Starting phenix.real_space_refine on Fri Jun 5 14:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g1k_4339/06_2026/6g1k_4339.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1k_4339/06_2026/6g1k_4339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6g1k_4339/06_2026/6g1k_4339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1k_4339/06_2026/6g1k_4339.map" model { file = "/net/cci-nas-00/data/ceres_data/6g1k_4339/06_2026/6g1k_4339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1k_4339/06_2026/6g1k_4339.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 4 5.49 5 S 108 5.16 5 C 14036 2.51 5 N 3484 2.21 5 O 3796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21428 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5298 Classifications: {'peptide': 648} Link IDs: {'PTRANS': 23, 'TRANS': 624} Chain breaks: 8 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'44E': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.46, per 1000 atoms: 0.25 Number of scatterers: 21428 At special positions: 0 Unit cell: (131.89, 131.89, 136.25, 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) S 108 16.00 P 4 15.00 O 3796 8.00 N 3484 7.00 C 14036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS D 549 " - pdb=" SG CYS D 554 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 961.5 milliseconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 73.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.584A pdb=" N LYS A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.558A pdb=" N ILE A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.605A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.637A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.575A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.776A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.656A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.902A pdb=" N ASP A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 361 through 382 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 400 through 423 Proline residue: A 408 - end of helix removed outlier: 4.273A pdb=" N GLY A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 457 removed outlier: 3.611A pdb=" N LEU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 472 through 491 removed outlier: 3.923A pdb=" N PHE A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.546A pdb=" N LEU A 495 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 539 removed outlier: 4.612A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.718A pdb=" N TYR A 604 " --> pdb=" O MET A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 630 through 645 removed outlier: 3.866A pdb=" N GLU A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 725 removed outlier: 3.858A pdb=" N ASP A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 725 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 751 removed outlier: 3.770A pdb=" N GLU A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 745 " --> pdb=" O ASP A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.584A pdb=" N LYS B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.558A pdb=" N ILE B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.605A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.637A pdb=" N ILE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.575A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.776A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.656A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 303 through 316 removed outlier: 3.902A pdb=" N ASP B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 361 through 382 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 400 through 423 Proline residue: B 408 - end of helix removed outlier: 4.273A pdb=" N GLY B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 removed outlier: 3.611A pdb=" N LEU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 472 through 491 removed outlier: 3.923A pdb=" N PHE B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.546A pdb=" N LEU B 495 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 539 removed outlier: 4.612A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.718A pdb=" N TYR B 604 " --> pdb=" O MET B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 630 through 645 removed outlier: 3.866A pdb=" N GLU B 634 " --> pdb=" O HIS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 725 removed outlier: 3.858A pdb=" N ASP B 723 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 725 " --> pdb=" O ILE B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 751 removed outlier: 3.770A pdb=" N GLU B 737 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 745 " --> pdb=" O ASP B 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.584A pdb=" N LYS C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.558A pdb=" N ILE C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.605A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.637A pdb=" N ILE C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.575A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.776A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.656A pdb=" N LEU C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.902A pdb=" N ASP C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 339 through 350 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 361 through 382 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 400 through 423 Proline residue: C 408 - end of helix removed outlier: 4.273A pdb=" N GLY C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 457 removed outlier: 3.611A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.923A pdb=" N PHE C 487 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 removed outlier: 3.546A pdb=" N LEU C 495 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 539 removed outlier: 4.612A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.718A pdb=" N TYR C 604 " --> pdb=" O MET C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 630 through 645 removed outlier: 3.866A pdb=" N GLU C 634 " --> pdb=" O HIS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 725 removed outlier: 3.858A pdb=" N ASP C 723 " --> pdb=" O ALA C 719 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 725 " --> pdb=" O ILE C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 751 removed outlier: 3.770A pdb=" N GLU C 737 " --> pdb=" O GLU C 733 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 745 " --> pdb=" O ASP C 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.584A pdb=" N LYS D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.558A pdb=" N ILE D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 116 removed outlier: 3.605A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.637A pdb=" N ILE D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.575A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.776A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.656A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.902A pdb=" N ASP D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 361 through 382 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 400 through 423 Proline residue: D 408 - end of helix removed outlier: 4.273A pdb=" N GLY D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 457 removed outlier: 3.611A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 491 removed outlier: 3.923A pdb=" N PHE D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.546A pdb=" N LEU D 495 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 539 removed outlier: 4.612A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN D 536 " --> pdb=" O ASN D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.718A pdb=" N TYR D 604 " --> pdb=" O MET D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 630 through 645 removed outlier: 3.866A pdb=" N GLU D 634 " --> pdb=" O HIS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 725 removed outlier: 3.858A pdb=" N ASP D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS D 725 " --> pdb=" O ILE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 751 removed outlier: 3.770A pdb=" N GLU D 737 " --> pdb=" O GLU D 733 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 745 " --> pdb=" O ASP D 741 " (cutoff:3.500A) 1248 hydrogen bonds defined for protein. 3708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3380 1.31 - 1.43: 5992 1.43 - 1.56: 12384 1.56 - 1.68: 8 1.68 - 1.81: 176 Bond restraints: 21940 Sorted by residual: bond pdb=" O13 44E C1002 " pdb=" P 44E C1002 " ideal model delta sigma weight residual 1.684 1.501 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" O13 44E D1002 " pdb=" P 44E D1002 " ideal model delta sigma weight residual 1.684 1.501 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" O13 44E A1002 " pdb=" P 44E A1002 " ideal model delta sigma weight residual 1.684 1.501 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" O13 44E B1002 " pdb=" P 44E B1002 " ideal model delta sigma weight residual 1.684 1.501 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" O14 44E C1002 " pdb=" P 44E C1002 " ideal model delta sigma weight residual 1.668 1.502 0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 21935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.72: 29692 10.72 - 21.44: 28 21.44 - 32.17: 0 32.17 - 42.89: 0 42.89 - 53.61: 4 Bond angle restraints: 29724 Sorted by residual: angle pdb=" O13 44E B1002 " pdb=" P 44E B1002 " pdb=" O14 44E B1002 " ideal model delta sigma weight residual 54.79 108.40 -53.61 3.00e+00 1.11e-01 3.19e+02 angle pdb=" O13 44E D1002 " pdb=" P 44E D1002 " pdb=" O14 44E D1002 " ideal model delta sigma weight residual 54.79 108.40 -53.61 3.00e+00 1.11e-01 3.19e+02 angle pdb=" O13 44E C1002 " pdb=" P 44E C1002 " pdb=" O14 44E C1002 " ideal model delta sigma weight residual 54.79 108.40 -53.61 3.00e+00 1.11e-01 3.19e+02 angle pdb=" O13 44E A1002 " pdb=" P 44E A1002 " pdb=" O14 44E A1002 " ideal model delta sigma weight residual 54.79 108.40 -53.61 3.00e+00 1.11e-01 3.19e+02 angle pdb=" O12 44E B1002 " pdb=" P 44E B1002 " pdb=" O14 44E B1002 " ideal model delta sigma weight residual 127.76 109.80 17.96 3.00e+00 1.11e-01 3.59e+01 ... (remaining 29719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.12: 12808 26.12 - 52.24: 432 52.24 - 78.36: 36 78.36 - 104.48: 4 104.48 - 130.60: 4 Dihedral angle restraints: 13284 sinusoidal: 5612 harmonic: 7672 Sorted by residual: dihedral pdb=" CB CYS A 549 " pdb=" SG CYS A 549 " pdb=" SG CYS A 554 " pdb=" CB CYS A 554 " ideal model delta sinusoidal sigma weight residual 93.00 151.52 -58.52 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 554 " pdb=" CB CYS B 554 " ideal model delta sinusoidal sigma weight residual 93.00 151.52 -58.52 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 554 " pdb=" CB CYS C 554 " ideal model delta sinusoidal sigma weight residual 93.00 151.52 -58.52 1 1.00e+01 1.00e-02 4.59e+01 ... (remaining 13281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2756 0.079 - 0.158: 540 0.158 - 0.238: 40 0.238 - 0.317: 12 0.317 - 0.396: 4 Chirality restraints: 3352 Sorted by residual: chirality pdb=" CBH Y01 A1001 " pdb=" CAT Y01 A1001 " pdb=" CAZ Y01 A1001 " pdb=" CBF Y01 A1001 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CBH Y01 C1001 " pdb=" CAT Y01 C1001 " pdb=" CAZ Y01 C1001 " pdb=" CBF Y01 C1001 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CBH Y01 B1001 " pdb=" CAT Y01 B1001 " pdb=" CAZ Y01 B1001 " pdb=" CBF Y01 B1001 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 3349 not shown) Planarity restraints: 3664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 168 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 169 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 168 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 169 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 168 " -0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO C 169 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 169 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 169 " -0.035 5.00e-02 4.00e+02 ... (remaining 3661 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5616 2.80 - 3.32: 20568 3.32 - 3.85: 35640 3.85 - 4.37: 40238 4.37 - 4.90: 68610 Nonbonded interactions: 170672 Sorted by model distance: nonbonded pdb=" OH TYR C 373 " pdb=" O SER C 488 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O SER A 488 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR B 373 " pdb=" O SER B 488 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR D 373 " pdb=" O SER D 488 " model vdw 2.272 3.040 nonbonded pdb=" O11 44E A1002 " pdb=" O21 44E A1002 " model vdw 2.300 2.432 ... (remaining 170667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.240 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.010 0.183 21944 Z= 0.430 Angle : 1.324 53.611 29732 Z= 0.626 Chirality : 0.063 0.396 3352 Planarity : 0.008 0.064 3664 Dihedral : 12.492 130.600 8264 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.13), residues: 2520 helix: -2.31 (0.09), residues: 1852 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 465 TYR 0.029 0.003 TYR A 541 PHE 0.030 0.004 PHE B 539 TRP 0.021 0.003 TRP A 434 HIS 0.006 0.002 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00952 / 0.43 (21940) covalent geometry : angle 1.32300 / 0.63 (29724) SS BOND : bond 0.00026 / 0.01 ( 4) SS BOND : angle 2.88757 / 1.54 ( 8) hydrogen bonds : bond 0.12616 / 8.15 ( 1248) hydrogen bonds : angle 6.10484 / 4.27 ( 3708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 628 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8763 (tp30) cc_final: 0.8547 (tp30) REVERT: A 92 PHE cc_start: 0.8278 (m-10) cc_final: 0.8063 (m-80) REVERT: A 234 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 238 LYS cc_start: 0.8660 (ptmm) cc_final: 0.8213 (ptmm) REVERT: A 429 TYR cc_start: 0.6517 (t80) cc_final: 0.6005 (t80) REVERT: A 516 ILE cc_start: 0.9434 (mt) cc_final: 0.9178 (mt) REVERT: A 520 LEU cc_start: 0.9070 (mp) cc_final: 0.8791 (mp) REVERT: A 636 LYS cc_start: 0.9021 (mttt) cc_final: 0.8736 (mttp) REVERT: A 737 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8559 (mt-10) REVERT: B 79 GLU cc_start: 0.8762 (tp30) cc_final: 0.8547 (tp30) REVERT: B 92 PHE cc_start: 0.8278 (m-10) cc_final: 0.8063 (m-80) REVERT: B 234 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 238 LYS cc_start: 0.8665 (ptmm) cc_final: 0.8214 (ptmm) REVERT: B 429 TYR cc_start: 0.6510 (t80) cc_final: 0.6004 (t80) REVERT: B 516 ILE cc_start: 0.9431 (mt) cc_final: 0.9185 (mt) REVERT: B 520 LEU cc_start: 0.9070 (mp) cc_final: 0.8796 (mp) REVERT: B 636 LYS cc_start: 0.9018 (mttt) cc_final: 0.8737 (mttp) REVERT: B 737 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8566 (mt-10) REVERT: C 79 GLU cc_start: 0.8766 (tp30) cc_final: 0.8553 (tp30) REVERT: C 92 PHE cc_start: 0.8285 (m-10) cc_final: 0.8065 (m-80) REVERT: C 234 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7744 (tm-30) REVERT: C 238 LYS cc_start: 0.8657 (ptmm) cc_final: 0.8212 (ptmm) REVERT: C 429 TYR cc_start: 0.6519 (t80) cc_final: 0.6007 (t80) REVERT: C 516 ILE cc_start: 0.9432 (mt) cc_final: 0.9183 (mt) REVERT: C 520 LEU cc_start: 0.9072 (mp) cc_final: 0.8800 (mp) REVERT: C 636 LYS cc_start: 0.9019 (mttt) cc_final: 0.8735 (mttp) REVERT: C 737 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8564 (mt-10) REVERT: D 79 GLU cc_start: 0.8764 (tp30) cc_final: 0.8547 (tp30) REVERT: D 92 PHE cc_start: 0.8268 (m-10) cc_final: 0.8056 (m-80) REVERT: D 234 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7743 (tm-30) REVERT: D 238 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8213 (ptmm) REVERT: D 429 TYR cc_start: 0.6518 (t80) cc_final: 0.6009 (t80) REVERT: D 516 ILE cc_start: 0.9433 (mt) cc_final: 0.9189 (mt) REVERT: D 520 LEU cc_start: 0.9070 (mp) cc_final: 0.8796 (mp) REVERT: D 636 LYS cc_start: 0.9018 (mttt) cc_final: 0.8735 (mttp) REVERT: D 737 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8563 (mt-10) outliers start: 4 outliers final: 4 residues processed: 632 average time/residue: 0.1734 time to fit residues: 162.9594 Evaluate side-chains 410 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 406 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 118 HIS A 153 ASN A 431 HIS A 506 GLN A 740 GLN B 80 ASN B 118 HIS B 153 ASN B 431 HIS B 506 GLN B 740 GLN C 80 ASN C 118 HIS C 153 ASN C 431 HIS C 506 GLN C 740 GLN D 80 ASN D 118 HIS D 153 ASN D 431 HIS D 506 GLN D 740 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.090068 restraints weight = 49344.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092777 restraints weight = 24030.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094441 restraints weight = 15572.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095522 restraints weight = 12158.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096195 restraints weight = 10489.044| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21944 Z= 0.130 Angle : 0.647 8.295 29732 Z= 0.324 Chirality : 0.042 0.164 3352 Planarity : 0.005 0.047 3664 Dihedral : 9.109 121.838 3164 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.41 % Allowed : 11.42 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2520 helix: -0.42 (0.11), residues: 1872 sheet: None (None), residues: 0 loop : -2.69 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 556 TYR 0.019 0.001 TYR A 582 PHE 0.023 0.001 PHE A 340 TRP 0.010 0.001 TRP A 434 HIS 0.002 0.000 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21940) covalent geometry : angle 0.64637 / 0.32 (29724) SS BOND : bond 0.00339 / 0.16 ( 4) SS BOND : angle 1.13836 / 0.51 ( 8) hydrogen bonds : bond 0.04045 / 2.65 ( 1248) hydrogen bonds : angle 4.17923 / 2.94 ( 3708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 520 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 92 PHE cc_start: 0.8274 (m-10) cc_final: 0.7896 (m-80) REVERT: A 234 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 238 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8399 (ptmm) REVERT: A 506 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: A 513 LEU cc_start: 0.9244 (mt) cc_final: 0.8937 (mp) REVERT: A 622 ASN cc_start: 0.7697 (p0) cc_final: 0.7474 (p0) REVERT: A 636 LYS cc_start: 0.9043 (mttt) cc_final: 0.8746 (mttp) REVERT: A 752 MET cc_start: 0.8613 (mmp) cc_final: 0.8319 (mmm) REVERT: B 92 PHE cc_start: 0.8280 (m-10) cc_final: 0.7900 (m-80) REVERT: B 234 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 238 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8397 (ptmm) REVERT: B 506 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: B 513 LEU cc_start: 0.9243 (mt) cc_final: 0.8930 (mp) REVERT: B 622 ASN cc_start: 0.7702 (p0) cc_final: 0.7483 (p0) REVERT: B 636 LYS cc_start: 0.9042 (mttt) cc_final: 0.8747 (mttp) REVERT: B 747 TYR cc_start: 0.8347 (m-80) cc_final: 0.8146 (m-10) REVERT: B 752 MET cc_start: 0.8541 (mmp) cc_final: 0.8292 (mmm) REVERT: C 81 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7551 (mm-30) REVERT: C 92 PHE cc_start: 0.8275 (m-10) cc_final: 0.7897 (m-80) REVERT: C 234 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7227 (tm-30) REVERT: C 238 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8397 (ptmm) REVERT: C 506 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: C 513 LEU cc_start: 0.9243 (mt) cc_final: 0.8937 (mp) REVERT: C 636 LYS cc_start: 0.9040 (mttt) cc_final: 0.8743 (mttp) REVERT: C 752 MET cc_start: 0.8614 (mmp) cc_final: 0.8319 (mmm) REVERT: D 81 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7550 (mm-30) REVERT: D 92 PHE cc_start: 0.8281 (m-10) cc_final: 0.7902 (m-80) REVERT: D 234 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7228 (tm-30) REVERT: D 238 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8397 (ptmm) REVERT: D 506 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: D 513 LEU cc_start: 0.9245 (mt) cc_final: 0.8936 (mp) REVERT: D 622 ASN cc_start: 0.7718 (p0) cc_final: 0.7499 (p0) REVERT: D 636 LYS cc_start: 0.9040 (mttt) cc_final: 0.8742 (mttp) REVERT: D 752 MET cc_start: 0.8544 (mmp) cc_final: 0.8293 (mmm) outliers start: 79 outliers final: 28 residues processed: 563 average time/residue: 0.1390 time to fit residues: 125.4248 Evaluate side-chains 454 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 422 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 185 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 605 ASN B 506 GLN B 605 ASN C 506 GLN C 605 ASN D 506 GLN D 605 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086067 restraints weight = 49684.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088572 restraints weight = 24641.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090190 restraints weight = 16113.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.091219 restraints weight = 12572.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091861 restraints weight = 10861.518| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21944 Z= 0.222 Angle : 0.700 9.417 29732 Z= 0.349 Chirality : 0.045 0.158 3352 Planarity : 0.004 0.044 3664 Dihedral : 8.772 123.084 3160 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.02 % Allowed : 14.27 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2520 helix: 0.34 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -2.33 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 194 TYR 0.017 0.002 TYR A 582 PHE 0.022 0.002 PHE A 136 TRP 0.012 0.001 TRP D 314 HIS 0.005 0.001 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (21940) covalent geometry : angle 0.69916 / 0.35 (29724) SS BOND : bond 0.00608 / 0.29 ( 4) SS BOND : angle 1.82362 / 0.89 ( 8) hydrogen bonds : bond 0.04074 / 2.68 ( 1248) hydrogen bonds : angle 4.15759 / 2.92 ( 3708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 436 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 92 PHE cc_start: 0.8303 (m-10) cc_final: 0.7849 (m-80) REVERT: A 513 LEU cc_start: 0.9332 (mt) cc_final: 0.9110 (mp) REVERT: A 532 ASN cc_start: 0.8899 (t0) cc_final: 0.8605 (t0) REVERT: A 622 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7608 (p0) REVERT: A 636 LYS cc_start: 0.9059 (mttt) cc_final: 0.8814 (mttp) REVERT: B 92 PHE cc_start: 0.8309 (m-10) cc_final: 0.7852 (m-80) REVERT: B 513 LEU cc_start: 0.9329 (mt) cc_final: 0.9105 (mp) REVERT: B 532 ASN cc_start: 0.8897 (t0) cc_final: 0.8605 (t0) REVERT: B 622 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7488 (p0) REVERT: B 636 LYS cc_start: 0.9057 (mttt) cc_final: 0.8811 (mttp) REVERT: B 737 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8200 (mt-10) REVERT: C 81 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 92 PHE cc_start: 0.8304 (m-10) cc_final: 0.7847 (m-80) REVERT: C 513 LEU cc_start: 0.9331 (mt) cc_final: 0.9098 (mp) REVERT: C 532 ASN cc_start: 0.8894 (t0) cc_final: 0.8600 (t0) REVERT: C 636 LYS cc_start: 0.9058 (mttt) cc_final: 0.8811 (mttp) REVERT: C 737 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8401 (mt-10) REVERT: D 41 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8619 (tt0) REVERT: D 81 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7583 (mm-30) REVERT: D 92 PHE cc_start: 0.8304 (m-10) cc_final: 0.7847 (m-80) REVERT: D 513 LEU cc_start: 0.9334 (mt) cc_final: 0.9108 (mp) REVERT: D 532 ASN cc_start: 0.8896 (t0) cc_final: 0.8610 (t0) REVERT: D 622 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7561 (p0) REVERT: D 636 LYS cc_start: 0.9055 (mttt) cc_final: 0.8807 (mttp) REVERT: D 737 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8394 (mt-10) outliers start: 70 outliers final: 37 residues processed: 475 average time/residue: 0.1284 time to fit residues: 101.6461 Evaluate side-chains 439 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 399 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 741 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 245 optimal weight: 0.8980 chunk 202 optimal weight: 0.0060 chunk 174 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN D 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088471 restraints weight = 49449.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.091075 restraints weight = 24768.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092777 restraints weight = 16389.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093840 restraints weight = 12852.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094390 restraints weight = 11126.691| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21944 Z= 0.123 Angle : 0.608 7.837 29732 Z= 0.301 Chirality : 0.042 0.153 3352 Planarity : 0.004 0.043 3664 Dihedral : 8.506 125.416 3160 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.53 % Allowed : 17.16 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2520 helix: 0.77 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -2.27 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 556 TYR 0.024 0.001 TYR C 429 PHE 0.023 0.001 PHE D 136 TRP 0.012 0.001 TRP D 314 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21940) covalent geometry : angle 0.60788 / 0.30 (29724) SS BOND : bond 0.00389 / 0.18 ( 4) SS BOND : angle 1.27042 / 0.61 ( 8) hydrogen bonds : bond 0.03545 / 2.34 ( 1248) hydrogen bonds : angle 3.83564 / 2.70 ( 3708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 456 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 92 PHE cc_start: 0.8245 (m-10) cc_final: 0.7806 (m-80) REVERT: A 267 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 409 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.7842 (m-90) REVERT: A 513 LEU cc_start: 0.9318 (mt) cc_final: 0.9065 (mp) REVERT: A 622 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7450 (p0) REVERT: B 92 PHE cc_start: 0.8239 (m-10) cc_final: 0.7802 (m-80) REVERT: B 267 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8270 (mt) REVERT: B 409 TRP cc_start: 0.8943 (OUTLIER) cc_final: 0.7791 (m-90) REVERT: B 513 LEU cc_start: 0.9314 (mt) cc_final: 0.9057 (mp) REVERT: B 622 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7630 (p0) REVERT: B 737 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8270 (mt-10) REVERT: B 752 MET cc_start: 0.8306 (mmm) cc_final: 0.8080 (mmm) REVERT: C 81 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 92 PHE cc_start: 0.8245 (m-10) cc_final: 0.7803 (m-80) REVERT: C 267 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8276 (mt) REVERT: C 409 TRP cc_start: 0.8943 (OUTLIER) cc_final: 0.7790 (m-90) REVERT: C 513 LEU cc_start: 0.9292 (mt) cc_final: 0.9055 (mp) REVERT: C 622 ASN cc_start: 0.7867 (p0) cc_final: 0.7607 (p0) REVERT: C 737 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8385 (mt-10) REVERT: D 81 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7483 (mm-30) REVERT: D 92 PHE cc_start: 0.8272 (m-10) cc_final: 0.7833 (m-80) REVERT: D 267 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8274 (mt) REVERT: D 409 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.7819 (m-90) REVERT: D 513 LEU cc_start: 0.9313 (mt) cc_final: 0.9059 (mp) REVERT: D 622 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7614 (p0) REVERT: D 737 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8379 (mt-10) REVERT: D 752 MET cc_start: 0.8296 (mmm) cc_final: 0.8065 (mmm) outliers start: 82 outliers final: 47 residues processed: 489 average time/residue: 0.1284 time to fit residues: 104.7661 Evaluate side-chains 453 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 395 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 622 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 391 ASN A 442 ASN A 506 GLN B 391 ASN B 442 ASN B 506 GLN C 80 ASN C 391 ASN C 442 ASN C 506 GLN D 80 ASN D 391 ASN D 442 ASN D 506 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081882 restraints weight = 50692.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084303 restraints weight = 25467.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085907 restraints weight = 16810.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086910 restraints weight = 13098.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087428 restraints weight = 11315.463| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 21944 Z= 0.366 Angle : 0.825 11.232 29732 Z= 0.412 Chirality : 0.050 0.166 3352 Planarity : 0.005 0.044 3664 Dihedral : 8.596 125.433 3160 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.84 % Allowed : 17.03 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2520 helix: 0.52 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -2.33 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 491 TYR 0.019 0.002 TYR A 459 PHE 0.025 0.002 PHE D 136 TRP 0.019 0.002 TRP B 404 HIS 0.004 0.001 HIS D 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.37 (21940) covalent geometry : angle 0.82425 / 0.41 (29724) SS BOND : bond 0.00795 / 0.38 ( 4) SS BOND : angle 2.03917 / 1.03 ( 8) hydrogen bonds : bond 0.04620 / 3.03 ( 1248) hydrogen bonds : angle 4.41609 / 3.08 ( 3708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 395 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 92 PHE cc_start: 0.8305 (m-10) cc_final: 0.7894 (m-80) REVERT: A 229 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: A 267 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 354 ARG cc_start: 0.7379 (ptm-80) cc_final: 0.7143 (ptm-80) REVERT: A 409 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.8095 (m-90) REVERT: A 429 TYR cc_start: 0.6830 (t80) cc_final: 0.6409 (t80) REVERT: A 506 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: A 622 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7721 (p0) REVERT: B 79 GLU cc_start: 0.8767 (tp30) cc_final: 0.8463 (tp30) REVERT: B 92 PHE cc_start: 0.8310 (m-10) cc_final: 0.7897 (m-80) REVERT: B 229 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8004 (pp20) REVERT: B 267 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8743 (mt) REVERT: B 354 ARG cc_start: 0.7378 (ptm-80) cc_final: 0.7141 (ptm-80) REVERT: B 409 TRP cc_start: 0.9034 (OUTLIER) cc_final: 0.8103 (m-90) REVERT: B 506 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: B 622 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7687 (p0) REVERT: C 81 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 92 PHE cc_start: 0.8307 (m-10) cc_final: 0.7893 (m-80) REVERT: C 229 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: C 267 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8745 (mt) REVERT: C 354 ARG cc_start: 0.7381 (ptm-80) cc_final: 0.7146 (ptm-80) REVERT: C 409 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.8102 (m-90) REVERT: C 506 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: C 622 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7729 (p0) REVERT: C 737 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8552 (mt-10) REVERT: D 81 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 92 PHE cc_start: 0.8308 (m-10) cc_final: 0.7894 (m-80) REVERT: D 229 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8004 (pp20) REVERT: D 267 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8744 (mt) REVERT: D 354 ARG cc_start: 0.7377 (ptm-80) cc_final: 0.7143 (ptm-80) REVERT: D 409 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.8107 (m-90) REVERT: D 429 TYR cc_start: 0.6826 (t80) cc_final: 0.6406 (t80) REVERT: D 506 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: D 622 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7733 (p0) REVERT: D 737 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8551 (mt-10) outliers start: 89 outliers final: 52 residues processed: 443 average time/residue: 0.1300 time to fit residues: 95.3557 Evaluate side-chains 440 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 368 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 600 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 741 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.0010 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 506 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 506 GLN ** D 621 ASN ** 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 = 0.3554 r_free = 0.3554 target = 0.113203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.088061 restraints weight = 49393.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090627 restraints weight = 24569.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092343 restraints weight = 16069.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093451 restraints weight = 12449.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094021 restraints weight = 10663.866| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21944 Z= 0.125 Angle : 0.644 9.321 29732 Z= 0.313 Chirality : 0.043 0.155 3352 Planarity : 0.004 0.044 3664 Dihedral : 8.310 128.652 3160 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.28 % Allowed : 19.35 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2520 helix: 0.96 (0.12), residues: 1880 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 556 TYR 0.015 0.001 TYR B 582 PHE 0.026 0.001 PHE C 519 TRP 0.014 0.001 TRP D 314 HIS 0.003 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21940) covalent geometry : angle 0.64400 / 0.31 (29724) SS BOND : bond 0.00338 / 0.16 ( 4) SS BOND : angle 1.22763 / 0.62 ( 8) hydrogen bonds : bond 0.03732 / 2.46 ( 1248) hydrogen bonds : angle 3.98380 / 2.81 ( 3708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 442 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8654 (tt0) REVERT: A 81 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 92 PHE cc_start: 0.8248 (m-10) cc_final: 0.7792 (m-80) REVERT: A 267 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 409 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.7750 (m-90) REVERT: A 535 ASN cc_start: 0.8827 (t0) cc_final: 0.8485 (t0) REVERT: A 622 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7586 (p0) REVERT: B 41 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8653 (tt0) REVERT: B 92 PHE cc_start: 0.8251 (m-10) cc_final: 0.7779 (m-80) REVERT: B 267 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8746 (mt) REVERT: B 409 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.7757 (m-90) REVERT: B 429 TYR cc_start: 0.6154 (t80) cc_final: 0.5380 (t80) REVERT: B 535 ASN cc_start: 0.8854 (t0) cc_final: 0.8505 (t0) REVERT: B 600 MET cc_start: 0.8993 (ptm) cc_final: 0.8722 (ttp) REVERT: B 622 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7608 (p0) REVERT: C 41 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8655 (tt0) REVERT: C 81 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 92 PHE cc_start: 0.8249 (m-10) cc_final: 0.7773 (m-80) REVERT: C 267 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8748 (mt) REVERT: C 409 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.7752 (m-90) REVERT: C 429 TYR cc_start: 0.6156 (t80) cc_final: 0.5381 (t80) REVERT: C 535 ASN cc_start: 0.8835 (t0) cc_final: 0.8503 (t0) REVERT: C 622 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7670 (p0) REVERT: C 737 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8504 (mt-10) REVERT: D 41 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8544 (tt0) REVERT: D 81 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7468 (mm-30) REVERT: D 92 PHE cc_start: 0.8248 (m-10) cc_final: 0.7774 (m-80) REVERT: D 267 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8748 (mt) REVERT: D 409 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.7757 (m-90) REVERT: D 535 ASN cc_start: 0.8852 (t0) cc_final: 0.8495 (t0) REVERT: D 600 MET cc_start: 0.8999 (ptm) cc_final: 0.8714 (ttp) REVERT: D 737 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8535 (mt-10) outliers start: 76 outliers final: 52 residues processed: 471 average time/residue: 0.1313 time to fit residues: 102.6497 Evaluate side-chains 473 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 410 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 622 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 181 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 506 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 506 GLN D 391 ASN D 506 GLN ** D 621 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 = 0.3559 r_free = 0.3559 target = 0.113528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088415 restraints weight = 49223.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090984 restraints weight = 24455.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092669 restraints weight = 16045.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093748 restraints weight = 12463.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094412 restraints weight = 10739.386| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21944 Z= 0.127 Angle : 0.670 11.530 29732 Z= 0.321 Chirality : 0.043 0.206 3352 Planarity : 0.004 0.042 3664 Dihedral : 8.133 128.002 3160 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.84 % Allowed : 19.83 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2520 helix: 1.03 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -2.19 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 700 TYR 0.019 0.001 TYR A 429 PHE 0.026 0.001 PHE A 136 TRP 0.013 0.001 TRP D 314 HIS 0.002 0.000 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21940) covalent geometry : angle 0.66963 / 0.32 (29724) SS BOND : bond 0.00390 / 0.18 ( 4) SS BOND : angle 1.15231 / 0.57 ( 8) hydrogen bonds : bond 0.03585 / 2.35 ( 1248) hydrogen bonds : angle 3.99965 / 2.83 ( 3708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 405 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 92 PHE cc_start: 0.8233 (m-10) cc_final: 0.7787 (m-80) REVERT: A 106 LYS cc_start: 0.8977 (tppt) cc_final: 0.8348 (tptp) REVERT: A 267 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8766 (mt) REVERT: A 409 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.7659 (m-90) REVERT: A 514 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8523 (mt) REVERT: A 622 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7595 (p0) REVERT: B 41 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8633 (tt0) REVERT: B 92 PHE cc_start: 0.8237 (m-10) cc_final: 0.7791 (m-80) REVERT: B 106 LYS cc_start: 0.9006 (tppt) cc_final: 0.8408 (tptp) REVERT: B 267 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8763 (mt) REVERT: B 409 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.7792 (m-90) REVERT: B 514 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8519 (mt) REVERT: B 535 ASN cc_start: 0.8867 (t0) cc_final: 0.8497 (t0) REVERT: B 622 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7695 (p0) REVERT: B 752 MET cc_start: 0.8156 (mmm) cc_final: 0.7918 (mmm) REVERT: C 41 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8648 (tt0) REVERT: C 81 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7139 (mm-30) REVERT: C 92 PHE cc_start: 0.8231 (m-10) cc_final: 0.7784 (m-80) REVERT: C 106 LYS cc_start: 0.8981 (tppt) cc_final: 0.8350 (tptp) REVERT: C 267 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8766 (mt) REVERT: C 409 TRP cc_start: 0.8883 (OUTLIER) cc_final: 0.7786 (m-90) REVERT: C 514 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 535 ASN cc_start: 0.8844 (t0) cc_final: 0.8494 (t0) REVERT: C 737 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8527 (mt-10) REVERT: D 81 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 92 PHE cc_start: 0.8239 (m-10) cc_final: 0.7795 (m-80) REVERT: D 106 LYS cc_start: 0.8983 (tppt) cc_final: 0.8351 (tptp) REVERT: D 267 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8765 (mt) REVERT: D 409 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.7665 (m-90) REVERT: D 506 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: D 514 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8514 (mt) REVERT: D 535 ASN cc_start: 0.8858 (t0) cc_final: 0.8488 (t0) REVERT: D 600 MET cc_start: 0.8948 (ptm) cc_final: 0.8624 (ttp) REVERT: D 737 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8517 (mt-10) REVERT: D 752 MET cc_start: 0.8136 (mmm) cc_final: 0.7907 (mmm) outliers start: 89 outliers final: 54 residues processed: 448 average time/residue: 0.1215 time to fit residues: 92.0087 Evaluate side-chains 452 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 640 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 0.0980 chunk 139 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087566 restraints weight = 49601.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090176 restraints weight = 24565.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091890 restraints weight = 16003.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092927 restraints weight = 12397.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093595 restraints weight = 10682.211| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21944 Z= 0.135 Angle : 0.667 12.073 29732 Z= 0.320 Chirality : 0.043 0.177 3352 Planarity : 0.004 0.042 3664 Dihedral : 8.053 128.104 3160 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.97 % Allowed : 20.00 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2520 helix: 1.11 (0.12), residues: 1880 sheet: None (None), residues: 0 loop : -2.14 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.028 0.001 TYR C 429 PHE 0.025 0.002 PHE B 335 TRP 0.013 0.001 TRP C 314 HIS 0.002 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (21940) covalent geometry : angle 0.66643 / 0.32 (29724) SS BOND : bond 0.00350 / 0.17 ( 4) SS BOND : angle 1.11742 / 0.55 ( 8) hydrogen bonds : bond 0.03531 / 2.32 ( 1248) hydrogen bonds : angle 3.92688 / 2.78 ( 3708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 398 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8539 (tt0) REVERT: A 92 PHE cc_start: 0.8234 (m-10) cc_final: 0.7811 (m-80) REVERT: A 106 LYS cc_start: 0.8969 (tppt) cc_final: 0.8314 (tptp) REVERT: A 267 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8782 (mt) REVERT: A 409 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.7730 (m-90) REVERT: A 514 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 622 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7619 (p0) REVERT: B 92 PHE cc_start: 0.8232 (m-10) cc_final: 0.7806 (m-80) REVERT: B 106 LYS cc_start: 0.8951 (tppt) cc_final: 0.8362 (tptp) REVERT: B 267 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 409 TRP cc_start: 0.8903 (OUTLIER) cc_final: 0.7765 (m-90) REVERT: B 470 MET cc_start: 0.7673 (mmm) cc_final: 0.7004 (mmm) REVERT: B 514 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 535 ASN cc_start: 0.8870 (t0) cc_final: 0.8533 (t0) REVERT: B 622 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7713 (p0) REVERT: B 752 MET cc_start: 0.8183 (mmm) cc_final: 0.7935 (mmm) REVERT: C 92 PHE cc_start: 0.8248 (m-10) cc_final: 0.7822 (m-80) REVERT: C 106 LYS cc_start: 0.8977 (tppt) cc_final: 0.8320 (tptp) REVERT: C 267 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8779 (mt) REVERT: C 409 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.7768 (m-90) REVERT: C 514 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8480 (mt) REVERT: C 535 ASN cc_start: 0.8869 (t0) cc_final: 0.8506 (t0) REVERT: D 41 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8512 (tt0) REVERT: D 42 LYS cc_start: 0.8484 (tttp) cc_final: 0.8004 (ttmm) REVERT: D 92 PHE cc_start: 0.8237 (m-10) cc_final: 0.7814 (m-80) REVERT: D 106 LYS cc_start: 0.8981 (tppt) cc_final: 0.8325 (tptp) REVERT: D 267 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 409 TRP cc_start: 0.8880 (OUTLIER) cc_final: 0.7735 (m-90) REVERT: D 470 MET cc_start: 0.7677 (mmm) cc_final: 0.7014 (mmm) REVERT: D 506 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: D 514 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8489 (mt) REVERT: D 535 ASN cc_start: 0.8859 (t0) cc_final: 0.8479 (t0) REVERT: D 600 MET cc_start: 0.8951 (ptm) cc_final: 0.8602 (ttp) REVERT: D 752 MET cc_start: 0.8239 (mmm) cc_final: 0.7999 (mmm) outliers start: 92 outliers final: 66 residues processed: 438 average time/residue: 0.1229 time to fit residues: 90.4026 Evaluate side-chains 475 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 394 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 600 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 426 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 640 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 147 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 506 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 154 ASN C 391 ASN C 506 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN D 506 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086350 restraints weight = 49788.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088943 restraints weight = 24785.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090612 restraints weight = 16158.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091642 restraints weight = 12531.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092086 restraints weight = 10778.797| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21944 Z= 0.171 Angle : 0.704 12.102 29732 Z= 0.339 Chirality : 0.044 0.201 3352 Planarity : 0.004 0.041 3664 Dihedral : 8.098 129.192 3160 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.53 % Allowed : 19.35 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2520 helix: 1.12 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -2.13 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.027 0.001 TYR A 429 PHE 0.024 0.002 PHE C 335 TRP 0.013 0.001 TRP A 314 HIS 0.002 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (21940) covalent geometry : angle 0.70408 / 0.34 (29724) SS BOND : bond 0.00411 / 0.19 ( 4) SS BOND : angle 1.28430 / 0.63 ( 8) hydrogen bonds : bond 0.03679 / 2.41 ( 1248) hydrogen bonds : angle 3.98187 / 2.82 ( 3708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 414 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8562 (tt0) REVERT: A 42 LYS cc_start: 0.8531 (tttp) cc_final: 0.8178 (ttmt) REVERT: A 92 PHE cc_start: 0.8243 (m-10) cc_final: 0.7834 (m-80) REVERT: A 106 LYS cc_start: 0.8981 (tppt) cc_final: 0.8315 (tptp) REVERT: A 267 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8809 (mt) REVERT: A 409 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.7942 (m-90) REVERT: A 514 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8519 (mt) REVERT: A 535 ASN cc_start: 0.8925 (t0) cc_final: 0.8654 (t0) REVERT: A 622 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 41 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8573 (tt0) REVERT: B 42 LYS cc_start: 0.8501 (tttp) cc_final: 0.8114 (ttmt) REVERT: B 92 PHE cc_start: 0.8161 (m-10) cc_final: 0.7781 (m-80) REVERT: B 106 LYS cc_start: 0.8967 (tppt) cc_final: 0.8356 (tptp) REVERT: B 267 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8808 (mt) REVERT: B 409 TRP cc_start: 0.8903 (OUTLIER) cc_final: 0.7898 (m-90) REVERT: B 470 MET cc_start: 0.7607 (mmm) cc_final: 0.6944 (mmm) REVERT: B 514 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 535 ASN cc_start: 0.8869 (t0) cc_final: 0.8554 (t0) REVERT: B 622 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7697 (p0) REVERT: B 752 MET cc_start: 0.8221 (mmm) cc_final: 0.7974 (mmm) REVERT: C 41 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8573 (tt0) REVERT: C 42 LYS cc_start: 0.8501 (tttp) cc_final: 0.8105 (ttmt) REVERT: C 92 PHE cc_start: 0.8242 (m-10) cc_final: 0.7830 (m-80) REVERT: C 106 LYS cc_start: 0.8977 (tppt) cc_final: 0.8320 (tptp) REVERT: C 267 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8811 (mt) REVERT: C 409 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.7866 (m-90) REVERT: C 470 MET cc_start: 0.7584 (mmm) cc_final: 0.6916 (mmm) REVERT: C 514 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 535 ASN cc_start: 0.8861 (t0) cc_final: 0.8494 (t0) REVERT: D 92 PHE cc_start: 0.8235 (m-10) cc_final: 0.7826 (m-80) REVERT: D 106 LYS cc_start: 0.8983 (tppt) cc_final: 0.8325 (tptp) REVERT: D 267 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8810 (mt) REVERT: D 409 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.7944 (m-90) REVERT: D 470 MET cc_start: 0.7595 (mmm) cc_final: 0.6925 (mmm) REVERT: D 506 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: D 514 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8520 (mt) REVERT: D 535 ASN cc_start: 0.8861 (t0) cc_final: 0.8491 (t0) REVERT: D 622 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7745 (p0) REVERT: D 752 MET cc_start: 0.8266 (mmm) cc_final: 0.8013 (mmm) outliers start: 105 outliers final: 76 residues processed: 454 average time/residue: 0.1237 time to fit residues: 94.4232 Evaluate side-chains 489 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 397 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 426 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 640 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 145 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 251 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 391 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 506 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 391 ASN D 501 HIS D 506 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086931 restraints weight = 49790.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089507 restraints weight = 24695.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091208 restraints weight = 16106.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092221 restraints weight = 12463.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092702 restraints weight = 10737.221| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21944 Z= 0.155 Angle : 0.702 12.509 29732 Z= 0.338 Chirality : 0.045 0.200 3352 Planarity : 0.004 0.042 3664 Dihedral : 8.096 129.012 3160 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.84 % Allowed : 20.26 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2520 helix: 1.09 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -2.06 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 288 TYR 0.027 0.001 TYR A 429 PHE 0.024 0.002 PHE A 335 TRP 0.013 0.001 TRP C 314 HIS 0.002 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (21940) covalent geometry : angle 0.70216 / 0.34 (29724) SS BOND : bond 0.00386 / 0.18 ( 4) SS BOND : angle 1.23761 / 0.61 ( 8) hydrogen bonds : bond 0.03657 / 2.39 ( 1248) hydrogen bonds : angle 4.01465 / 2.84 ( 3708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 406 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8557 (tt0) REVERT: A 42 LYS cc_start: 0.8533 (tttp) cc_final: 0.8170 (ttmt) REVERT: A 92 PHE cc_start: 0.8160 (m-10) cc_final: 0.7795 (m-80) REVERT: A 106 LYS cc_start: 0.8977 (tppt) cc_final: 0.8306 (tptp) REVERT: A 267 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8812 (mt) REVERT: A 514 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 535 ASN cc_start: 0.8949 (t0) cc_final: 0.8662 (t0) REVERT: A 622 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7691 (p0) REVERT: B 41 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8561 (tt0) REVERT: B 42 LYS cc_start: 0.8526 (tttp) cc_final: 0.8170 (ttmt) REVERT: B 92 PHE cc_start: 0.8152 (m-10) cc_final: 0.7768 (m-80) REVERT: B 106 LYS cc_start: 0.8956 (tppt) cc_final: 0.8363 (tptp) REVERT: B 267 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 430 ILE cc_start: 0.7813 (mp) cc_final: 0.7258 (mt) REVERT: B 470 MET cc_start: 0.7703 (mmm) cc_final: 0.7090 (mmm) REVERT: B 514 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8510 (mt) REVERT: B 535 ASN cc_start: 0.8873 (t0) cc_final: 0.8549 (t0) REVERT: B 622 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7747 (p0) REVERT: B 752 MET cc_start: 0.8257 (mmm) cc_final: 0.7997 (mmm) REVERT: C 41 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8559 (tt0) REVERT: C 42 LYS cc_start: 0.8550 (tttp) cc_final: 0.8228 (ttmt) REVERT: C 92 PHE cc_start: 0.8154 (m-10) cc_final: 0.7768 (m-80) REVERT: C 106 LYS cc_start: 0.8973 (tppt) cc_final: 0.8319 (tptp) REVERT: C 267 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8786 (mt) REVERT: C 430 ILE cc_start: 0.7804 (mp) cc_final: 0.7284 (mt) REVERT: C 470 MET cc_start: 0.7499 (mmm) cc_final: 0.7094 (mmm) REVERT: C 514 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8543 (mt) REVERT: C 535 ASN cc_start: 0.8865 (t0) cc_final: 0.8498 (t0) REVERT: D 41 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8568 (tt0) REVERT: D 42 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8560 (ttmt) REVERT: D 92 PHE cc_start: 0.8148 (m-10) cc_final: 0.7781 (m-80) REVERT: D 106 LYS cc_start: 0.8981 (tppt) cc_final: 0.8336 (tptp) REVERT: D 267 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8786 (mt) REVERT: D 470 MET cc_start: 0.7594 (mmm) cc_final: 0.7151 (mmm) REVERT: D 514 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8515 (mt) REVERT: D 535 ASN cc_start: 0.8862 (t0) cc_final: 0.8485 (t0) REVERT: D 622 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (p0) REVERT: D 752 MET cc_start: 0.8284 (mmm) cc_final: 0.8026 (mmm) outliers start: 89 outliers final: 70 residues processed: 435 average time/residue: 0.1209 time to fit residues: 88.2737 Evaluate side-chains 477 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 395 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 600 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 426 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 640 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 148 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083937 restraints weight = 50157.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086509 restraints weight = 25395.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088197 restraints weight = 16806.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089245 restraints weight = 13094.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089883 restraints weight = 11317.046| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21944 Z= 0.221 Angle : 0.756 12.405 29732 Z= 0.367 Chirality : 0.046 0.181 3352 Planarity : 0.004 0.042 3664 Dihedral : 8.220 128.465 3160 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.88 % Allowed : 20.56 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2520 helix: 0.98 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -2.00 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 288 TYR 0.028 0.002 TYR A 429 PHE 0.029 0.002 PHE B 136 TRP 0.013 0.001 TRP B 314 HIS 0.003 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (21940) covalent geometry : angle 0.75573 / 0.37 (29724) SS BOND : bond 0.00506 / 0.24 ( 4) SS BOND : angle 1.59035 / 0.77 ( 8) hydrogen bonds : bond 0.03941 / 2.57 ( 1248) hydrogen bonds : angle 4.12564 / 2.91 ( 3708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4038.26 seconds wall clock time: 70 minutes 27.13 seconds (4227.13 seconds total)