Starting phenix.real_space_refine on Sun Sep 13 06:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6g1k_4339/09_2026/6g1k_4339.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1k_4339/09_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_4339/09_2026/6g1k_4339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1k_4339/09_2026/6g1k_4339.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6g1k_4339/09_2026/6g1k_4339.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6g1k_4339/09_2026/6g1k_4339.cif" model { file = "/net/cci-nas-00/data/ceres_data/6g1k_4339/09_2026/6g1k_4339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1k_4339/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.86, per 1000 atoms: 0.27 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.49 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: 3.59 Time building geometry restraints manager: 2.38 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: 12596 26.12 - 52.24: 412 52.24 - 78.36: 36 78.36 - 104.48: 4 104.48 - 130.60: 4 Dihedral angle restraints: 13052 sinusoidal: 5380 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 13049 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: 0.07 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: 0.730 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.760 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 12.511 130.600 8032 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 : 0.850 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: 0.1703 time to fit residues: 161.8597 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 : 0.800 ------------------------------------------------------------------------------- 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... 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 = 0.3599 r_free = 0.3599 target = 0.115674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090195 restraints weight = 49359.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092893 restraints weight = 24013.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094610 restraints weight = 15558.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095698 restraints weight = 12084.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096260 restraints weight = 10434.754| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2785 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= 0.130 Angle : 0.642 8.041 29732 Z= 0.321 Chirality : 0.042 0.164 3352 Planarity : 0.005 0.048 3664 Dihedral : 9.013 122.861 2932 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.32 % Allowed : 11.42 % Favored : 85.26 % 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: -1.55 (0.16), residues: 2520 helix: -0.41 (0.11), residues: 1880 sheet: None (None), residues: 0 loop : -2.62 (0.22), residues: 640 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 0.024 0.001 PHE A 340 TRP 0.010 0.001 TRP D 314 HIS 0.002 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21940) covalent geometry : angle 0.64214 / 0.32 (29724) SS BOND : bond 0.00221 / 0.10 ( 4) SS BOND : angle 1.09425 / 0.50 ( 8) hydrogen bonds : bond 0.03990 / 2.62 ( 1248) hydrogen bonds : angle 4.15844 / 2.93 ( 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 597 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 520 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 92 PHE cc_start: 0.8270 (m-10) cc_final: 0.7880 (m-80) REVERT: A 105 ARG cc_start: 0.8682 (ttp-170) cc_final: 0.8288 (ttp-170) REVERT: A 234 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 238 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8404 (ptmm) REVERT: A 445 TYR cc_start: 0.9188 (m-80) cc_final: 0.8939 (m-80) REVERT: A 506 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: A 513 LEU cc_start: 0.9243 (mt) cc_final: 0.8925 (mp) REVERT: A 636 LYS cc_start: 0.9038 (mttt) cc_final: 0.8742 (mttp) REVERT: A 752 MET cc_start: 0.8615 (mmp) cc_final: 0.8326 (mmm) REVERT: A 753 MET cc_start: 0.6484 (mmm) cc_final: 0.6279 (mmt) REVERT: B 92 PHE cc_start: 0.8272 (m-10) cc_final: 0.7880 (m-80) REVERT: B 105 ARG cc_start: 0.8682 (ttp-170) cc_final: 0.8286 (ttp-170) REVERT: B 234 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 238 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8402 (ptmm) REVERT: B 445 TYR cc_start: 0.9189 (m-80) cc_final: 0.8939 (m-80) REVERT: B 506 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: B 513 LEU cc_start: 0.9241 (mt) cc_final: 0.8922 (mp) REVERT: B 622 ASN cc_start: 0.7682 (p0) cc_final: 0.7461 (p0) REVERT: B 636 LYS cc_start: 0.9038 (mttt) cc_final: 0.8745 (mttp) REVERT: B 752 MET cc_start: 0.8565 (mmp) cc_final: 0.8323 (mmm) REVERT: C 81 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 92 PHE cc_start: 0.8268 (m-10) cc_final: 0.7877 (m-80) REVERT: C 105 ARG cc_start: 0.8680 (ttp-170) cc_final: 0.8286 (ttp-170) REVERT: C 234 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 238 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8403 (ptmm) REVERT: C 445 TYR cc_start: 0.9187 (m-80) cc_final: 0.8939 (m-80) REVERT: C 506 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: C 513 LEU cc_start: 0.9241 (mt) cc_final: 0.8927 (mp) REVERT: C 636 LYS cc_start: 0.9037 (mttt) cc_final: 0.8743 (mttp) REVERT: C 752 MET cc_start: 0.8614 (mmp) cc_final: 0.8326 (mmm) REVERT: C 753 MET cc_start: 0.6473 (mmm) cc_final: 0.6271 (mmt) REVERT: D 81 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 92 PHE cc_start: 0.8273 (m-10) cc_final: 0.7882 (m-80) REVERT: D 105 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.8296 (ttp-170) REVERT: D 234 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7233 (tm-30) REVERT: D 238 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8403 (ptmm) REVERT: D 445 TYR cc_start: 0.9191 (m-80) cc_final: 0.8941 (m-80) REVERT: D 506 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: D 513 LEU cc_start: 0.9243 (mt) cc_final: 0.8927 (mp) REVERT: D 636 LYS cc_start: 0.9036 (mttt) cc_final: 0.8741 (mttp) REVERT: D 752 MET cc_start: 0.8566 (mmp) cc_final: 0.8325 (mmm) outliers start: 77 outliers final: 28 residues processed: 563 average time/residue: 0.1399 time to fit residues: 126.6221 Evaluate side-chains 462 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 430 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 2.9990 chunk 110 optimal weight: 4.9990 chunk 232 optimal weight: 0.0470 chunk 250 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3579 r_free = 0.3579 target = 0.114487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089139 restraints weight = 49111.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091727 restraints weight = 24317.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093385 restraints weight = 15916.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094425 restraints weight = 12389.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094990 restraints weight = 10703.858| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21944 Z= 0.142 Angle : 0.640 8.737 29732 Z= 0.316 Chirality : 0.042 0.157 3352 Planarity : 0.004 0.043 3664 Dihedral : 8.747 123.620 2928 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.93 % Allowed : 13.71 % Favored : 83.36 % 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: -0.50 (0.17), residues: 2520 helix: 0.36 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -2.30 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.017 0.001 TYR D 747 PHE 0.021 0.001 PHE A 136 TRP 0.013 0.001 TRP B 314 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (21940) covalent geometry : angle 0.63944 / 0.32 (29724) SS BOND : bond 0.00481 / 0.23 ( 4) SS BOND : angle 1.41547 / 0.68 ( 8) hydrogen bonds : bond 0.03737 / 2.46 ( 1248) hydrogen bonds : angle 4.01741 / 2.83 ( 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 521 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 453 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8550 (tt0) REVERT: A 81 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 107 GLU cc_start: 0.8320 (pm20) cc_final: 0.7955 (pm20) REVERT: A 315 TYR cc_start: 0.8370 (m-10) cc_final: 0.7982 (m-80) REVERT: A 513 LEU cc_start: 0.9299 (mt) cc_final: 0.9022 (mp) REVERT: A 532 ASN cc_start: 0.8788 (t0) cc_final: 0.8457 (t0) REVERT: A 752 MET cc_start: 0.8539 (mmp) cc_final: 0.8325 (mmm) REVERT: B 41 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8547 (tt0) REVERT: B 79 GLU cc_start: 0.8688 (tp30) cc_final: 0.8475 (tp30) REVERT: B 107 GLU cc_start: 0.8323 (pm20) cc_final: 0.7954 (pm20) REVERT: B 315 TYR cc_start: 0.8363 (m-10) cc_final: 0.8006 (m-80) REVERT: B 513 LEU cc_start: 0.9288 (mt) cc_final: 0.9003 (mp) REVERT: B 532 ASN cc_start: 0.8794 (t0) cc_final: 0.8466 (t0) REVERT: B 622 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7467 (p0) REVERT: B 737 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 752 MET cc_start: 0.8522 (mmp) cc_final: 0.8310 (mmm) REVERT: C 41 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8551 (tt0) REVERT: C 81 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 107 GLU cc_start: 0.8318 (pm20) cc_final: 0.7953 (pm20) REVERT: C 315 TYR cc_start: 0.8362 (m-10) cc_final: 0.8003 (m-80) REVERT: C 513 LEU cc_start: 0.9303 (mt) cc_final: 0.9020 (mp) REVERT: C 532 ASN cc_start: 0.8793 (t0) cc_final: 0.8442 (t0) REVERT: C 737 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 752 MET cc_start: 0.8539 (mmp) cc_final: 0.8327 (mmm) REVERT: D 41 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8551 (tt0) REVERT: D 81 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7670 (mm-30) REVERT: D 107 GLU cc_start: 0.8327 (pm20) cc_final: 0.7960 (pm20) REVERT: D 315 TYR cc_start: 0.8373 (m-10) cc_final: 0.7985 (m-80) REVERT: D 513 LEU cc_start: 0.9305 (mt) cc_final: 0.9021 (mp) REVERT: D 532 ASN cc_start: 0.8798 (t0) cc_final: 0.8473 (t0) REVERT: D 622 ASN cc_start: 0.7805 (p0) cc_final: 0.7590 (p0) REVERT: D 737 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8314 (mt-10) REVERT: D 752 MET cc_start: 0.8528 (mmp) cc_final: 0.8324 (mmm) outliers start: 68 outliers final: 40 residues processed: 486 average time/residue: 0.1280 time to fit residues: 104.0157 Evaluate side-chains 440 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 399 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 741 ASP 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 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 377 LEU 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 741 ASP 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 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 741 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 245 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 506 GLN 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 = 0.3579 r_free = 0.3579 target = 0.114604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089284 restraints weight = 49350.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091868 restraints weight = 24348.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093526 restraints weight = 15958.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094625 restraints weight = 12403.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.095187 restraints weight = 10648.041| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21944 Z= 0.124 Angle : 0.610 8.516 29732 Z= 0.302 Chirality : 0.042 0.152 3352 Planarity : 0.004 0.042 3664 Dihedral : 8.571 124.072 2928 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.36 % Allowed : 16.25 % Favored : 80.39 % 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: 0.02 (0.17), residues: 2520 helix: 0.76 (0.12), residues: 1892 sheet: None (None), residues: 0 loop : -2.20 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 556 TYR 0.024 0.001 TYR C 429 PHE 0.023 0.001 PHE D 136 TRP 0.012 0.001 TRP C 314 HIS 0.004 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21940) covalent geometry : angle 0.60995 / 0.30 (29724) SS BOND : bond 0.00400 / 0.19 ( 4) SS BOND : angle 1.10627 / 0.54 ( 8) hydrogen bonds : bond 0.03555 / 2.34 ( 1248) hydrogen bonds : angle 3.87437 / 2.73 ( 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 515 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 437 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 143 ILE cc_start: 0.8613 (mt) cc_final: 0.8325 (tt) REVERT: A 267 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8774 (mt) REVERT: A 315 TYR cc_start: 0.8313 (m-10) cc_final: 0.8009 (m-80) REVERT: A 409 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.7808 (m-90) REVERT: A 622 ASN cc_start: 0.7785 (p0) cc_final: 0.7571 (p0) REVERT: A 752 MET cc_start: 0.8544 (mmp) cc_final: 0.8296 (mmm) REVERT: B 267 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 315 TYR cc_start: 0.8321 (m-10) cc_final: 0.8033 (m-80) REVERT: B 409 TRP cc_start: 0.8944 (OUTLIER) cc_final: 0.7805 (m-90) REVERT: B 622 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7476 (p0) REVERT: B 737 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 752 MET cc_start: 0.8572 (mmp) cc_final: 0.8271 (mmm) REVERT: C 81 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7650 (mm-30) REVERT: C 267 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8782 (mt) REVERT: C 315 TYR cc_start: 0.8321 (m-10) cc_final: 0.8034 (m-80) REVERT: C 409 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.7806 (m-90) REVERT: C 622 ASN cc_start: 0.7848 (p0) cc_final: 0.7632 (p0) REVERT: C 737 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8349 (mt-10) REVERT: C 752 MET cc_start: 0.8547 (mmp) cc_final: 0.8302 (mmm) REVERT: D 79 GLU cc_start: 0.8646 (tp30) cc_final: 0.8401 (tp30) REVERT: D 81 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7657 (mm-30) REVERT: D 267 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8774 (mt) REVERT: D 315 TYR cc_start: 0.8313 (m-10) cc_final: 0.8012 (m-80) REVERT: D 409 TRP cc_start: 0.8945 (OUTLIER) cc_final: 0.7813 (m-90) REVERT: D 622 ASN cc_start: 0.7796 (p0) cc_final: 0.7585 (p0) REVERT: D 737 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8351 (mt-10) REVERT: D 752 MET cc_start: 0.8576 (mmp) cc_final: 0.8276 (mmm) outliers start: 78 outliers final: 43 residues processed: 476 average time/residue: 0.1262 time to fit residues: 100.9203 Evaluate side-chains 434 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 382 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 326 TRP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 377 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 517 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 267 LEU Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 409 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 517 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 C residue 144 THR 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 377 LEU Chi-restraints excluded: chain C residue 409 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 517 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 600 MET Chi-restraints excluded: chain D residue 144 THR 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 377 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 517 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 552 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 506 GLN B 80 ASN B 506 GLN C 80 ASN C 506 GLN D 80 ASN D 506 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083614 restraints weight = 49885.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.086048 restraints weight = 25062.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087660 restraints weight = 16473.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088674 restraints weight = 12836.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089145 restraints weight = 11056.174| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 21944 Z= 0.275 Angle : 0.730 8.353 29732 Z= 0.366 Chirality : 0.047 0.168 3352 Planarity : 0.004 0.043 3664 Dihedral : 8.631 124.882 2928 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.14 % Allowed : 16.12 % Favored : 79.74 % 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: -0.11 (0.17), residues: 2520 helix: 0.71 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 491 TYR 0.019 0.002 TYR C 429 PHE 0.025 0.002 PHE A 136 TRP 0.016 0.002 TRP D 404 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 (21940) covalent geometry : angle 0.72921 / 0.37 (29724) SS BOND : bond 0.00666 / 0.31 ( 4) SS BOND : angle 1.77671 / 0.88 ( 8) hydrogen bonds : bond 0.04254 / 2.79 ( 1248) hydrogen bonds : angle 4.16851 / 2.92 ( 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 488 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 392 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8682 (tp30) cc_final: 0.8470 (tp30) REVERT: A 81 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 92 PHE cc_start: 0.8406 (m-80) cc_final: 0.7578 (m-80) REVERT: A 267 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (mt) REVERT: A 409 TRP cc_start: 0.8979 (OUTLIER) cc_final: 0.7974 (m-90) REVERT: A 470 MET cc_start: 0.7777 (mmm) cc_final: 0.7242 (mmm) REVERT: A 622 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7667 (p0) REVERT: B 79 GLU cc_start: 0.8646 (tp30) cc_final: 0.8408 (tp30) REVERT: B 92 PHE cc_start: 0.8404 (m-80) cc_final: 0.7577 (m-80) REVERT: B 267 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 409 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.7970 (m-90) REVERT: B 470 MET cc_start: 0.7775 (mmm) cc_final: 0.7240 (mmm) REVERT: B 622 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7663 (p0) REVERT: B 737 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8382 (mt-10) REVERT: C 79 GLU cc_start: 0.8684 (tp30) cc_final: 0.8470 (tp30) REVERT: C 81 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7649 (mm-30) REVERT: C 92 PHE cc_start: 0.8408 (m-80) cc_final: 0.7578 (m-80) REVERT: C 267 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8784 (mt) REVERT: C 409 TRP cc_start: 0.8979 (OUTLIER) cc_final: 0.7972 (m-90) REVERT: C 622 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7648 (p0) REVERT: C 737 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8466 (mt-10) REVERT: D 81 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7503 (mm-30) REVERT: D 92 PHE cc_start: 0.8405 (m-80) cc_final: 0.7580 (m-80) REVERT: D 267 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (mt) REVERT: D 409 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.7975 (m-90) REVERT: D 622 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7671 (p0) REVERT: D 737 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8460 (mt-10) outliers start: 96 outliers final: 55 residues processed: 439 average time/residue: 0.1253 time to fit residues: 92.9204 Evaluate side-chains 444 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 377 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 205 SER 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 409 TRP Chi-restraints excluded: chain A residue 418 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 528 LEU Chi-restraints excluded: chain A residue 552 ILE 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 205 SER 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 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 507 ILE Chi-restraints excluded: chain B residue 509 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 622 ASN Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER 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 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 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 528 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 600 MET Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 205 SER 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 348 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 509 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 622 ASN 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: 2.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.084137 restraints weight = 49788.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086582 restraints weight = 25165.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088172 restraints weight = 16610.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089195 restraints weight = 13011.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089643 restraints weight = 11252.748| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3910 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= 0.231 Angle : 0.682 8.837 29732 Z= 0.342 Chirality : 0.045 0.156 3352 Planarity : 0.004 0.045 3664 Dihedral : 8.563 128.092 2928 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.18 % Allowed : 18.02 % Favored : 77.80 % 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: 0.08 (0.17), residues: 2520 helix: 0.82 (0.12), residues: 1880 sheet: None (None), residues: 0 loop : -2.19 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 746 TYR 0.015 0.002 TYR B 582 PHE 0.021 0.002 PHE C 519 TRP 0.016 0.001 TRP D 404 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (21940) covalent geometry : angle 0.68154 / 0.34 (29724) SS BOND : bond 0.00589 / 0.28 ( 4) SS BOND : angle 1.72168 / 0.84 ( 8) hydrogen bonds : bond 0.04039 / 2.65 ( 1248) hydrogen bonds : angle 4.03383 / 2.82 ( 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 486 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 389 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8457 (tttp) cc_final: 0.8246 (ttmt) REVERT: A 79 GLU cc_start: 0.8717 (tp30) cc_final: 0.8501 (tp30) REVERT: A 81 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 267 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8800 (mt) REVERT: A 409 TRP cc_start: 0.8962 (OUTLIER) cc_final: 0.7903 (m-90) REVERT: A 622 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7565 (p0) REVERT: B 267 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8801 (mt) REVERT: B 409 TRP cc_start: 0.8965 (OUTLIER) cc_final: 0.7901 (m-90) REVERT: B 622 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7641 (p0) REVERT: B 737 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 79 GLU cc_start: 0.8718 (tp30) cc_final: 0.8504 (tp30) REVERT: C 81 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 267 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8803 (mt) REVERT: C 409 TRP cc_start: 0.8978 (OUTLIER) cc_final: 0.7937 (m-90) REVERT: C 622 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7741 (p0) REVERT: D 81 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 106 LYS cc_start: 0.9027 (tppt) cc_final: 0.8411 (tptp) REVERT: D 267 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8800 (mt) REVERT: D 409 TRP cc_start: 0.8962 (OUTLIER) cc_final: 0.7904 (m-90) REVERT: D 622 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7681 (p0) outliers start: 97 outliers final: 65 residues processed: 432 average time/residue: 0.1300 time to fit residues: 94.1418 Evaluate side-chains 467 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 390 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 205 SER 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 409 TRP Chi-restraints excluded: chain A residue 418 ILE 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 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 205 SER 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 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 493 ILE Chi-restraints excluded: chain B residue 499 ASN 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 622 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER 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 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 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 599 THR Chi-restraints excluded: chain C residue 600 MET Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 205 SER 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 348 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 ASN 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 528 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: 0.7980 chunk 118 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN ** 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 = 0.3566 r_free = 0.3566 target = 0.114030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087923 restraints weight = 48993.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090521 restraints weight = 25062.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.092217 restraints weight = 16628.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093256 restraints weight = 13034.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093820 restraints weight = 11300.790| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21944 Z= 0.119 Angle : 0.641 9.192 29732 Z= 0.312 Chirality : 0.043 0.163 3352 Planarity : 0.004 0.043 3664 Dihedral : 8.415 129.058 2928 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.62 % Allowed : 19.31 % Favored : 77.07 % 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: 0.41 (0.17), residues: 2520 helix: 1.06 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -2.12 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 556 TYR 0.027 0.001 TYR C 429 PHE 0.027 0.001 PHE C 136 TRP 0.014 0.001 TRP D 314 HIS 0.003 0.001 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21940) covalent geometry : angle 0.64105 / 0.31 (29724) SS BOND : bond 0.00339 / 0.16 ( 4) SS BOND : angle 1.11576 / 0.55 ( 8) hydrogen bonds : bond 0.03604 / 2.36 ( 1248) hydrogen bonds : angle 3.91713 / 2.77 ( 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 522 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 438 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8499 (tt0) REVERT: A 42 LYS cc_start: 0.8409 (tttp) cc_final: 0.8047 (ttmt) REVERT: A 81 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 267 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8816 (mt) REVERT: A 315 TYR cc_start: 0.8305 (m-10) cc_final: 0.8070 (m-80) REVERT: A 409 TRP cc_start: 0.8890 (OUTLIER) cc_final: 0.7700 (m-90) REVERT: A 470 MET cc_start: 0.7457 (mmm) cc_final: 0.7082 (mmm) REVERT: A 514 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8513 (mt) REVERT: A 535 ASN cc_start: 0.8887 (t0) cc_final: 0.8516 (t0) REVERT: A 622 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7551 (p0) REVERT: B 41 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8487 (tt0) REVERT: B 42 LYS cc_start: 0.8409 (tttp) cc_final: 0.7996 (ttmt) REVERT: B 92 PHE cc_start: 0.8280 (m-80) cc_final: 0.8015 (m-80) REVERT: B 106 LYS cc_start: 0.9086 (tppt) cc_final: 0.8412 (tptp) REVERT: B 267 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8816 (mt) REVERT: B 409 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.7698 (m-90) REVERT: B 417 GLU cc_start: 0.8018 (tp30) cc_final: 0.7803 (tp30) REVERT: B 470 MET cc_start: 0.7452 (mmm) cc_final: 0.7078 (mmm) REVERT: B 514 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8454 (mt) REVERT: B 535 ASN cc_start: 0.8885 (t0) cc_final: 0.8463 (t0) REVERT: B 600 MET cc_start: 0.8923 (ptm) cc_final: 0.8638 (ttp) REVERT: B 622 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7659 (p0) REVERT: C 41 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8567 (tt0) REVERT: C 42 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8284 (tttt) REVERT: C 81 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 143 ILE cc_start: 0.8801 (mt) cc_final: 0.8403 (tt) REVERT: C 267 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8779 (mt) REVERT: C 409 TRP cc_start: 0.8887 (OUTLIER) cc_final: 0.7697 (m-90) REVERT: C 470 MET cc_start: 0.7449 (mmm) cc_final: 0.7069 (mmm) REVERT: C 514 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 535 ASN cc_start: 0.8879 (t0) cc_final: 0.8496 (t0) REVERT: C 622 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7757 (p0) REVERT: C 737 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8332 (mt-10) REVERT: D 41 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8623 (tt0) REVERT: D 42 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8062 (ttpp) REVERT: D 106 LYS cc_start: 0.8978 (tppt) cc_final: 0.8332 (tptp) REVERT: D 267 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8815 (mt) REVERT: D 315 TYR cc_start: 0.8306 (m-10) cc_final: 0.8076 (m-80) REVERT: D 409 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.7703 (m-90) REVERT: D 470 MET cc_start: 0.7480 (mmm) cc_final: 0.7111 (mmm) REVERT: D 514 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8638 (mm) REVERT: D 535 ASN cc_start: 0.8877 (t0) cc_final: 0.8463 (t0) REVERT: D 600 MET cc_start: 0.8942 (ptm) cc_final: 0.8643 (ttp) REVERT: D 622 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7717 (p0) REVERT: D 737 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8323 (mt-10) REVERT: D 747 TYR cc_start: 0.8406 (m-10) cc_final: 0.7616 (m-10) outliers start: 84 outliers final: 56 residues processed: 471 average time/residue: 0.1267 time to fit residues: 98.8589 Evaluate side-chains 482 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 408 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 377 LEU 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 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 640 THR Chi-restraints excluded: chain B residue 144 THR 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 377 LEU 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 499 ASN 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 640 THR Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 144 THR 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 377 LEU 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 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 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 377 LEU 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 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 528 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: 0.0270 chunk 139 optimal weight: 4.9990 chunk 207 optimal weight: 0.0070 chunk 54 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 501 HIS B 506 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088916 restraints weight = 49371.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091518 restraints weight = 25269.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093246 restraints weight = 16802.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094313 restraints weight = 13156.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094949 restraints weight = 11414.744| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21944 Z= 0.124 Angle : 0.644 9.547 29732 Z= 0.320 Chirality : 0.043 0.157 3352 Planarity : 0.004 0.042 3664 Dihedral : 8.329 127.338 2928 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.27 % Allowed : 20.00 % Favored : 75.73 % 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: 0.48 (0.17), residues: 2520 helix: 1.10 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 700 TYR 0.023 0.001 TYR B 429 PHE 0.025 0.001 PHE A 335 TRP 0.015 0.001 TRP B 314 HIS 0.002 0.000 HIS B 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21940) covalent geometry : angle 0.64387 / 0.32 (29724) SS BOND : bond 0.00321 / 0.15 ( 4) SS BOND : angle 1.12295 / 0.54 ( 8) hydrogen bonds : bond 0.03475 / 2.27 ( 1248) hydrogen bonds : angle 3.89290 / 2.75 ( 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 546 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 447 time to evaluate : 0.755 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 41 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8543 (tt0) REVERT: A 42 LYS cc_start: 0.8531 (tttp) cc_final: 0.8168 (ttmt) REVERT: A 81 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 106 LYS cc_start: 0.9047 (tppt) cc_final: 0.8391 (tptp) REVERT: A 267 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8811 (mt) REVERT: A 405 MET cc_start: 0.8187 (mmp) cc_final: 0.7751 (mmm) REVERT: A 409 TRP cc_start: 0.8830 (OUTLIER) cc_final: 0.7728 (m-90) REVERT: A 470 MET cc_start: 0.7519 (mmm) cc_final: 0.7182 (mmm) REVERT: A 514 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 535 ASN cc_start: 0.8881 (t0) cc_final: 0.8460 (t0) REVERT: A 622 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7605 (p0) REVERT: B 106 LYS cc_start: 0.9082 (tppt) cc_final: 0.8393 (tptp) REVERT: B 267 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8809 (mt) REVERT: B 405 MET cc_start: 0.8189 (mmp) cc_final: 0.7749 (mmm) REVERT: B 409 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.7737 (m-90) REVERT: B 470 MET cc_start: 0.7467 (mmm) cc_final: 0.7145 (mmm) REVERT: B 514 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 535 ASN cc_start: 0.8869 (t0) cc_final: 0.8424 (t0) REVERT: B 600 MET cc_start: 0.8871 (ptm) cc_final: 0.8529 (ttp) REVERT: B 622 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7671 (p0) REVERT: C 81 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7335 (mm-30) REVERT: C 106 LYS cc_start: 0.9063 (tppt) cc_final: 0.8388 (tptp) REVERT: C 143 ILE cc_start: 0.8758 (mt) cc_final: 0.8402 (tt) REVERT: C 267 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 405 MET cc_start: 0.8186 (mmp) cc_final: 0.7749 (mmm) REVERT: C 409 TRP cc_start: 0.8824 (OUTLIER) cc_final: 0.7719 (m-90) REVERT: C 470 MET cc_start: 0.7461 (mmm) cc_final: 0.7130 (mmm) REVERT: C 514 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 535 ASN cc_start: 0.8873 (t0) cc_final: 0.8459 (t0) REVERT: C 737 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8441 (mt-10) REVERT: D 81 GLU cc_start: 0.7939 (mm-30) cc_final: 0.6970 (mm-30) REVERT: D 106 LYS cc_start: 0.8964 (tppt) cc_final: 0.8299 (tptp) REVERT: D 267 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8809 (mt) REVERT: D 405 MET cc_start: 0.8189 (mmp) cc_final: 0.7753 (mmm) REVERT: D 409 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.7727 (m-90) REVERT: D 470 MET cc_start: 0.7510 (mmm) cc_final: 0.7172 (mmm) REVERT: D 514 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8436 (mt) REVERT: D 535 ASN cc_start: 0.8869 (t0) cc_final: 0.8419 (t0) REVERT: D 600 MET cc_start: 0.8895 (ptm) cc_final: 0.8550 (ttp) REVERT: D 622 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7727 (p0) REVERT: D 737 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8373 (mt-10) outliers start: 99 outliers final: 63 residues processed: 478 average time/residue: 0.1219 time to fit residues: 97.8254 Evaluate side-chains 493 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 415 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 377 LEU 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 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 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 377 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 499 ASN 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 640 THR Chi-restraints excluded: chain C residue 144 THR 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 377 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 493 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 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 377 LEU 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 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 528 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 147 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN A 435 ASN A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 506 GLN C 308 GLN C 435 ASN C 506 GLN D 308 GLN D 435 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087613 restraints weight = 49434.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090162 restraints weight = 25498.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091772 restraints weight = 17061.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092812 restraints weight = 13471.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093371 restraints weight = 11710.327| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4266 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= 0.150 Angle : 0.678 10.126 29732 Z= 0.333 Chirality : 0.044 0.155 3352 Planarity : 0.004 0.044 3664 Dihedral : 8.303 126.228 2928 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.09 % Allowed : 20.34 % 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: 0.51 (0.17), residues: 2520 helix: 1.13 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 700 TYR 0.019 0.001 TYR B 429 PHE 0.024 0.002 PHE A 335 TRP 0.013 0.001 TRP B 314 HIS 0.002 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (21940) covalent geometry : angle 0.67758 / 0.33 (29724) SS BOND : bond 0.00354 / 0.17 ( 4) SS BOND : angle 1.22174 / 0.59 ( 8) hydrogen bonds : bond 0.03589 / 2.34 ( 1248) hydrogen bonds : angle 3.95518 / 2.79 ( 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 517 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 422 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 106 LYS cc_start: 0.9051 (tppt) cc_final: 0.8378 (tptp) REVERT: A 267 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 514 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8467 (mt) REVERT: A 535 ASN cc_start: 0.8858 (t0) cc_final: 0.8466 (t0) REVERT: A 622 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7636 (p0) REVERT: B 41 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8543 (tt0) REVERT: B 42 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8046 (ttpp) REVERT: B 106 LYS cc_start: 0.8998 (tppt) cc_final: 0.8319 (tptp) REVERT: B 267 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8797 (mt) REVERT: B 430 ILE cc_start: 0.7843 (mp) cc_final: 0.7304 (mt) REVERT: B 470 MET cc_start: 0.7587 (mmm) cc_final: 0.6958 (tpt) REVERT: B 514 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 535 ASN cc_start: 0.8856 (t0) cc_final: 0.8479 (t0) REVERT: B 622 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7759 (p0) REVERT: C 42 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8195 (ttpp) REVERT: C 81 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7368 (mm-30) REVERT: C 106 LYS cc_start: 0.9072 (tppt) cc_final: 0.8385 (tptp) REVERT: C 143 ILE cc_start: 0.8791 (mt) cc_final: 0.8435 (tt) REVERT: C 267 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8775 (mt) REVERT: C 430 ILE cc_start: 0.7765 (mp) cc_final: 0.7427 (mm) REVERT: C 514 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 535 ASN cc_start: 0.8884 (t0) cc_final: 0.8519 (t0) REVERT: C 737 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8370 (mt-10) REVERT: D 42 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8155 (ttpp) REVERT: D 106 LYS cc_start: 0.8970 (tppt) cc_final: 0.8278 (tptp) REVERT: D 267 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8795 (mt) REVERT: D 430 ILE cc_start: 0.7758 (mp) cc_final: 0.7410 (mm) REVERT: D 514 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8466 (mt) REVERT: D 535 ASN cc_start: 0.8880 (t0) cc_final: 0.8484 (t0) REVERT: D 622 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7754 (p0) REVERT: D 737 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8367 (mt-10) outliers start: 95 outliers final: 69 residues processed: 456 average time/residue: 0.1256 time to fit residues: 96.6643 Evaluate side-chains 482 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 401 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 348 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 PHE 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 600 MET Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 205 SER 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 418 ILE Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 493 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 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 640 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER 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 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 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 418 ILE Chi-restraints excluded: chain D residue 426 PHE Chi-restraints excluded: chain D residue 499 ASN 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 528 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: 3.9990 chunk 154 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN B 506 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3539 r_free = 0.3539 target = 0.112152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.086842 restraints weight = 49583.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089336 restraints weight = 24944.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090976 restraints weight = 16469.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091996 restraints weight = 12863.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092547 restraints weight = 11128.387| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21944 Z= 0.172 Angle : 0.695 11.245 29732 Z= 0.343 Chirality : 0.045 0.160 3352 Planarity : 0.004 0.041 3664 Dihedral : 8.313 126.066 2928 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.01 % Allowed : 20.60 % Favored : 75.39 % 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: 0.53 (0.17), residues: 2520 helix: 1.12 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.96 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 746 TYR 0.018 0.001 TYR B 429 PHE 0.024 0.002 PHE A 335 TRP 0.014 0.001 TRP D 314 HIS 0.002 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (21940) covalent geometry : angle 0.69432 / 0.34 (29724) SS BOND : bond 0.00408 / 0.19 ( 4) SS BOND : angle 1.32298 / 0.64 ( 8) hydrogen bonds : bond 0.03679 / 2.40 ( 1248) hydrogen bonds : angle 3.99806 / 2.82 ( 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 510 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 417 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 92 PHE cc_start: 0.8287 (m-80) cc_final: 0.8054 (m-80) REVERT: A 267 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8802 (mt) REVERT: A 405 MET cc_start: 0.8338 (mmm) cc_final: 0.8035 (mmm) REVERT: A 409 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.7872 (m-90) REVERT: A 514 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 622 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7646 (p0) REVERT: B 41 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8585 (tt0) REVERT: B 92 PHE cc_start: 0.8235 (m-80) cc_final: 0.7999 (m-80) REVERT: B 106 LYS cc_start: 0.8991 (tppt) cc_final: 0.8326 (tptp) REVERT: B 267 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8798 (mt) REVERT: B 470 MET cc_start: 0.7667 (mmm) cc_final: 0.7165 (tpt) REVERT: B 514 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8509 (mt) REVERT: B 622 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7722 (p0) REVERT: C 42 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8228 (ttpp) REVERT: C 81 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 92 PHE cc_start: 0.8222 (m-80) cc_final: 0.7989 (m-80) REVERT: C 106 LYS cc_start: 0.9002 (tppt) cc_final: 0.8314 (tptp) REVERT: C 143 ILE cc_start: 0.8844 (mt) cc_final: 0.8511 (tt) REVERT: C 267 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8776 (mt) REVERT: C 514 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8532 (mt) REVERT: C 737 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8335 (mt-10) REVERT: D 81 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 92 PHE cc_start: 0.8278 (m-80) cc_final: 0.8049 (m-80) REVERT: D 106 LYS cc_start: 0.8966 (tppt) cc_final: 0.8279 (tptp) REVERT: D 267 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8796 (mt) REVERT: D 405 MET cc_start: 0.8343 (mmm) cc_final: 0.8046 (mmm) REVERT: D 409 TRP cc_start: 0.8853 (OUTLIER) cc_final: 0.7892 (m-90) REVERT: D 514 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8538 (mt) REVERT: D 622 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7777 (p0) REVERT: D 737 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8370 (mt-10) outliers start: 93 outliers final: 74 residues processed: 452 average time/residue: 0.1267 time to fit residues: 96.2620 Evaluate side-chains 491 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 404 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 205 SER 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 379 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 418 ILE 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 505 LEU 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 640 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 205 SER 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 426 PHE Chi-restraints excluded: chain B residue 499 ASN 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 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 640 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER 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 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 622 ASN Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 205 SER 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 409 TRP Chi-restraints excluded: chain D residue 418 ILE 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 505 LEU 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 528 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: 0.6980 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 224 optimal weight: 0.0010 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088176 restraints weight = 49495.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090729 restraints weight = 25518.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092366 restraints weight = 17039.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.093429 restraints weight = 13465.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094084 restraints weight = 11667.813| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4409 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= 0.126 Angle : 0.669 10.016 29732 Z= 0.326 Chirality : 0.043 0.172 3352 Planarity : 0.004 0.041 3664 Dihedral : 8.245 125.975 2928 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.58 % Allowed : 20.86 % 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: 0.67 (0.17), residues: 2520 helix: 1.20 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.84 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 556 TYR 0.016 0.001 TYR B 429 PHE 0.028 0.001 PHE B 136 TRP 0.014 0.001 TRP B 314 HIS 0.002 0.001 HIS B 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (21940) covalent geometry : angle 0.66870 / 0.33 (29724) SS BOND : bond 0.00306 / 0.14 ( 4) SS BOND : angle 1.08126 / 0.53 ( 8) hydrogen bonds : bond 0.03445 / 2.25 ( 1248) hydrogen bonds : angle 3.90704 / 2.76 ( 3708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3917.28 seconds wall clock time: 68 minutes 31.68 seconds (4111.68 seconds total)