowed : 17.71 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.15), residues: 2947 helix: 0.20 (0.25), residues: 497 sheet: 0.66 (0.16), residues: 910 loop : -0.45 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 470 TYR 0.012 0.001 TYR C 411 PHE 0.012 0.001 PHE B 493 TRP 0.014 0.001 TRP D 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00368 (23709) covalent geometry : angle 0.52183 (32228) hydrogen bonds : bond 0.02923 ( 805) hydrogen bonds : angle 6.15624 ( 2184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 276 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6335 (mtt90) cc_final: 0.5944 (tmt170) REVERT: A 343 GLU cc_start: 0.7840 (tt0) cc_final: 0.7501 (tt0) REVERT: A 344 ARG cc_start: 0.7048 (ttp-110) cc_final: 0.6685 (ttp80) REVERT: A 350 MET cc_start: 0.7907 (mmm) cc_final: 0.7255 (tmt) REVERT: A 388 ASN cc_start: 0.8606 (p0) cc_final: 0.8393 (p0) REVERT: A 541 GLN cc_start: 0.7869 (mt0) cc_final: 0.7575 (mt0) REVERT: A 545 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8042 (mtpt) REVERT: A 560 GLN cc_start: 0.8441 (tp40) cc_final: 0.7992 (tp40) REVERT: A 570 ASN cc_start: 0.8595 (m-40) cc_final: 0.8093 (p0) REVERT: A 586 LYS cc_start: 0.8895 (mttm) cc_final: 0.8666 (mtpt) REVERT: B 287 ARG cc_start: 0.6525 (mtt90) cc_final: 0.5883 (ttp-170) REVERT: B 350 MET cc_start: 0.7854 (mmm) cc_final: 0.7323 (tmt) REVERT: B 447 GLN cc_start: 0.7573 (mt0) cc_final: 0.7232 (mp10) REVERT: B 465 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 541 GLN cc_start: 0.7952 (mt0) cc_final: 0.7515 (mt0) REVERT: B 557 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8280 (mp10) REVERT: B 563 LYS cc_start: 0.8647 (tppp) cc_final: 0.8368 (ttmm) REVERT: C 287 ARG cc_start: 0.6447 (mtt90) cc_final: 0.5920 (ttp-110) REVERT: C 344 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7239 (tmt170) REVERT: C 350 MET cc_start: 0.7628 (mmm) cc_final: 0.7163 (tmt) REVERT: C 398 GLU cc_start: 0.8236 (pt0) cc_final: 0.8022 (pm20) REVERT: C 404 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9005 (tp) REVERT: C 447 GLN cc_start: 0.7708 (mt0) cc_final: 0.7468 (mp10) REVERT: C 541 GLN cc_start: 0.8165 (mt0) cc_final: 0.7857 (mt0) REVERT: C 587 MET cc_start: 0.8694 (mtt) cc_final: 0.8407 (mtp) REVERT: C 595 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7297 (ptt180) REVERT: D 180 ASN cc_start: 0.8553 (t0) cc_final: 0.8092 (t0) REVERT: D 287 ARG cc_start: 0.6436 (mtt90) cc_final: 0.5785 (ttp-110) REVERT: D 294 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6821 (t) REVERT: D 465 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7653 (mm-30) REVERT: E 287 ARG cc_start: 0.6469 (mtt90) cc_final: 0.5821 (ttp-110) REVERT: E 344 ARG cc_start: 0.6689 (ttp-110) cc_final: 0.6309 (ttp80) REVERT: E 348 GLU cc_start: 0.7893 (tt0) cc_final: 0.7008 (tm-30) REVERT: E 486 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: E 551 ASP cc_start: 0.7468 (p0) cc_final: 0.7265 (p0) REVERT: E 595 ARG cc_start: 0.7887 (mpp80) cc_final: 0.7413 (ptt180) REVERT: F 271 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8051 (pp) REVERT: F 287 ARG cc_start: 0.6556 (mtt90) cc_final: 0.5745 (tmt170) REVERT: F 330 SER cc_start: 0.6274 (m) cc_final: 0.5583 (t) REVERT: F 344 ARG cc_start: 0.6795 (ttp-110) cc_final: 0.6590 (ttp80) REVERT: F 350 MET cc_start: 0.7833 (mmm) cc_final: 0.7480 (tmt) REVERT: F 398 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: F 441 GLU cc_start: 0.7863 (tt0) cc_final: 0.7659 (tm-30) REVERT: F 444 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7847 (mtpp) REVERT: F 541 GLN cc_start: 0.7960 (mt0) cc_final: 0.7630 (mt0) REVERT: F 595 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7163 (ptt-90) REVERT: G 212 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: G 287 ARG cc_start: 0.6601 (mtt90) cc_final: 0.5662 (ttp-170) REVERT: G 294 SER cc_start: 0.7265 (OUTLIER) cc_final: 0.6575 (t) REVERT: G 344 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6799 (ttp-170) REVERT: G 357 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8470 (t) REVERT: G 403 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8770 (mt0) REVERT: G 414 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8938 (mmtt) REVERT: G 436 TYR cc_start: 0.8558 (t80) cc_final: 0.8292 (t80) REVERT: G 465 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7578 (mm-30) REVERT: G 500 LEU cc_start: 0.8997 (mm) cc_final: 0.8744 (mt) REVERT: G 541 GLN cc_start: 0.8065 (mt0) cc_final: 0.7754 (mt0) REVERT: G 563 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8587 (mttm) outliers start: 110 outliers final: 63 residues processed: 346 average time/residue: 0.8375 time to fit residues: 323.8514 Evaluate side-chains 335 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 THR Chi-restraints excluded: chain A residue 475 SER 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 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 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 204 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 385 LEU 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 447 GLN Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 394 ILE 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 563 LYS 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 21 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 183 optimal weight: 40.0000 chunk 140 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 476 ASN D 476 ASN E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN F 422 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102529 restraints weight = 32371.388| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.81 r_work: 0.3070 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: 0.8439 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23709 Z= 0.188 Angle : 0.545 7.140 32228 Z= 0.287 Chirality : 0.047 0.166 3696 Planarity : 0.004 0.039 4249 Dihedral : 5.150 39.508 3170 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.46 % Allowed : 18.02 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 2947 helix: 0.17 (0.25), residues: 497 sheet: 0.86 (0.16), residues: 875 loop : -0.60 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 470 TYR 0.013 0.002 TYR C 411 PHE 0.013 0.001 PHE B 493 TRP 0.015 0.002 TRP D 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00453 (23709) covalent geometry : angle 0.54487 (32228) hydrogen bonds : bond 0.03049 ( 805) hydrogen bonds : angle 6.19516 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 263 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.6372 (mtt90) cc_final: 0.5978 (tmt170) REVERT: A 299 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.6045 (p90) REVERT: A 343 GLU cc_start: 0.7859 (tt0) cc_final: 0.7525 (tt0) REVERT: A 344 ARG cc_start: 0.7138 (ttp-110) cc_final: 0.6888 (ttp-170) REVERT: A 350 MET cc_start: 0.7967 (mmm) cc_final: 0.7293 (tmt) REVERT: A 541 GLN cc_start: 0.7968 (mt0) cc_final: 0.7674 (mt0) REVERT: A 560 GLN cc_start: 0.8435 (tp40) cc_final: 0.8009 (tp40) REVERT: A 570 ASN cc_start: 0.8634 (m-40) cc_final: 0.8087 (p0) REVERT: A 586 LYS cc_start: 0.8877 (mttm) cc_final: 0.8670 (mtpt) REVERT: B 180 ASN cc_start: 0.8609 (t0) cc_final: 0.8108 (t0) REVERT: B 287 ARG cc_start: 0.6513 (mtt90) cc_final: 0.5878 (ttp-170) REVERT: B 334 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7053 (pp) REVERT: B 350 MET cc_start: 0.7905 (mmm) cc_final: 0.7352 (tmt) REVERT: B 447 GLN cc_start: 0.7598 (mt0) cc_final: 0.7236 (mp10) REVERT: B 465 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 541 GLN cc_start: 0.8023 (mt0) cc_final: 0.7629 (mt0) REVERT: B 557 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8248 (mp10) REVERT: B 563 LYS cc_start: 0.8671 (tppp) cc_final: 0.8382 (ttmm) REVERT: B 595 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7437 (ptt180) REVERT: C 287 ARG cc_start: 0.6505 (mtt90) cc_final: 0.5816 (tmt170) REVERT: C 350 MET cc_start: 0.7663 (mmm) cc_final: 0.7138 (tmt) REVERT: C 356 ASP cc_start: 0.7763 (t0) cc_final: 0.7468 (t0) REVERT: C 389 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: C 404 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9009 (tp) REVERT: C 441 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7742 (pt0) REVERT: C 447 GLN cc_start: 0.7708 (mt0) cc_final: 0.7451 (mp10) REVERT: C 541 GLN cc_start: 0.8180 (mt0) cc_final: 0.7963 (mt0) REVERT: C 587 MET cc_start: 0.8758 (mtt) cc_final: 0.8481 (mtp) REVERT: C 595 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7326 (ptt180) REVERT: D 180 ASN cc_start: 0.8584 (t0) cc_final: 0.8109 (t0) REVERT: D 212 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: D 221 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8984 (p) REVERT: D 287 ARG cc_start: 0.6408 (mtt90) cc_final: 0.5909 (ttp-110) REVERT: D 294 SER cc_start: 0.7178 (OUTLIER) cc_final: 0.6789 (t) REVERT: D 297 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5620 (mmt90) REVERT: E 287 ARG cc_start: 0.6491 (mtt90) cc_final: 0.5861 (ttp-110) REVERT: E 344 ARG cc_start: 0.6831 (ttp-110) cc_final: 0.6394 (ttp80) REVERT: E 348 GLU cc_start: 0.7990 (tt0) cc_final: 0.7106 (tm-30) REVERT: E 486 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: E 541 GLN cc_start: 0.8121 (mt0) cc_final: 0.7891 (tt0) REVERT: E 545 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7893 (mtpm) REVERT: E 551 ASP cc_start: 0.7491 (p0) cc_final: 0.7285 (p0) REVERT: E 586 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8745 (mtpt) REVERT: E 595 ARG cc_start: 0.7883 (mpp80) cc_final: 0.7458 (ptt-90) REVERT: F 271 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8079 (pp) REVERT: F 287 ARG cc_start: 0.6588 (mtt90) cc_final: 0.5713 (tmt170) REVERT: F 297 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5077 (mmt90) REVERT: F 330 SER cc_start: 0.6155 (m) cc_final: 0.5290 (p) REVERT: F 344 ARG cc_start: 0.6909 (ttp-110) cc_final: 0.6673 (ttp80) REVERT: F 350 MET cc_start: 0.7886 (mmm) cc_final: 0.7498 (tmt) REVERT: F 356 ASP cc_start: 0.7832 (t0) cc_final: 0.7546 (t0) REVERT: F 441 GLU cc_start: 0.7906 (tt0) cc_final: 0.7664 (tm-30) REVERT: F 595 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7156 (ptt-90) REVERT: G 212 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: G 287 ARG cc_start: 0.6624 (mtt90) cc_final: 0.5683 (ttp-170) REVERT: G 294 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6587 (t) REVERT: G 344 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6790 (ttp-170) REVERT: G 357 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8447 (t) REVERT: G 403 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: G 414 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8939 (mmtt) REVERT: G 436 TYR cc_start: 0.8567 (t80) cc_final: 0.8308 (t80) REVERT: G 465 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7605 (mm-30) REVERT: G 500 LEU cc_start: 0.9013 (mm) cc_final: 0.8767 (mt) REVERT: G 541 GLN cc_start: 0.8114 (mt0) cc_final: 0.7797 (mt0) REVERT: G 563 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8599 (mttm) outliers start: 117 outliers final: 72 residues processed: 340 average time/residue: 0.8264 time to fit residues: 314.3979 Evaluate side-chains 339 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 250 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 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 475 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR 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 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 212 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 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 385 LEU 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 486 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 271 LEU 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 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 293 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 394 ILE 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 563 LYS Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 153 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 184 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 476 ASN D 476 ASN E 285 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN E 476 ASN E 499 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.101491 restraints weight = 32395.047| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.81 r_work: 0.3042 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23709 Z= 0.225 Angle : 0.576 8.705 32228 Z= 0.302 Chirality : 0.048 0.166 3696 Planarity : 0.005 0.040 4249 Dihedral : 5.263 40.081 3170 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.22 % Allowed : 17.64 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 2947 helix: 0.07 (0.24), residues: 497 sheet: 0.93 (0.16), residues: 903 loop : -0.68 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 470 TYR 0.013 0.002 TYR G 462 PHE 0.013 0.002 PHE B 493 TRP 0.015 0.002 TRP D 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00542 (23709) covalent geometry : angle 0.57558 (32228) hydrogen bonds : bond 0.03217 ( 805) hydrogen bonds : angle 6.30288 ( 2184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 252 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7840 (m-30) cc_final: 0.7341 (t70) REVERT: A 287 ARG cc_start: 0.6291 (mtt90) cc_final: 0.5965 (tmt170) REVERT: A 299 HIS cc_start: 0.6491 (OUTLIER) cc_final: 0.6072 (p90) REVERT: A 344 ARG cc_start: 0.7144 (ttp-110) cc_final: 0.6872 (ttp-170) REVERT: A 350 MET cc_start: 0.8033 (mmm) cc_final: 0.7335 (tmt) REVERT: A 541 GLN cc_start: 0.8004 (mt0) cc_final: 0.7729 (mt0) REVERT: A 560 GLN cc_start: 0.8434 (tp40) cc_final: 0.8019 (tp40) REVERT: A 570 ASN cc_start: 0.8471 (m-40) cc_final: 0.8075 (p0) REVERT: B 287 ARG cc_start: 0.6537 (mtt90) cc_final: 0.5920 (ttp-170) REVERT: B 297 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5860 (mmt90) REVERT: B 334 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7054 (pp) REVERT: B 350 MET cc_start: 0.7979 (mmm) cc_final: 0.7392 (tmt) REVERT: B 403 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8888 (mt0) REVERT: B 447 GLN cc_start: 0.7573 (mt0) cc_final: 0.7219 (mp10) REVERT: B 465 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 541 GLN cc_start: 0.8103 (mt0) cc_final: 0.7183 (mm-40) REVERT: B 557 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8169 (mp10) REVERT: B 563 LYS cc_start: 0.8699 (tppp) cc_final: 0.8333 (mmtp) REVERT: C 287 ARG cc_start: 0.6582 (mtt90) cc_final: 0.5835 (tmt170) REVERT: C 344 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7309 (tmt170) REVERT: C 350 MET cc_start: 0.7739 (mmm) cc_final: 0.7260 (tmt) REVERT: C 389 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: C 404 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9025 (tp) REVERT: C 441 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7691 (pt0) REVERT: C 447 GLN cc_start: 0.7825 (mt0) cc_final: 0.7474 (mp10) REVERT: C 496 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7226 (tptm) REVERT: C 541 GLN cc_start: 0.8141 (mt0) cc_final: 0.7585 (mm-40) REVERT: C 587 MET cc_start: 0.8785 (mtt) cc_final: 0.8522 (mtp) REVERT: D 180 ASN cc_start: 0.8613 (t0) cc_final: 0.8120 (t0) REVERT: D 221 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.9004 (p) REVERT: D 287 ARG cc_start: 0.6395 (mtt90) cc_final: 0.5900 (ttp-110) REVERT: D 294 SER cc_start: 0.7270 (OUTLIER) cc_final: 0.6854 (t) REVERT: D 297 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5584 (mmt90) REVERT: D 465 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7029 (mm-30) REVERT: E 287 ARG cc_start: 0.6565 (mtt90) cc_final: 0.5919 (ttp-110) REVERT: E 294 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.6961 (t) REVERT: E 344 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6470 (ttp80) REVERT: E 348 GLU cc_start: 0.8056 (tt0) cc_final: 0.7217 (tm-30) REVERT: E 486 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: E 541 GLN cc_start: 0.8196 (mt0) cc_final: 0.7959 (tt0) REVERT: E 545 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7868 (mtpm) REVERT: E 551 ASP cc_start: 0.7495 (p0) cc_final: 0.7271 (p0) REVERT: E 595 ARG cc_start: 0.7818 (mpp80) cc_final: 0.7365 (ptt-90) REVERT: F 209 ASN cc_start: 0.7427 (m-40) cc_final: 0.7037 (p0) REVERT: F 271 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8117 (pp) REVERT: F 287 ARG cc_start: 0.6749 (mtt90) cc_final: 0.5771 (tmt170) REVERT: F 297 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5251 (mmt90) REVERT: F 330 SER cc_start: 0.6180 (m) cc_final: 0.5286 (p) REVERT: F 344 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6609 (ttp80) REVERT: F 350 MET cc_start: 0.7976 (mmm) cc_final: 0.7462 (tmt) REVERT: F 356 ASP cc_start: 0.7898 (t0) cc_final: 0.7595 (t0) REVERT: F 389 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: F 555 ASP cc_start: 0.7016 (p0) cc_final: 0.6772 (p0) REVERT: F 557 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8280 (mp10) REVERT: F 595 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7009 (ptt180) REVERT: G 212 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: G 287 ARG cc_start: 0.6556 (mtt90) cc_final: 0.5538 (ttp-170) REVERT: G 294 SER cc_start: 0.7327 (OUTLIER) cc_final: 0.6610 (t) REVERT: G 299 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5514 (p-80) REVERT: G 344 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6785 (ttp-170) REVERT: G 403 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8734 (mt0) REVERT: G 414 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8965 (mmtt) REVERT: G 436 TYR cc_start: 0.8586 (t80) cc_final: 0.8359 (t80) REVERT: G 465 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7690 (mm-30) REVERT: G 486 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: G 500 LEU cc_start: 0.9077 (mm) cc_final: 0.8844 (mt) REVERT: G 541 GLN cc_start: 0.8165 (mt0) cc_final: 0.7833 (mt0) REVERT: G 563 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8591 (mttm) REVERT: G 586 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8916 (mtpt) outliers start: 137 outliers final: 79 residues processed: 346 average time/residue: 0.8210 time to fit residues: 317.8769 Evaluate side-chains 347 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 246 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 475 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 345 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 381 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 433 THR 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 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 511 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 271 LEU 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 345 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 294 SER 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 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 563 LYS Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 72 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 57 optimal weight: 40.0000 chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 403 GLN 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 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 476 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3708 r_free = 0.3708 target = 0.139284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105742 restraints weight = 32034.649| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.81 r_work: 0.3120 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23709 Z= 0.102 Angle : 0.503 7.095 32228 Z= 0.265 Chirality : 0.044 0.164 3696 Planarity : 0.004 0.035 4249 Dihedral : 4.642 30.952 3169 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.70 % Allowed : 19.96 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.16), residues: 2947 helix: 0.77 (0.27), residues: 455 sheet: 1.22 (0.16), residues: 875 loop : -0.31 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 470 TYR 0.012 0.001 TYR B 410 PHE 0.011 0.001 PHE A 493 TRP 0.015 0.001 TRP D 226 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00234 (23709) covalent geometry : angle 0.50310 (32228) hydrogen bonds : bond 0.02667 ( 805) hydrogen bonds : angle 5.86390 ( 2184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 287 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7774 (m-30) cc_final: 0.7259 (t0) REVERT: A 287 ARG cc_start: 0.6336 (mtt90) cc_final: 0.5871 (tmt170) REVERT: A 344 ARG cc_start: 0.7066 (ttp-110) cc_final: 0.6680 (ttp80) REVERT: A 350 MET cc_start: 0.7900 (mmm) cc_final: 0.7120 (tmt) REVERT: A 388 ASN cc_start: 0.8588 (p0) cc_final: 0.8382 (p0) REVERT: A 541 GLN cc_start: 0.7960 (mt0) cc_final: 0.7747 (mt0) REVERT: A 560 GLN cc_start: 0.8268 (tp40) cc_final: 0.7833 (tp40) REVERT: A 570 ASN cc_start: 0.8445 (m-40) cc_final: 0.7942 (p0) REVERT: A 595 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7056 (ptt180) REVERT: B 180 ASN cc_start: 0.8566 (t0) cc_final: 0.8083 (t0) REVERT: B 287 ARG cc_start: 0.6537 (mtt90) cc_final: 0.5908 (ttp-170) REVERT: B 335 ASP cc_start: 0.7536 (m-30) cc_final: 0.7213 (t0) REVERT: B 350 MET cc_start: 0.7867 (mmm) cc_final: 0.7284 (tmt) REVERT: B 403 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: B 447 GLN cc_start: 0.7511 (mt0) cc_final: 0.7208 (mp10) REVERT: B 465 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 541 GLN cc_start: 0.8029 (mt0) cc_final: 0.7677 (mt0) REVERT: B 557 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8335 (mp10) REVERT: B 563 LYS cc_start: 0.8641 (tppp) cc_final: 0.8329 (mmtp) REVERT: B 595 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7484 (ptt180) REVERT: C 287 ARG cc_start: 0.6611 (mtt90) cc_final: 0.5862 (tmt170) REVERT: C 344 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7219 (tmt170) REVERT: C 350 MET cc_start: 0.7606 (mmm) cc_final: 0.7051 (tmt) REVERT: C 441 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7809 (pt0) REVERT: C 447 GLN cc_start: 0.7683 (mt0) cc_final: 0.7438 (mp10) REVERT: C 496 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7311 (tptm) REVERT: C 587 MET cc_start: 0.8672 (mtt) cc_final: 0.8292 (mtp) REVERT: C 595 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7298 (ptt180) REVERT: D 180 ASN cc_start: 0.8492 (t0) cc_final: 0.8068 (t0) REVERT: D 221 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8940 (p) REVERT: D 287 ARG cc_start: 0.6364 (mtt90) cc_final: 0.5844 (ttp-110) REVERT: D 294 SER cc_start: 0.7258 (OUTLIER) cc_final: 0.6795 (t) REVERT: D 500 LEU cc_start: 0.8801 (mm) cc_final: 0.8512 (mt) REVERT: D 595 ARG cc_start: 0.7897 (mtm180) cc_final: 0.7480 (ptt-90) REVERT: E 180 ASN cc_start: 0.8498 (t0) cc_final: 0.8062 (t0) REVERT: E 287 ARG cc_start: 0.6556 (mtt90) cc_final: 0.5883 (ttp-110) REVERT: E 344 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.6301 (ttp80) REVERT: E 348 GLU cc_start: 0.8006 (tt0) cc_final: 0.7162 (tm-30) REVERT: E 541 GLN cc_start: 0.8056 (mt0) cc_final: 0.7795 (tt0) REVERT: E 545 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7803 (mtpm) REVERT: E 551 ASP cc_start: 0.7512 (p0) cc_final: 0.7306 (p0) REVERT: E 570 ASN cc_start: 0.8296 (m-40) cc_final: 0.8080 (p0) REVERT: E 595 ARG cc_start: 0.7827 (mpp80) cc_final: 0.7394 (ptt-90) REVERT: F 209 ASN cc_start: 0.7381 (m-40) cc_final: 0.7007 (p0) REVERT: F 271 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7960 (pp) REVERT: F 287 ARG cc_start: 0.6717 (mtt90) cc_final: 0.5742 (tmt170) REVERT: F 344 ARG cc_start: 0.6849 (ttp-110) cc_final: 0.6594 (ttp80) REVERT: F 350 MET cc_start: 0.7893 (mmm) cc_final: 0.7440 (tmt) REVERT: F 356 ASP cc_start: 0.7676 (t0) cc_final: 0.7412 (t0) REVERT: F 595 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7392 (ptt-90) REVERT: G 180 ASN cc_start: 0.8671 (t0) cc_final: 0.8256 (t0) REVERT: G 287 ARG cc_start: 0.6578 (mtt90) cc_final: 0.5522 (ttp-170) REVERT: G 294 SER cc_start: 0.7284 (OUTLIER) cc_final: 0.6604 (t) REVERT: G 344 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6915 (ttp-170) REVERT: G 403 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: G 414 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8954 (mmtt) REVERT: G 436 TYR cc_start: 0.8471 (t80) cc_final: 0.8261 (t80) REVERT: G 465 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7615 (mm-30) REVERT: G 500 LEU cc_start: 0.9036 (mm) cc_final: 0.8796 (mt) REVERT: G 541 GLN cc_start: 0.8098 (mt0) cc_final: 0.7829 (mt0) REVERT: G 545 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7633 (mtpt) REVERT: G 562 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8667 (tp) REVERT: G 563 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8572 (ttmm) REVERT: G 595 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7272 (ptt-90) outliers start: 71 outliers final: 31 residues processed: 331 average time/residue: 0.8483 time to fit residues: 312.8514 Evaluate side-chains 296 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 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 A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain G residue 294 SER 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 563 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 231 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 180 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 280 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 422 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 274 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 422 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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** ** 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 = 0.3717 r_free = 0.3717 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106501 restraints weight = 32177.406| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.81 r_work: 0.3120 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23709 Z= 0.102 Angle : 0.512 8.153 32228 Z= 0.269 Chirality : 0.044 0.165 3696 Planarity : 0.004 0.034 4249 Dihedral : 4.445 18.949 3165 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.94 % Allowed : 21.18 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2947 helix: 0.83 (0.27), residues: 462 sheet: 1.08 (0.16), residues: 952 loop : -0.04 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 470 TYR 0.012 0.001 TYR B 411 PHE 0.012 0.001 PHE F 493 TRP 0.014 0.001 TRP D 226 HIS 0.004 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00237 (23709) covalent geometry : angle 0.51228 (32228) hydrogen bonds : bond 0.02565 ( 805) hydrogen bonds : angle 5.66053 ( 2184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8633 (t0) cc_final: 0.8164 (t0) REVERT: A 283 ASP cc_start: 0.7826 (m-30) cc_final: 0.7328 (t0) REVERT: A 287 ARG cc_start: 0.6253 (mtt90) cc_final: 0.5803 (tmt170) REVERT: A 344 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6798 (ttp-170) REVERT: A 350 MET cc_start: 0.7927 (mmm) cc_final: 0.7168 (tmt) REVERT: A 388 ASN cc_start: 0.8564 (p0) cc_final: 0.8336 (p0) REVERT: A 541 GLN cc_start: 0.7983 (mt0) cc_final: 0.7783 (mt0) REVERT: A 560 GLN cc_start: 0.8240 (tp40) cc_final: 0.7792 (tp40) REVERT: A 570 ASN cc_start: 0.8458 (m-40) cc_final: 0.7993 (p0) REVERT: A 595 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7093 (ptt180) REVERT: B 180 ASN cc_start: 0.8553 (t0) cc_final: 0.8097 (t0) REVERT: B 287 ARG cc_start: 0.6426 (mtt90) cc_final: 0.5937 (ttp-170) REVERT: B 335 ASP cc_start: 0.7536 (m-30) cc_final: 0.7192 (t0) REVERT: B 350 MET cc_start: 0.7825 (mmm) cc_final: 0.7179 (tmt) REVERT: B 441 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7458 (mt-10) REVERT: B 447 GLN cc_start: 0.7470 (mt0) cc_final: 0.7234 (mp10) REVERT: B 465 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 541 GLN cc_start: 0.8037 (mt0) cc_final: 0.7693 (mt0) REVERT: B 563 LYS cc_start: 0.8637 (tppp) cc_final: 0.8364 (mmtp) REVERT: B 595 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7470 (ptt180) REVERT: C 287 ARG cc_start: 0.6586 (mtt90) cc_final: 0.6030 (ttp-110) REVERT: C 344 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7223 (tmt170) REVERT: C 350 MET cc_start: 0.7572 (mmm) cc_final: 0.6983 (tmt) REVERT: C 441 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7834 (pt0) REVERT: C 496 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7188 (tptm) REVERT: C 587 MET cc_start: 0.8699 (mtt) cc_final: 0.8440 (mtp) REVERT: C 595 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7287 (ptt180) REVERT: D 180 ASN cc_start: 0.8424 (t0) cc_final: 0.8027 (t0) REVERT: D 287 ARG cc_start: 0.6404 (mtt90) cc_final: 0.5908 (ttp-110) REVERT: D 294 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.6777 (t) REVERT: D 465 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6949 (mm-30) REVERT: D 500 LEU cc_start: 0.8748 (mm) cc_final: 0.8478 (mt) REVERT: D 595 ARG cc_start: 0.7843 (mtm180) cc_final: 0.7437 (ptt-90) REVERT: E 180 ASN cc_start: 0.8464 (t0) cc_final: 0.8052 (t0) REVERT: E 287 ARG cc_start: 0.6433 (mtt90) cc_final: 0.5821 (ttp-110) REVERT: E 344 ARG cc_start: 0.6606 (ttp-110) cc_final: 0.6256 (ttp80) REVERT: E 348 GLU cc_start: 0.7949 (tt0) cc_final: 0.7069 (tm-30) REVERT: E 541 GLN cc_start: 0.8048 (mt0) cc_final: 0.7811 (tt0) REVERT: E 545 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7774 (mtpm) REVERT: E 595 ARG cc_start: 0.7798 (mpp80) cc_final: 0.7386 (ptt-90) REVERT: F 209 ASN cc_start: 0.7270 (m-40) cc_final: 0.6945 (p0) REVERT: F 271 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7996 (pp) REVERT: F 287 ARG cc_start: 0.6715 (mtt90) cc_final: 0.5758 (tmt170) REVERT: F 344 ARG cc_start: 0.6771 (ttp-110) cc_final: 0.6549 (ttp80) REVERT: F 346 TRP cc_start: 0.7246 (OUTLIER) cc_final: 0.6788 (t60) REVERT: F 350 MET cc_start: 0.7875 (mmm) cc_final: 0.7396 (tmt) REVERT: F 356 ASP cc_start: 0.7725 (t0) cc_final: 0.7477 (t0) REVERT: F 560 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: F 595 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7389 (ptt-90) REVERT: G 180 ASN cc_start: 0.8636 (t0) cc_final: 0.8235 (t0) REVERT: G 287 ARG cc_start: 0.6560 (mtt90) cc_final: 0.5541 (ttp-170) REVERT: G 294 SER cc_start: 0.7189 (OUTLIER) cc_final: 0.6472 (t) REVERT: G 344 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6788 (ttp80) REVERT: G 403 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: G 465 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7423 (mm-30) REVERT: G 500 LEU cc_start: 0.9019 (mm) cc_final: 0.8790 (mt) REVERT: G 541 GLN cc_start: 0.8115 (mt0) cc_final: 0.7842 (mt0) REVERT: G 563 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8626 (ttmm) REVERT: G 595 ARG cc_start: 0.7740 (mtp180) cc_final: 0.6977 (ptt180) outliers start: 51 outliers final: 28 residues processed: 304 average time/residue: 0.8800 time to fit residues: 297.6777 Evaluate side-chains 298 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 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 A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain 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 D residue 294 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 346 TRP Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 560 GLN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 563 LYS Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 176 optimal weight: 0.0970 chunk 25 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 422 ASN B 424 GLN B 476 ASN B 499 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102455 restraints weight = 32359.561| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.82 r_work: 0.3071 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 23709 Z= 0.211 Angle : 0.580 9.517 32228 Z= 0.305 Chirality : 0.048 0.181 3696 Planarity : 0.004 0.039 4249 Dihedral : 4.811 18.675 3164 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.36 % Allowed : 21.18 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 2947 helix: 0.61 (0.26), residues: 455 sheet: 1.01 (0.16), residues: 959 loop : -0.35 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 470 TYR 0.017 0.002 TYR C 410 PHE 0.013 0.001 PHE A 493 TRP 0.015 0.002 TRP C 226 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00508 (23709) covalent geometry : angle 0.57975 (32228) hydrogen bonds : bond 0.03032 ( 805) hydrogen bonds : angle 5.99726 ( 2184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7874 (m-30) cc_final: 0.7390 (t70) REVERT: A 287 ARG cc_start: 0.6300 (mtt90) cc_final: 0.6007 (tmt170) REVERT: A 344 ARG cc_start: 0.7150 (ttp-110) cc_final: 0.6857 (ttp-170) REVERT: A 350 MET cc_start: 0.7996 (mmm) cc_final: 0.7291 (tmt) REVERT: A 388 ASN cc_start: 0.8602 (p0) cc_final: 0.8400 (p0) REVERT: A 541 GLN cc_start: 0.8065 (mt0) cc_final: 0.7851 (mt0) REVERT: A 560 GLN cc_start: 0.8335 (tp40) cc_final: 0.7938 (tp40) REVERT: A 570 ASN cc_start: 0.8297 (m-40) cc_final: 0.8024 (p0) REVERT: B 180 ASN cc_start: 0.8591 (t0) cc_final: 0.8122 (t0) REVERT: B 287 ARG cc_start: 0.6584 (mtt90) cc_final: 0.5948 (ttp-170) REVERT: B 350 MET cc_start: 0.8029 (mmm) cc_final: 0.7347 (tmt) REVERT: B 447 GLN cc_start: 0.7541 (mt0) cc_final: 0.7243 (mp10) REVERT: B 541 GLN cc_start: 0.8116 (mt0) cc_final: 0.7800 (mt0) REVERT: B 563 LYS cc_start: 0.8645 (tppp) cc_final: 0.8391 (ttmm) REVERT: B 595 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7453 (ptt180) REVERT: C 287 ARG cc_start: 0.6603 (mtt90) cc_final: 0.5886 (tmt170) REVERT: C 344 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7328 (tmt170) REVERT: C 350 MET cc_start: 0.7697 (mmm) cc_final: 0.7140 (tmt) REVERT: C 441 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7782 (pt0) REVERT: C 496 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7173 (tptm) REVERT: C 587 MET cc_start: 0.8748 (mtt) cc_final: 0.8459 (mtp) REVERT: C 595 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7322 (ptt180) REVERT: D 180 ASN cc_start: 0.8585 (t0) cc_final: 0.8138 (t0) REVERT: D 287 ARG cc_start: 0.6478 (mtt90) cc_final: 0.5990 (ttp-110) REVERT: D 294 SER cc_start: 0.7390 (OUTLIER) cc_final: 0.6841 (t) REVERT: D 465 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6934 (mm-30) REVERT: D 595 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7430 (ptt-90) REVERT: E 287 ARG cc_start: 0.6532 (mtt90) cc_final: 0.5937 (ttp-110) REVERT: E 344 ARG cc_start: 0.6771 (ttp-110) cc_final: 0.6380 (ttp80) REVERT: E 348 GLU cc_start: 0.8039 (tt0) cc_final: 0.7200 (tm-30) REVERT: E 541 GLN cc_start: 0.8184 (mt0) cc_final: 0.7912 (tt0) REVERT: E 545 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7794 (mtpm) REVERT: F 209 ASN cc_start: 0.7261 (m-40) cc_final: 0.6929 (p0) REVERT: F 271 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8090 (pp) REVERT: F 287 ARG cc_start: 0.6833 (mtt90) cc_final: 0.5857 (tmt170) REVERT: F 344 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.6495 (ttp80) REVERT: F 350 MET cc_start: 0.7958 (mmm) cc_final: 0.7465 (tmt) REVERT: F 356 ASP cc_start: 0.7866 (t0) cc_final: 0.7601 (t0) REVERT: F 560 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7708 (mm-40) REVERT: F 595 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7313 (ptt-90) REVERT: G 287 ARG cc_start: 0.6565 (mtt90) cc_final: 0.5572 (ttp-170) REVERT: G 294 SER cc_start: 0.7346 (OUTLIER) cc_final: 0.6619 (t) REVERT: G 344 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6729 (ttp80) REVERT: G 403 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: G 465 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7392 (mm-30) REVERT: G 500 LEU cc_start: 0.9074 (mm) cc_final: 0.8845 (mt) REVERT: G 541 GLN cc_start: 0.8105 (mt0) cc_final: 0.7418 (mm-40) REVERT: G 563 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8676 (ttmm) REVERT: G 595 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7186 (ptt180) outliers start: 62 outliers final: 38 residues processed: 291 average time/residue: 0.7854 time to fit residues: 255.3136 Evaluate side-chains 294 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 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 A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 293 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 294 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 560 GLN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 563 LYS Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 99 optimal weight: 40.0000 chunk 132 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 274 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** F 438 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 = 0.3674 r_free = 0.3674 target = 0.136641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102820 restraints weight = 32347.208| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.81 r_work: 0.3061 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23709 Z= 0.199 Angle : 0.576 7.527 32228 Z= 0.303 Chirality : 0.048 0.173 3696 Planarity : 0.004 0.038 4249 Dihedral : 4.838 18.406 3164 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.32 % Allowed : 20.95 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 2947 helix: 0.57 (0.26), residues: 455 sheet: 1.15 (0.16), residues: 903 loop : -0.45 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 470 TYR 0.014 0.002 TYR F 410 PHE 0.013 0.001 PHE A 493 TRP 0.015 0.002 TRP D 226 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00479 (23709) covalent geometry : angle 0.57588 (32228) hydrogen bonds : bond 0.02999 ( 805) hydrogen bonds : angle 6.04143 ( 2184) =============================================================================== Job complete usr+sys time: 10223.48 seconds wall clock time: 174 minutes 48.78 seconds (10488.78 seconds total)