Starting phenix.real_space_refine on Mon Apr 6 06:30:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eft_47979/04_2026/9eft_47979.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eft_47979/04_2026/9eft_47979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eft_47979/04_2026/9eft_47979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eft_47979/04_2026/9eft_47979.map" model { file = "/net/cci-nas-00/data/ceres_data/9eft_47979/04_2026/9eft_47979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eft_47979/04_2026/9eft_47979.cif" } resolution = 2.4 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= 0.054 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10290 2.51 5 N 2835 2.21 5 O 3018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16224 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5380 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 31, 'TRANS': 645} Chain breaks: 4 Chain: "B" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5380 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 31, 'TRANS': 645} Chain breaks: 4 Chain: "C" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5380 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 31, 'TRANS': 645} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.82, per 1000 atoms: 0.24 Number of scatterers: 16224 At special positions: 0 Unit cell: (123.42, 116.16, 169.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3018 8.00 N 2835 7.00 C 10290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.06 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.06 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 398 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 398 " " NAG C1001 " - " ASN C 141 " " NAG C1002 " - " ASN C 398 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 786.1 milliseconds 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3804 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 32 sheets defined 35.3% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.965A pdb=" N VAL A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.802A pdb=" N ARG A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 546 Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 685 through 691 removed outlier: 4.080A pdb=" N TYR A 689 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 726 through 739 removed outlier: 4.131A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 773 removed outlier: 3.758A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.746A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 removed outlier: 3.576A pdb=" N ALA A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.939A pdb=" N VAL B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.803A pdb=" N ARG B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 546 Proline residue: B 516 - end of helix Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 685 through 691 removed outlier: 4.077A pdb=" N TYR B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 726 through 739 removed outlier: 4.109A pdb=" N ALA B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 773 removed outlier: 3.766A pdb=" N ASN B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.799A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 removed outlier: 3.754A pdb=" N ALA B 808 " --> pdb=" O ASN B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.952A pdb=" N VAL C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.809A pdb=" N ARG C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 546 Proline residue: C 516 - end of helix Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 685 through 691 removed outlier: 4.078A pdb=" N TYR C 689 " --> pdb=" O PRO C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 724 Processing helix chain 'C' and resid 726 through 739 removed outlier: 4.142A pdb=" N ALA C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 773 removed outlier: 3.770A pdb=" N ASN C 773 " --> pdb=" O SER C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 removed outlier: 3.791A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 removed outlier: 3.507A pdb=" N ALA C 808 " --> pdb=" O ASN C 804 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.037A pdb=" N THR C 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 5.377A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 397 removed outlier: 5.377A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.271A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 324 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA9, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.679A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.537A pdb=" N THR A 665 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.379A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 395 through 397 removed outlier: 5.338A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 397 removed outlier: 5.338A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 191 Processing sheet with id=AB8, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.330A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC2, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.663A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 665 through 667 removed outlier: 6.549A pdb=" N THR B 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC6, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.808A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP C 373 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLY C 145 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET C 375 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR C 143 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.808A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP C 373 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLY C 145 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET C 375 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR C 143 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AC9, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.302A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD2, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD3, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD4, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD5, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.664A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2484 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: 3.70 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5355 1.34 - 1.46: 4109 1.46 - 1.58: 7021 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 16617 Sorted by residual: bond pdb=" N ILE C 526 " pdb=" CA ILE C 526 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.60e+00 bond pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.26e-02 6.30e+03 9.05e+00 bond pdb=" N ILE A 526 " pdb=" CA ILE A 526 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.95e+00 bond pdb=" N TRP A 528 " pdb=" CA TRP A 528 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.57e+00 bond pdb=" N GLU C 530 " pdb=" CA GLU C 530 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.47e+00 ... (remaining 16612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 21922 1.18 - 2.36: 495 2.36 - 3.53: 118 3.53 - 4.71: 9 4.71 - 5.89: 13 Bond angle restraints: 22557 Sorted by residual: angle pdb=" CA CYS A 529 " pdb=" C CYS A 529 " pdb=" O CYS A 529 " ideal model delta sigma weight residual 120.82 117.56 3.26 1.05e+00 9.07e-01 9.66e+00 angle pdb=" CA CYS C 529 " pdb=" C CYS C 529 " pdb=" O CYS C 529 " ideal model delta sigma weight residual 120.82 117.60 3.22 1.05e+00 9.07e-01 9.42e+00 angle pdb=" O VAL A 524 " pdb=" C VAL A 524 " pdb=" N ALA A 525 " ideal model delta sigma weight residual 121.87 124.67 -2.80 1.01e+00 9.80e-01 7.70e+00 angle pdb=" CA CYS B 529 " pdb=" CB CYS B 529 " pdb=" SG CYS B 529 " ideal model delta sigma weight residual 114.40 120.29 -5.89 2.30e+00 1.89e-01 6.56e+00 angle pdb=" CA ALA C 527 " pdb=" C ALA C 527 " pdb=" O ALA C 527 " ideal model delta sigma weight residual 120.55 117.90 2.65 1.06e+00 8.90e-01 6.27e+00 ... (remaining 22552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 8585 16.98 - 33.96: 993 33.96 - 50.94: 262 50.94 - 67.92: 82 67.92 - 84.90: 23 Dihedral angle restraints: 9945 sinusoidal: 4020 harmonic: 5925 Sorted by residual: dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual -86.00 -159.10 73.10 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual 93.00 154.02 -61.02 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 633 " pdb=" CB CYS A 633 " ideal model delta sinusoidal sigma weight residual 93.00 37.62 55.38 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 9942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1826 0.038 - 0.076: 456 0.076 - 0.114: 159 0.114 - 0.152: 36 0.152 - 0.190: 1 Chirality restraints: 2478 Sorted by residual: chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL A 524 " pdb=" CA VAL A 524 " pdb=" CG1 VAL A 524 " pdb=" CG2 VAL A 524 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE A 146 " pdb=" N ILE A 146 " pdb=" C ILE A 146 " pdb=" CB ILE A 146 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 2475 not shown) Planarity restraints: 2934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 347 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 348 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 347 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO C 348 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 347 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 348 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 348 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 348 " 0.019 5.00e-02 4.00e+02 ... (remaining 2931 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3861 2.80 - 3.32: 13827 3.32 - 3.85: 26983 3.85 - 4.37: 32096 4.37 - 4.90: 54637 Nonbonded interactions: 131404 Sorted by model distance: nonbonded pdb=" O LEU A 506 " pdb=" OG1 THR A 509 " model vdw 2.272 3.040 nonbonded pdb=" O LEU B 506 " pdb=" OG1 THR B 509 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP B 373 " pdb=" NH2 ARG B 427 " model vdw 2.279 3.120 nonbonded pdb=" O LEU C 506 " pdb=" OG1 THR C 509 " model vdw 2.282 3.040 nonbonded pdb=" OG SER C 244 " pdb=" OE1 GLU C 274 " model vdw 2.293 3.040 ... (remaining 131399 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.002 0.039 16638 Z= 0.132 Angle : 0.478 6.763 22605 Z= 0.270 Chirality : 0.040 0.190 2478 Planarity : 0.003 0.034 2928 Dihedral : 16.289 84.904 6096 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 22.71 % Favored : 75.18 % 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: 1.82 (0.19), residues: 2001 helix: 2.92 (0.20), residues: 630 sheet: 1.41 (0.23), residues: 477 loop : -0.17 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.012 0.001 TYR C 282 PHE 0.012 0.001 PHE C 287 TRP 0.013 0.001 TRP C 528 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00232 (16617) covalent geometry : angle 0.46754 (22557) SS BOND : bond 0.01262 ( 15) SS BOND : angle 2.58662 ( 30) hydrogen bonds : bond 0.13424 ( 792) hydrogen bonds : angle 6.37371 ( 2484) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.37527 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 305 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5251 (mp0) REVERT: A 622 GLU cc_start: 0.8323 (tt0) cc_final: 0.8006 (tm-30) REVERT: C 305 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5412 (mt-10) REVERT: C 318 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6989 (mmt-90) REVERT: C 622 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7920 (tm-30) outliers start: 36 outliers final: 17 residues processed: 211 average time/residue: 0.6791 time to fit residues: 157.1074 Evaluate side-chains 193 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 796 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 622 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 0.2980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 534 HIS B 248 HIS B 308 HIS B 534 HIS C 248 HIS C 804 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.203702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.166142 restraints weight = 13865.576| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.03 r_work: 0.3516 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16638 Z= 0.124 Angle : 0.517 7.086 22605 Z= 0.280 Chirality : 0.042 0.154 2478 Planarity : 0.004 0.036 2928 Dihedral : 5.910 66.615 2434 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.76 % Allowed : 21.19 % Favored : 76.06 % 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: 1.77 (0.19), residues: 2001 helix: 2.92 (0.20), residues: 633 sheet: 1.23 (0.22), residues: 537 loop : -0.26 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 427 TYR 0.011 0.001 TYR B 429 PHE 0.017 0.001 PHE A 287 TRP 0.011 0.001 TRP A 528 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00261 (16617) covalent geometry : angle 0.50939 (22557) SS BOND : bond 0.00762 ( 15) SS BOND : angle 2.19518 ( 30) hydrogen bonds : bond 0.04858 ( 792) hydrogen bonds : angle 4.66074 ( 2484) link_NAG-ASN : bond 0.00223 ( 6) link_NAG-ASN : angle 1.51081 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.617 Fit side-chains REVERT: A 167 ASP cc_start: 0.7875 (p0) cc_final: 0.7542 (m-30) REVERT: A 399 LEU cc_start: 0.7857 (mm) cc_final: 0.7645 (mt) REVERT: A 622 GLU cc_start: 0.8723 (tt0) cc_final: 0.8456 (tm-30) REVERT: A 753 VAL cc_start: 0.6872 (OUTLIER) cc_final: 0.6329 (p) REVERT: A 772 SER cc_start: 0.6775 (OUTLIER) cc_final: 0.6436 (p) REVERT: B 167 ASP cc_start: 0.7801 (p0) cc_final: 0.7406 (m-30) REVERT: B 232 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7491 (mtt) REVERT: B 411 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6962 (t0) REVERT: B 651 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: B 772 SER cc_start: 0.6746 (OUTLIER) cc_final: 0.6311 (p) REVERT: C 167 ASP cc_start: 0.7764 (p0) cc_final: 0.7415 (m-30) REVERT: C 218 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6537 (tt) REVERT: C 232 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7652 (mtt) REVERT: C 235 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: C 318 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7174 (mmt180) REVERT: C 411 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6942 (t0) REVERT: C 622 GLU cc_start: 0.8747 (tt0) cc_final: 0.8359 (tm-30) REVERT: C 651 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: C 726 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5346 (t0) REVERT: C 772 SER cc_start: 0.6723 (OUTLIER) cc_final: 0.6336 (p) outliers start: 47 outliers final: 16 residues processed: 215 average time/residue: 0.6953 time to fit residues: 163.9857 Evaluate side-chains 199 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 35 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 804 ASN B 112 ASN B 248 HIS B 308 HIS C 248 HIS C 534 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.200620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162778 restraints weight = 14008.536| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.06 r_work: 0.3471 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16638 Z= 0.170 Angle : 0.583 8.961 22605 Z= 0.316 Chirality : 0.045 0.202 2478 Planarity : 0.004 0.038 2928 Dihedral : 5.391 49.842 2413 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.99 % Allowed : 20.60 % Favored : 75.41 % 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: 1.60 (0.18), residues: 2001 helix: 2.81 (0.20), residues: 633 sheet: 1.12 (0.22), residues: 537 loop : -0.38 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 558 TYR 0.012 0.002 TYR B 702 PHE 0.021 0.002 PHE B 287 TRP 0.010 0.001 TRP C 539 HIS 0.005 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00375 (16617) covalent geometry : angle 0.57381 (22557) SS BOND : bond 0.00821 ( 15) SS BOND : angle 2.50501 ( 30) hydrogen bonds : bond 0.05610 ( 792) hydrogen bonds : angle 4.64342 ( 2484) link_NAG-ASN : bond 0.00185 ( 6) link_NAG-ASN : angle 1.78000 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 169 time to evaluate : 0.756 Fit side-chains REVERT: A 305 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: A 362 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7173 (m) REVERT: A 622 GLU cc_start: 0.8693 (tt0) cc_final: 0.8396 (tm-30) REVERT: A 651 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: A 753 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6333 (p) REVERT: A 772 SER cc_start: 0.6931 (OUTLIER) cc_final: 0.6532 (p) REVERT: B 318 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7111 (mmt180) REVERT: B 349 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8098 (mtmt) REVERT: B 362 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7113 (m) REVERT: B 411 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6961 (t0) REVERT: B 772 SER cc_start: 0.6811 (OUTLIER) cc_final: 0.6365 (p) REVERT: C 218 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6495 (tt) REVERT: C 232 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7588 (mtt) REVERT: C 235 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8168 (mtmt) REVERT: C 305 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.5330 (mp0) REVERT: C 362 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7088 (m) REVERT: C 411 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7023 (t0) REVERT: C 622 GLU cc_start: 0.8713 (tt0) cc_final: 0.8348 (tm-30) REVERT: C 651 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: C 772 SER cc_start: 0.6821 (OUTLIER) cc_final: 0.6424 (p) REVERT: C 806 MET cc_start: 0.6920 (tpp) cc_final: 0.6695 (tpp) outliers start: 68 outliers final: 22 residues processed: 218 average time/residue: 0.6905 time to fit residues: 165.3419 Evaluate side-chains 202 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 772 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 36 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 140 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 136 optimal weight: 0.0000 chunk 127 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 112 ASN B 248 HIS B 308 HIS C 248 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.200803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.160456 restraints weight = 13900.340| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.05 r_work: 0.3473 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16638 Z= 0.158 Angle : 0.566 8.649 22605 Z= 0.307 Chirality : 0.044 0.194 2478 Planarity : 0.004 0.038 2928 Dihedral : 5.359 51.650 2412 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.58 % Allowed : 20.13 % Favored : 75.29 % 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: 1.56 (0.18), residues: 2001 helix: 2.81 (0.20), residues: 636 sheet: 1.09 (0.22), residues: 537 loop : -0.43 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.011 0.002 TYR B 282 PHE 0.020 0.002 PHE B 287 TRP 0.008 0.001 TRP A 539 HIS 0.003 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00348 (16617) covalent geometry : angle 0.55786 (22557) SS BOND : bond 0.00808 ( 15) SS BOND : angle 2.30866 ( 30) hydrogen bonds : bond 0.05379 ( 792) hydrogen bonds : angle 4.56590 ( 2484) link_NAG-ASN : bond 0.00238 ( 6) link_NAG-ASN : angle 1.79049 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.608 Fit side-chains REVERT: A 235 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7684 (mtmt) REVERT: A 305 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: A 362 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.7259 (m) REVERT: A 411 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6903 (t0) REVERT: A 416 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6551 (m-30) REVERT: A 622 GLU cc_start: 0.8731 (tt0) cc_final: 0.8413 (tm-30) REVERT: A 651 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: A 753 VAL cc_start: 0.6948 (OUTLIER) cc_final: 0.6523 (m) REVERT: A 772 SER cc_start: 0.6945 (OUTLIER) cc_final: 0.6571 (p) REVERT: B 204 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7849 (mttt) REVERT: B 305 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.5448 (mt-10) REVERT: B 326 TYR cc_start: 0.8295 (m-80) cc_final: 0.8052 (m-80) REVERT: B 349 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: B 362 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7221 (m) REVERT: B 411 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6939 (t0) REVERT: B 753 VAL cc_start: 0.7217 (OUTLIER) cc_final: 0.6872 (p) REVERT: B 772 SER cc_start: 0.6899 (OUTLIER) cc_final: 0.6478 (p) REVERT: C 218 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6476 (tt) REVERT: C 232 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: C 235 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8237 (mtmt) REVERT: C 362 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7075 (m) REVERT: C 411 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6934 (t0) REVERT: C 622 GLU cc_start: 0.8728 (tt0) cc_final: 0.8350 (tm-30) REVERT: C 651 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: C 753 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6951 (p) REVERT: C 772 SER cc_start: 0.6896 (OUTLIER) cc_final: 0.6539 (p) outliers start: 78 outliers final: 23 residues processed: 234 average time/residue: 0.6740 time to fit residues: 173.6644 Evaluate side-chains 213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 772 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 88 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 112 ASN B 248 HIS B 308 HIS C 248 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.201959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 203)---------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158358 restraints weight = 13961.988| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.01 r_work: 0.3502 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16638 Z= 0.130 Angle : 0.524 7.958 22605 Z= 0.282 Chirality : 0.042 0.162 2478 Planarity : 0.004 0.036 2928 Dihedral : 5.127 51.130 2411 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.23 % Allowed : 20.42 % Favored : 75.35 % 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: 1.64 (0.18), residues: 2001 helix: 2.92 (0.20), residues: 636 sheet: 1.13 (0.22), residues: 537 loop : -0.43 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 427 TYR 0.010 0.001 TYR B 282 PHE 0.018 0.001 PHE B 287 TRP 0.006 0.001 TRP A 354 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00280 (16617) covalent geometry : angle 0.51763 (22557) SS BOND : bond 0.00652 ( 15) SS BOND : angle 1.90470 ( 30) hydrogen bonds : bond 0.04918 ( 792) hydrogen bonds : angle 4.45276 ( 2484) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 1.65773 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7589 (mtp) REVERT: A 235 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7623 (mtmt) REVERT: A 305 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.5647 (mt-10) REVERT: A 362 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.7334 (m) REVERT: A 399 LEU cc_start: 0.7863 (mm) cc_final: 0.7625 (mt) REVERT: A 411 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6884 (t0) REVERT: A 416 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: A 622 GLU cc_start: 0.8647 (tt0) cc_final: 0.8332 (tm-30) REVERT: A 651 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: A 753 VAL cc_start: 0.6817 (OUTLIER) cc_final: 0.6452 (m) REVERT: A 772 SER cc_start: 0.6809 (OUTLIER) cc_final: 0.6461 (p) REVERT: B 204 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7798 (mttt) REVERT: B 305 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.5592 (mt-10) REVERT: B 326 TYR cc_start: 0.8285 (m-80) cc_final: 0.8078 (m-80) REVERT: B 349 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8051 (mtmt) REVERT: B 411 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6829 (t0) REVERT: B 506 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6056 (pp) REVERT: B 772 SER cc_start: 0.6839 (OUTLIER) cc_final: 0.6411 (p) REVERT: C 218 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6559 (tt) REVERT: C 232 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7520 (mtt) REVERT: C 235 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8130 (mtmt) REVERT: C 305 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.5301 (mp0) REVERT: C 411 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6891 (t0) REVERT: C 622 GLU cc_start: 0.8650 (tt0) cc_final: 0.8272 (tm-30) REVERT: C 651 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: C 772 SER cc_start: 0.6809 (OUTLIER) cc_final: 0.6449 (p) REVERT: C 798 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6812 (m) outliers start: 72 outliers final: 33 residues processed: 230 average time/residue: 0.6570 time to fit residues: 166.5201 Evaluate side-chains 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 798 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.0870 chunk 50 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 248 HIS B 308 HIS C 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.202325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162591 restraints weight = 13941.464| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.07 r_work: 0.3491 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16638 Z= 0.120 Angle : 0.510 9.057 22605 Z= 0.273 Chirality : 0.042 0.157 2478 Planarity : 0.003 0.035 2928 Dihedral : 5.011 50.874 2411 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.40 % Allowed : 20.36 % Favored : 75.23 % 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: 1.68 (0.18), residues: 2001 helix: 2.98 (0.20), residues: 636 sheet: 1.15 (0.22), residues: 537 loop : -0.43 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 599 TYR 0.010 0.001 TYR B 282 PHE 0.016 0.001 PHE B 287 TRP 0.006 0.001 TRP C 174 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00257 (16617) covalent geometry : angle 0.50482 (22557) SS BOND : bond 0.00588 ( 15) SS BOND : angle 1.75877 ( 30) hydrogen bonds : bond 0.04713 ( 792) hydrogen bonds : angle 4.38376 ( 2484) link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 1.59699 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7691 (mtmt) REVERT: A 305 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.5605 (mt-10) REVERT: A 411 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6864 (t0) REVERT: A 416 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: A 622 GLU cc_start: 0.8721 (tt0) cc_final: 0.8421 (tm-30) REVERT: A 651 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 753 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6504 (m) REVERT: A 772 SER cc_start: 0.6804 (OUTLIER) cc_final: 0.6466 (p) REVERT: B 204 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7826 (mttt) REVERT: B 212 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8004 (mtpp) REVERT: B 305 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5519 (mt-10) REVERT: B 326 TYR cc_start: 0.8292 (m-80) cc_final: 0.8070 (m-80) REVERT: B 349 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8139 (mtmt) REVERT: B 399 LEU cc_start: 0.7682 (mm) cc_final: 0.7445 (mt) REVERT: B 411 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6819 (t0) REVERT: B 772 SER cc_start: 0.6867 (OUTLIER) cc_final: 0.6447 (p) REVERT: B 798 VAL cc_start: 0.7135 (OUTLIER) cc_final: 0.6810 (m) REVERT: C 218 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6413 (tt) REVERT: C 232 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7646 (mtt) REVERT: C 235 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8177 (mtmt) REVERT: C 305 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.5257 (mp0) REVERT: C 622 GLU cc_start: 0.8703 (tt0) cc_final: 0.8326 (tm-30) REVERT: C 651 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: C 772 SER cc_start: 0.6813 (OUTLIER) cc_final: 0.6435 (p) REVERT: C 798 VAL cc_start: 0.7139 (OUTLIER) cc_final: 0.6842 (m) outliers start: 75 outliers final: 32 residues processed: 229 average time/residue: 0.6677 time to fit residues: 168.1409 Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 798 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 153 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 248 HIS C 248 HIS C 584 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.195094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.164949 restraints weight = 13877.184| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 0.91 r_work: 0.3465 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16638 Z= 0.234 Angle : 0.679 10.108 22605 Z= 0.366 Chirality : 0.048 0.245 2478 Planarity : 0.005 0.046 2928 Dihedral : 5.782 56.112 2411 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.64 % Allowed : 20.13 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.35 (0.18), residues: 2001 helix: 2.58 (0.19), residues: 639 sheet: 1.03 (0.22), residues: 537 loop : -0.56 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 599 TYR 0.017 0.002 TYR A 702 PHE 0.026 0.002 PHE B 287 TRP 0.012 0.002 TRP C 539 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00529 (16617) covalent geometry : angle 0.66885 (22557) SS BOND : bond 0.01294 ( 15) SS BOND : angle 2.90792 ( 30) hydrogen bonds : bond 0.06295 ( 792) hydrogen bonds : angle 4.73327 ( 2484) link_NAG-ASN : bond 0.00115 ( 6) link_NAG-ASN : angle 2.15333 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 178 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7691 (mtmt) REVERT: A 305 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.5667 (mt-10) REVERT: A 362 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7175 (m) REVERT: A 411 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7242 (t0) REVERT: A 416 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: A 622 GLU cc_start: 0.8674 (tt0) cc_final: 0.8349 (tm-30) REVERT: A 651 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 753 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6617 (m) REVERT: A 772 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6637 (p) REVERT: A 798 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.7001 (m) REVERT: B 204 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7840 (mttt) REVERT: B 212 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7984 (mtpp) REVERT: B 305 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.5360 (mt-10) REVERT: B 349 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8177 (mtmt) REVERT: B 753 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.6984 (p) REVERT: B 772 SER cc_start: 0.7052 (OUTLIER) cc_final: 0.6637 (p) REVERT: B 798 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6989 (m) REVERT: C 218 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6494 (tt) REVERT: C 232 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: C 235 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8262 (mtmt) REVERT: C 305 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.5283 (mp0) REVERT: C 651 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: C 753 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.7117 (p) REVERT: C 772 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6634 (p) REVERT: C 798 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7110 (m) outliers start: 79 outliers final: 37 residues processed: 246 average time/residue: 0.6644 time to fit residues: 179.5926 Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 675 ILE Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 798 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.198506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166706 restraints weight = 13974.018| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 0.88 r_work: 0.3513 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16638 Z= 0.115 Angle : 0.519 8.051 22605 Z= 0.277 Chirality : 0.042 0.137 2478 Planarity : 0.003 0.036 2928 Dihedral : 5.184 53.408 2411 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.05 % Allowed : 21.89 % Favored : 75.06 % 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: 1.58 (0.18), residues: 2001 helix: 2.93 (0.20), residues: 633 sheet: 1.10 (0.22), residues: 537 loop : -0.52 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.011 0.001 TYR B 282 PHE 0.016 0.001 PHE B 287 TRP 0.007 0.001 TRP A 354 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00246 (16617) covalent geometry : angle 0.51193 (22557) SS BOND : bond 0.00514 ( 15) SS BOND : angle 2.14225 ( 30) hydrogen bonds : bond 0.04688 ( 792) hydrogen bonds : angle 4.42093 ( 2484) link_NAG-ASN : bond 0.00334 ( 6) link_NAG-ASN : angle 1.60391 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7619 (mtmt) REVERT: A 305 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.5650 (mt-10) REVERT: A 349 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8073 (mtmt) REVERT: A 399 LEU cc_start: 0.7848 (mm) cc_final: 0.7605 (mt) REVERT: A 411 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7063 (t0) REVERT: A 416 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6541 (m-30) REVERT: A 622 GLU cc_start: 0.8705 (tt0) cc_final: 0.8382 (tm-30) REVERT: A 651 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: A 772 SER cc_start: 0.6804 (OUTLIER) cc_final: 0.6475 (p) REVERT: B 204 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7812 (mttt) REVERT: B 212 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7905 (mttt) REVERT: B 305 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5505 (mt-10) REVERT: B 399 LEU cc_start: 0.7676 (mm) cc_final: 0.7473 (mt) REVERT: B 772 SER cc_start: 0.6869 (OUTLIER) cc_final: 0.6464 (p) REVERT: C 218 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6435 (tt) REVERT: C 232 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7584 (mtt) REVERT: C 233 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 235 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8121 (mtmt) REVERT: C 305 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.5276 (mp0) REVERT: C 622 GLU cc_start: 0.8664 (tt0) cc_final: 0.8287 (tm-30) REVERT: C 651 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: C 772 SER cc_start: 0.6824 (OUTLIER) cc_final: 0.6487 (p) outliers start: 52 outliers final: 25 residues processed: 213 average time/residue: 0.7168 time to fit residues: 167.2083 Evaluate side-chains 210 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 796 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 82 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 112 ASN B 248 HIS C 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.195469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163338 restraints weight = 13884.677| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 0.87 r_work: 0.3470 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16638 Z= 0.201 Angle : 0.638 9.943 22605 Z= 0.342 Chirality : 0.046 0.216 2478 Planarity : 0.005 0.043 2928 Dihedral : 5.625 56.924 2411 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.87 % Allowed : 21.19 % Favored : 74.94 % 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: 1.37 (0.18), residues: 2001 helix: 2.68 (0.19), residues: 633 sheet: 1.05 (0.22), residues: 537 loop : -0.62 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 599 TYR 0.014 0.002 TYR C 702 PHE 0.023 0.002 PHE B 287 TRP 0.011 0.002 TRP C 539 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00452 (16617) covalent geometry : angle 0.62964 (22557) SS BOND : bond 0.01070 ( 15) SS BOND : angle 2.57884 ( 30) hydrogen bonds : bond 0.05883 ( 792) hydrogen bonds : angle 4.64331 ( 2484) link_NAG-ASN : bond 0.00137 ( 6) link_NAG-ASN : angle 2.00777 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7963 (mttt) REVERT: A 235 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7656 (mtmt) REVERT: A 305 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5667 (mt-10) REVERT: A 349 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8116 (mtmt) REVERT: A 416 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: A 622 GLU cc_start: 0.8640 (tt0) cc_final: 0.8315 (tm-30) REVERT: A 651 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 772 SER cc_start: 0.6891 (OUTLIER) cc_final: 0.6573 (p) REVERT: B 204 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7834 (mttt) REVERT: B 212 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7945 (mttt) REVERT: B 305 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.5516 (mt-10) REVERT: B 349 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8145 (mtmt) REVERT: B 772 SER cc_start: 0.7014 (OUTLIER) cc_final: 0.6629 (p) REVERT: B 798 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6939 (m) REVERT: C 218 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6564 (tt) REVERT: C 232 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: C 235 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8185 (mtmt) REVERT: C 305 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: C 651 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: C 772 SER cc_start: 0.6878 (OUTLIER) cc_final: 0.6560 (p) REVERT: C 798 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7057 (m) outliers start: 66 outliers final: 36 residues processed: 225 average time/residue: 0.6796 time to fit residues: 168.0768 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 675 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 143 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.197016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.167195 restraints weight = 13905.184| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 0.87 r_work: 0.3506 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16638 Z= 0.143 Angle : 0.566 9.777 22605 Z= 0.301 Chirality : 0.043 0.176 2478 Planarity : 0.004 0.037 2928 Dihedral : 5.363 56.022 2411 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.35 % Allowed : 21.83 % Favored : 74.82 % 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: 1.47 (0.18), residues: 2001 helix: 2.80 (0.20), residues: 633 sheet: 1.08 (0.22), residues: 537 loop : -0.57 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.011 0.001 TYR B 282 PHE 0.019 0.002 PHE B 287 TRP 0.006 0.001 TRP B 174 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00313 (16617) covalent geometry : angle 0.55858 (22557) SS BOND : bond 0.00743 ( 15) SS BOND : angle 2.17558 ( 30) hydrogen bonds : bond 0.05139 ( 792) hydrogen bonds : angle 4.50011 ( 2484) link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 1.74193 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7940 (mttt) REVERT: A 235 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7637 (mtmt) REVERT: A 305 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.5635 (mt-10) REVERT: A 349 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8107 (mtmt) REVERT: A 399 LEU cc_start: 0.7841 (mm) cc_final: 0.7613 (mt) REVERT: A 416 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: A 622 GLU cc_start: 0.8659 (tt0) cc_final: 0.8339 (tm-30) REVERT: A 651 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 772 SER cc_start: 0.6774 (OUTLIER) cc_final: 0.6456 (p) REVERT: B 204 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7844 (mttt) REVERT: B 212 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7930 (mttt) REVERT: B 305 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5512 (mt-10) REVERT: B 349 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8141 (mtmt) REVERT: B 399 LEU cc_start: 0.7755 (mm) cc_final: 0.7539 (mt) REVERT: B 772 SER cc_start: 0.6954 (OUTLIER) cc_final: 0.6533 (p) REVERT: B 798 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6807 (m) REVERT: C 218 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6470 (tt) REVERT: C 232 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7603 (mtt) REVERT: C 233 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 235 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: C 305 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5300 (mp0) REVERT: C 399 LEU cc_start: 0.7849 (mm) cc_final: 0.7642 (mt) REVERT: C 651 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: C 772 SER cc_start: 0.6770 (OUTLIER) cc_final: 0.6428 (p) outliers start: 57 outliers final: 33 residues processed: 212 average time/residue: 0.7324 time to fit residues: 169.5276 Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 675 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 796 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.195208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165162 restraints weight = 13867.233| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 0.89 r_work: 0.3475 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16638 Z= 0.205 Angle : 0.652 10.754 22605 Z= 0.348 Chirality : 0.047 0.222 2478 Planarity : 0.005 0.039 2928 Dihedral : 5.681 58.511 2411 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.58 % Allowed : 21.65 % Favored : 74.77 % 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: 1.33 (0.18), residues: 2001 helix: 2.56 (0.20), residues: 639 sheet: 0.98 (0.21), residues: 561 loop : -0.60 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 599 TYR 0.014 0.002 TYR C 702 PHE 0.024 0.002 PHE B 287 TRP 0.010 0.002 TRP C 539 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00463 (16617) covalent geometry : angle 0.64294 (22557) SS BOND : bond 0.01117 ( 15) SS BOND : angle 2.56446 ( 30) hydrogen bonds : bond 0.05954 ( 792) hydrogen bonds : angle 4.66556 ( 2484) link_NAG-ASN : bond 0.00133 ( 6) link_NAG-ASN : angle 2.05350 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8154.10 seconds wall clock time: 138 minutes 53.71 seconds (8333.71 seconds total)