Starting phenix.real_space_refine on Sun May 3 09:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egg_47988/05_2026/9egg_47988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egg_47988/05_2026/9egg_47988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9egg_47988/05_2026/9egg_47988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egg_47988/05_2026/9egg_47988.map" model { file = "/net/cci-nas-00/data/ceres_data/9egg_47988/05_2026/9egg_47988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egg_47988/05_2026/9egg_47988.cif" } resolution = 2.65 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= 0.001 sd= 0.042 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 60 5.16 5 C 7467 2.51 5 N 2058 2.21 5 O 2247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3916 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 463} Chain breaks: 5 Chain: "B" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3916 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 463} Chain breaks: 5 Chain: "C" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3916 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 463} Chain breaks: 5 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: 3.25, per 1000 atoms: 0.27 Number of scatterers: 11832 At special positions: 0 Unit cell: (124.74, 124.08, 95.7, 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 60 16.00 O 2247 8.00 N 2058 7.00 C 7467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 430 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 430 " " NAG C1001 " - " ASN C 141 " " NAG C1002 " - " ASN C 430 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 616.4 milliseconds 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 28 sheets defined 22.4% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.648A pdb=" N ASP A 226 " --> pdb=" O PHE A 223 " (cutoff:3.500A) 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 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.543A pdb=" N ARG A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.938A pdb=" N HIS A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.876A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) 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 'B' and resid 193 through 201 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 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.518A pdb=" N THR B 393 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.530A pdb=" N ARG B 406 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.986A pdb=" N HIS B 516 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 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 662 through 667 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.664A pdb=" N ASP C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) 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 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.515A pdb=" N ARG C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.907A pdb=" N HIS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 543 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 663 through 667 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.288A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 125 removed outlier: 4.465A pdb=" N THR A 123 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 5.585A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER A 378 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 141 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 13.963A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.109A 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: 5.585A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER A 378 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 141 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 13.963A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.049A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.533A 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 207 Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 642 removed outlier: 3.754A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.310A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 125 removed outlier: 4.462A pdb=" N THR B 123 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.689A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B 373 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLY B 145 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 375 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 143 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG B 377 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN B 141 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 13.974A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.689A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B 373 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLY B 145 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 375 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 143 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG B 377 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN B 141 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 13.974A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AB6, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.076A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AB9, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC1, first strand: chain 'B' and resid 638 through 642 removed outlier: 3.827A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.307A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 123 through 125 removed outlier: 4.497A pdb=" N THR C 123 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 395 through 398 removed outlier: 5.627A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 374 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 145 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 376 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR C 143 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER C 378 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN C 141 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 13.974A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 395 through 398 removed outlier: 5.627A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 374 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 145 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 376 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR C 143 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER C 378 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN C 141 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 13.974A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 189 through 191 Processing sheet with id=AC7, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.051A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AC9, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD1, first strand: chain 'C' and resid 638 through 642 removed outlier: 3.723A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1479 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: 2.31 Time building geometry restraints manager: 1.25 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: 3886 1.34 - 1.46: 2368 1.46 - 1.57: 5776 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12120 Sorted by residual: bond pdb=" N VAL C 667 " pdb=" CA VAL C 667 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.14e-02 7.69e+03 1.27e+01 bond pdb=" N VAL B 667 " pdb=" CA VAL B 667 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.69e+00 bond pdb=" N ILE B 664 " pdb=" CA ILE B 664 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 7.95e+00 bond pdb=" N ILE C 664 " pdb=" CA ILE C 664 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.85e+00 bond pdb=" N TYR A 655 " pdb=" CA TYR A 655 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.69e+00 ... (remaining 12115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 15560 1.13 - 2.27: 688 2.27 - 3.40: 176 3.40 - 4.54: 29 4.54 - 5.67: 11 Bond angle restraints: 16464 Sorted by residual: angle pdb=" N ARG C 505 " pdb=" CA ARG C 505 " pdb=" C ARG C 505 " ideal model delta sigma weight residual 114.04 108.37 5.67 1.24e+00 6.50e-01 2.09e+01 angle pdb=" N ARG C 661 " pdb=" CA ARG C 661 " pdb=" C ARG C 661 " ideal model delta sigma weight residual 113.02 108.37 4.65 1.20e+00 6.94e-01 1.50e+01 angle pdb=" N ALA C 662 " pdb=" CA ALA C 662 " pdb=" C ALA C 662 " ideal model delta sigma weight residual 113.97 109.42 4.55 1.28e+00 6.10e-01 1.27e+01 angle pdb=" CA GLU B 652 " pdb=" C GLU B 652 " pdb=" O GLU B 652 " ideal model delta sigma weight residual 121.65 117.84 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" CA GLU A 652 " pdb=" C GLU A 652 " pdb=" O GLU A 652 " ideal model delta sigma weight residual 121.65 117.85 3.80 1.17e+00 7.31e-01 1.06e+01 ... (remaining 16459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6298 17.70 - 35.40: 696 35.40 - 53.10: 216 53.10 - 70.80: 53 70.80 - 88.50: 15 Dihedral angle restraints: 7278 sinusoidal: 2976 harmonic: 4302 Sorted by residual: dihedral pdb=" CA GLY A 644 " pdb=" C GLY A 644 " pdb=" N GLY A 645 " pdb=" CA GLY A 645 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLY C 644 " pdb=" C GLY C 644 " pdb=" N GLY C 645 " pdb=" CA GLY C 645 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLY B 644 " pdb=" C GLY B 644 " pdb=" N GLY B 645 " pdb=" CA GLY B 645 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1297 0.045 - 0.089: 385 0.089 - 0.134: 101 0.134 - 0.178: 13 0.178 - 0.223: 4 Chirality restraints: 1800 Sorted by residual: chirality pdb=" C1 NAG A1002 " pdb=" ND2 ASN A 430 " pdb=" C2 NAG A1002 " pdb=" O5 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1 NAG C1002 " pdb=" ND2 ASN C 430 " pdb=" C2 NAG C1002 " pdb=" O5 NAG C1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1797 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 661 " 0.210 9.50e-02 1.11e+02 9.42e-02 5.45e+00 pdb=" NE ARG C 661 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 661 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 661 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 661 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 347 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.87e+00 pdb=" N PRO B 348 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 348 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 348 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 347 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 348 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " 0.031 5.00e-02 4.00e+02 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2569 2.79 - 3.31: 9485 3.31 - 3.84: 19142 3.84 - 4.37: 23939 4.37 - 4.90: 41438 Nonbonded interactions: 96573 Sorted by model distance: nonbonded pdb=" O LEU B 536 " pdb=" ND2 ASN B 540 " model vdw 2.258 3.120 nonbonded pdb=" NH2 ARG A 304 " pdb=" OD2 ASP A 323 " model vdw 2.272 3.120 nonbonded pdb=" OH TYR C 649 " pdb=" OE2 GLU C 651 " model vdw 2.276 3.040 nonbonded pdb=" NZ LYS C 160 " pdb=" OD1 ASP C 277 " model vdw 2.278 3.120 nonbonded pdb=" O LEU C 536 " pdb=" ND2 ASN C 540 " model vdw 2.287 3.120 ... (remaining 96568 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: 14.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.004 0.041 12132 Z= 0.222 Angle : 0.598 5.672 16494 Z= 0.348 Chirality : 0.045 0.223 1800 Planarity : 0.005 0.094 2139 Dihedral : 17.077 88.503 4494 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.67 % Allowed : 20.10 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1431 helix: 0.74 (0.33), residues: 252 sheet: 1.17 (0.25), residues: 393 loop : -0.70 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 406 TYR 0.013 0.001 TYR C 296 PHE 0.015 0.002 PHE C 194 TRP 0.012 0.001 TRP C 354 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00441 (12120) covalent geometry : angle 0.59399 (16464) SS BOND : bond 0.00268 ( 6) SS BOND : angle 1.01397 ( 12) hydrogen bonds : bond 0.16893 ( 466) hydrogen bonds : angle 7.14308 ( 1479) link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 1.97274 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6782 (ttm110) REVERT: A 212 LYS cc_start: 0.7467 (mtpt) cc_final: 0.6834 (mttp) REVERT: A 286 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: B 128 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: B 212 LYS cc_start: 0.7557 (mtpt) cc_final: 0.6858 (mttp) REVERT: B 367 THR cc_start: 0.8854 (p) cc_final: 0.8485 (m) REVERT: B 505 ARG cc_start: 0.6799 (pmt170) cc_final: 0.6572 (pmt-80) REVERT: B 651 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6863 (mt-10) REVERT: B 663 ASP cc_start: 0.6660 (m-30) cc_final: 0.6452 (m-30) REVERT: C 107 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: C 212 LYS cc_start: 0.7480 (mtpt) cc_final: 0.6847 (mttp) REVERT: C 367 THR cc_start: 0.8875 (p) cc_final: 0.8544 (m) REVERT: C 609 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6781 (pp30) outliers start: 46 outliers final: 31 residues processed: 194 average time/residue: 0.6572 time to fit residues: 137.1120 Evaluate side-chains 190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 248 HIS A 445 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN C 511 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118897 restraints weight = 13430.629| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.89 r_work: 0.3277 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12132 Z= 0.178 Angle : 0.553 4.971 16494 Z= 0.298 Chirality : 0.045 0.213 1800 Planarity : 0.005 0.057 2139 Dihedral : 8.652 79.562 1833 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 6.30 % Allowed : 17.86 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1431 helix: 0.55 (0.31), residues: 258 sheet: 1.34 (0.25), residues: 384 loop : -0.86 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.012 0.001 TYR C 296 PHE 0.015 0.002 PHE A 287 TRP 0.014 0.001 TRP C 354 HIS 0.003 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00427 (12120) covalent geometry : angle 0.54901 (16464) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.06063 ( 12) hydrogen bonds : bond 0.04562 ( 466) hydrogen bonds : angle 5.15972 ( 1479) link_NAG-ASN : bond 0.00416 ( 6) link_NAG-ASN : angle 1.95383 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: A 136 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.7032 (ttm110) REVERT: A 158 LYS cc_start: 0.8906 (mttm) cc_final: 0.8652 (mtpp) REVERT: A 212 LYS cc_start: 0.7561 (mtpt) cc_final: 0.6970 (mttp) REVERT: A 584 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6604 (mm-40) REVERT: A 609 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6946 (pp30) REVERT: B 107 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: B 128 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: B 136 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7832 (mtm-85) REVERT: B 158 LYS cc_start: 0.8869 (mttm) cc_final: 0.8624 (mtpp) REVERT: B 505 ARG cc_start: 0.6968 (pmt170) cc_final: 0.6766 (pmt-80) REVERT: B 541 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: B 619 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: B 663 ASP cc_start: 0.7287 (m-30) cc_final: 0.6825 (m-30) REVERT: B 666 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6532 (p) REVERT: C 212 LYS cc_start: 0.7574 (mtpt) cc_final: 0.6974 (mttp) REVERT: C 367 THR cc_start: 0.8952 (p) cc_final: 0.8613 (m) REVERT: C 582 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8115 (mp) REVERT: C 663 ASP cc_start: 0.7394 (m-30) cc_final: 0.7137 (m-30) outliers start: 79 outliers final: 44 residues processed: 217 average time/residue: 0.6404 time to fit residues: 149.5263 Evaluate side-chains 208 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 540 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 512 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113221 restraints weight = 13018.718| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.09 r_work: 0.3116 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12132 Z= 0.125 Angle : 0.492 4.512 16494 Z= 0.266 Chirality : 0.043 0.198 1800 Planarity : 0.004 0.056 2139 Dihedral : 7.898 71.581 1813 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.34 % Allowed : 19.38 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1431 helix: 0.71 (0.31), residues: 258 sheet: 1.19 (0.25), residues: 414 loop : -0.87 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.009 0.001 TYR A 296 PHE 0.014 0.001 PHE C 287 TRP 0.012 0.001 TRP B 354 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00290 (12120) covalent geometry : angle 0.48904 (16464) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.94182 ( 12) hydrogen bonds : bond 0.03885 ( 466) hydrogen bonds : angle 4.82823 ( 1479) link_NAG-ASN : bond 0.00366 ( 6) link_NAG-ASN : angle 1.69031 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: A 136 ARG cc_start: 0.7435 (ttp-110) cc_final: 0.6939 (ttm110) REVERT: A 158 LYS cc_start: 0.8962 (mttm) cc_final: 0.8713 (mtpp) REVERT: A 212 LYS cc_start: 0.7589 (mtpt) cc_final: 0.6962 (mttm) REVERT: A 232 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6834 (mtm) REVERT: A 609 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6912 (pp30) REVERT: B 107 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: B 158 LYS cc_start: 0.8916 (mttm) cc_final: 0.8671 (mtpp) REVERT: B 232 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6834 (mtm) REVERT: B 541 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: B 619 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: B 663 ASP cc_start: 0.7196 (m-30) cc_final: 0.6857 (m-30) REVERT: B 666 THR cc_start: 0.6662 (OUTLIER) cc_final: 0.6453 (p) REVERT: C 212 LYS cc_start: 0.7596 (mtpt) cc_final: 0.6962 (mttp) REVERT: C 235 LYS cc_start: 0.7017 (mtmt) cc_final: 0.5903 (mmtm) REVERT: C 304 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6082 (ptt90) REVERT: C 367 THR cc_start: 0.8959 (p) cc_final: 0.8621 (m) REVERT: C 663 ASP cc_start: 0.7257 (m-30) cc_final: 0.6716 (m-30) outliers start: 67 outliers final: 38 residues processed: 211 average time/residue: 0.7056 time to fit residues: 159.3905 Evaluate side-chains 207 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111261 restraints weight = 13033.566| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.09 r_work: 0.3091 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12132 Z= 0.181 Angle : 0.547 4.896 16494 Z= 0.292 Chirality : 0.045 0.220 1800 Planarity : 0.004 0.058 2139 Dihedral : 7.631 56.921 1803 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.90 % Allowed : 18.98 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1431 helix: 0.59 (0.32), residues: 258 sheet: 1.31 (0.25), residues: 384 loop : -0.95 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 406 TYR 0.012 0.001 TYR A 296 PHE 0.016 0.002 PHE C 287 TRP 0.014 0.001 TRP C 354 HIS 0.003 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00439 (12120) covalent geometry : angle 0.54240 (16464) SS BOND : bond 0.00344 ( 6) SS BOND : angle 1.12880 ( 12) hydrogen bonds : bond 0.04338 ( 466) hydrogen bonds : angle 4.93778 ( 1479) link_NAG-ASN : bond 0.00412 ( 6) link_NAG-ASN : angle 2.05072 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 164 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: A 128 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: A 136 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.6976 (ttm110) REVERT: A 158 LYS cc_start: 0.8961 (mttm) cc_final: 0.8698 (mtpp) REVERT: A 212 LYS cc_start: 0.7571 (mtpt) cc_final: 0.6957 (mttp) REVERT: A 232 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6832 (mtm) REVERT: A 445 ASN cc_start: 0.8038 (m110) cc_final: 0.7611 (p0) REVERT: A 609 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6857 (pp30) REVERT: B 107 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: B 128 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: B 158 LYS cc_start: 0.8925 (mttm) cc_final: 0.8664 (mtpp) REVERT: B 232 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6879 (mtm) REVERT: B 505 ARG cc_start: 0.6988 (pmt-80) cc_final: 0.6453 (pmt-80) REVERT: B 541 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: B 619 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: B 663 ASP cc_start: 0.7286 (m-30) cc_final: 0.6851 (m-30) REVERT: B 666 THR cc_start: 0.6713 (OUTLIER) cc_final: 0.6488 (p) REVERT: C 107 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: C 128 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7425 (mm-30) REVERT: C 212 LYS cc_start: 0.7592 (mtpt) cc_final: 0.6958 (mttp) REVERT: C 304 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6059 (ptt90) REVERT: C 367 THR cc_start: 0.8920 (p) cc_final: 0.8582 (m) REVERT: C 663 ASP cc_start: 0.7358 (m-30) cc_final: 0.7056 (m-30) outliers start: 74 outliers final: 49 residues processed: 215 average time/residue: 0.6339 time to fit residues: 146.7422 Evaluate side-chains 220 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 512 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108913 restraints weight = 12898.500| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.14 r_work: 0.3052 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 12132 Z= 0.336 Angle : 0.690 7.025 16494 Z= 0.366 Chirality : 0.052 0.253 1800 Planarity : 0.006 0.063 2139 Dihedral : 8.270 58.823 1803 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.62 % Allowed : 19.38 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1431 helix: 0.19 (0.31), residues: 255 sheet: 1.00 (0.25), residues: 384 loop : -1.05 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 558 TYR 0.018 0.003 TYR A 296 PHE 0.020 0.002 PHE C 287 TRP 0.018 0.003 TRP C 354 HIS 0.005 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00830 (12120) covalent geometry : angle 0.68460 (16464) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.64633 ( 12) hydrogen bonds : bond 0.05456 ( 466) hydrogen bonds : angle 5.24992 ( 1479) link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 2.53179 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 165 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: A 128 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: A 136 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7109 (ttm110) REVERT: A 158 LYS cc_start: 0.8977 (mttm) cc_final: 0.8688 (mtpp) REVERT: A 212 LYS cc_start: 0.7506 (mtpt) cc_final: 0.6893 (mttp) REVERT: A 232 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.7020 (mtm) REVERT: A 584 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6723 (mm-40) REVERT: A 638 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6868 (ttp-170) REVERT: B 104 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7373 (mm) REVERT: B 107 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6958 (mt-10) REVERT: B 128 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: B 158 LYS cc_start: 0.8951 (mttm) cc_final: 0.8670 (mtpp) REVERT: B 304 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5922 (ptt90) REVERT: B 505 ARG cc_start: 0.7091 (pmt-80) cc_final: 0.6620 (pmt-80) REVERT: B 619 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: B 663 ASP cc_start: 0.7492 (m-30) cc_final: 0.7090 (m-30) REVERT: B 666 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6538 (p) REVERT: C 107 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: C 212 LYS cc_start: 0.7569 (mtpt) cc_final: 0.6939 (mttp) REVERT: C 304 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.5993 (ptt90) REVERT: C 663 ASP cc_start: 0.7406 (m-30) cc_final: 0.7104 (m-30) outliers start: 83 outliers final: 53 residues processed: 222 average time/residue: 0.6469 time to fit residues: 154.6869 Evaluate side-chains 226 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 112 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN C 112 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112059 restraints weight = 12939.725| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.11 r_work: 0.3101 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12132 Z= 0.123 Angle : 0.504 4.638 16494 Z= 0.273 Chirality : 0.043 0.223 1800 Planarity : 0.004 0.059 2139 Dihedral : 7.619 56.733 1803 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.78 % Allowed : 21.69 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1431 helix: 0.59 (0.32), residues: 255 sheet: 0.98 (0.25), residues: 414 loop : -1.01 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 406 TYR 0.009 0.001 TYR A 296 PHE 0.014 0.001 PHE C 287 TRP 0.015 0.001 TRP C 354 HIS 0.005 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00285 (12120) covalent geometry : angle 0.49962 (16464) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.03068 ( 12) hydrogen bonds : bond 0.03820 ( 466) hydrogen bonds : angle 4.80513 ( 1479) link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 2.01779 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: A 128 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: A 136 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7027 (ttm110) REVERT: A 158 LYS cc_start: 0.8980 (mttm) cc_final: 0.8715 (mtpp) REVERT: A 212 LYS cc_start: 0.7584 (mtpt) cc_final: 0.6976 (mttp) REVERT: A 445 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7591 (p0) REVERT: A 609 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6837 (pp30) REVERT: B 107 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: B 128 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: B 158 LYS cc_start: 0.8932 (mttm) cc_final: 0.8672 (mtpp) REVERT: B 505 ARG cc_start: 0.6913 (pmt-80) cc_final: 0.6638 (pmt-80) REVERT: B 609 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6818 (pp30) REVERT: B 619 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: B 663 ASP cc_start: 0.7330 (m-30) cc_final: 0.6917 (m-30) REVERT: B 666 THR cc_start: 0.6654 (OUTLIER) cc_final: 0.6383 (p) REVERT: C 107 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: C 212 LYS cc_start: 0.7613 (mtpt) cc_final: 0.6985 (mttp) REVERT: C 235 LYS cc_start: 0.7042 (mtmt) cc_final: 0.5911 (mmtm) REVERT: C 304 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6097 (ptt90) REVERT: C 367 THR cc_start: 0.8942 (p) cc_final: 0.8603 (m) REVERT: C 663 ASP cc_start: 0.7292 (m-30) cc_final: 0.6848 (m-30) outliers start: 60 outliers final: 39 residues processed: 203 average time/residue: 0.6769 time to fit residues: 147.3077 Evaluate side-chains 208 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 512 HIS A 540 ASN B 112 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN C 112 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113200 restraints weight = 12798.454| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.09 r_work: 0.3119 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12132 Z= 0.112 Angle : 0.489 4.573 16494 Z= 0.263 Chirality : 0.042 0.225 1800 Planarity : 0.004 0.057 2139 Dihedral : 7.323 57.123 1803 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.94 % Allowed : 21.77 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1431 helix: 0.71 (0.32), residues: 258 sheet: 1.09 (0.25), residues: 414 loop : -0.98 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 406 TYR 0.008 0.001 TYR A 296 PHE 0.013 0.001 PHE A 287 TRP 0.013 0.001 TRP B 354 HIS 0.006 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00258 (12120) covalent geometry : angle 0.48381 (16464) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.93076 ( 12) hydrogen bonds : bond 0.03596 ( 466) hydrogen bonds : angle 4.64899 ( 1479) link_NAG-ASN : bond 0.00442 ( 6) link_NAG-ASN : angle 2.04238 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: A 128 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: A 136 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.6966 (ttm110) REVERT: A 158 LYS cc_start: 0.8962 (mttm) cc_final: 0.8709 (mtpp) REVERT: A 212 LYS cc_start: 0.7597 (mtpt) cc_final: 0.6992 (mttp) REVERT: A 232 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6839 (mtm) REVERT: A 445 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 107 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: B 128 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: B 158 LYS cc_start: 0.8922 (mttm) cc_final: 0.8682 (mtpp) REVERT: B 505 ARG cc_start: 0.6872 (pmt-80) cc_final: 0.6595 (pmt-80) REVERT: B 609 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6781 (pp30) REVERT: B 619 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: B 663 ASP cc_start: 0.7262 (m-30) cc_final: 0.6951 (m-30) REVERT: B 666 THR cc_start: 0.6618 (OUTLIER) cc_final: 0.6325 (p) REVERT: C 107 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: C 212 LYS cc_start: 0.7612 (mtpt) cc_final: 0.6985 (mttp) REVERT: C 235 LYS cc_start: 0.7025 (mtmt) cc_final: 0.5906 (mmtm) REVERT: C 304 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6081 (ptt90) REVERT: C 367 THR cc_start: 0.8936 (p) cc_final: 0.8591 (m) REVERT: C 663 ASP cc_start: 0.7260 (m-30) cc_final: 0.6986 (m-30) outliers start: 62 outliers final: 39 residues processed: 205 average time/residue: 0.6892 time to fit residues: 151.5842 Evaluate side-chains 212 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 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 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 112 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111468 restraints weight = 12794.816| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.09 r_work: 0.3094 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12132 Z= 0.162 Angle : 0.534 4.813 16494 Z= 0.285 Chirality : 0.044 0.217 1800 Planarity : 0.004 0.058 2139 Dihedral : 7.446 55.909 1803 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.34 % Allowed : 21.37 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1431 helix: 0.61 (0.32), residues: 258 sheet: 1.03 (0.25), residues: 414 loop : -0.98 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 406 TYR 0.012 0.001 TYR A 640 PHE 0.015 0.002 PHE C 287 TRP 0.013 0.001 TRP B 354 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00389 (12120) covalent geometry : angle 0.52856 (16464) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.07193 ( 12) hydrogen bonds : bond 0.04077 ( 466) hydrogen bonds : angle 4.78621 ( 1479) link_NAG-ASN : bond 0.00332 ( 6) link_NAG-ASN : angle 2.22612 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: A 128 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: A 136 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6982 (ttm110) REVERT: A 158 LYS cc_start: 0.8969 (mttm) cc_final: 0.8704 (mtpp) REVERT: A 212 LYS cc_start: 0.7591 (mtpt) cc_final: 0.6982 (mttp) REVERT: A 232 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6894 (mtm) REVERT: A 445 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7604 (p0) REVERT: B 107 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: B 128 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: B 158 LYS cc_start: 0.8930 (mttm) cc_final: 0.8664 (mtpp) REVERT: B 505 ARG cc_start: 0.6893 (pmt-80) cc_final: 0.6388 (pmt-80) REVERT: B 609 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6806 (pp30) REVERT: B 619 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: B 663 ASP cc_start: 0.7277 (m-30) cc_final: 0.6859 (m-30) REVERT: B 666 THR cc_start: 0.6623 (OUTLIER) cc_final: 0.6312 (p) REVERT: C 107 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: C 128 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7450 (mm-30) REVERT: C 212 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7010 (mttp) REVERT: C 235 LYS cc_start: 0.7019 (mtmt) cc_final: 0.5895 (mmtm) REVERT: C 304 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6075 (ptt90) REVERT: C 663 ASP cc_start: 0.7228 (m-30) cc_final: 0.6924 (m-30) outliers start: 67 outliers final: 43 residues processed: 206 average time/residue: 0.6427 time to fit residues: 142.3620 Evaluate side-chains 216 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 118 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 512 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112765 restraints weight = 12788.875| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.09 r_work: 0.3111 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12132 Z= 0.124 Angle : 0.505 6.842 16494 Z= 0.270 Chirality : 0.043 0.228 1800 Planarity : 0.004 0.057 2139 Dihedral : 7.249 57.267 1803 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.86 % Allowed : 21.77 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1431 helix: 0.71 (0.32), residues: 258 sheet: 1.07 (0.25), residues: 414 loop : -0.94 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 406 TYR 0.013 0.001 TYR A 640 PHE 0.014 0.001 PHE C 287 TRP 0.014 0.001 TRP B 354 HIS 0.006 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00288 (12120) covalent geometry : angle 0.49902 (16464) SS BOND : bond 0.00300 ( 6) SS BOND : angle 0.96482 ( 12) hydrogen bonds : bond 0.03693 ( 466) hydrogen bonds : angle 4.66590 ( 1479) link_NAG-ASN : bond 0.00386 ( 6) link_NAG-ASN : angle 2.30619 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: A 128 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: A 136 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.6977 (ttm110) REVERT: A 158 LYS cc_start: 0.8966 (mttm) cc_final: 0.8706 (mtpp) REVERT: A 212 LYS cc_start: 0.7560 (mtpt) cc_final: 0.6949 (mttp) REVERT: A 232 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6866 (mtm) REVERT: A 374 GLU cc_start: 0.8735 (tt0) cc_final: 0.7819 (tp30) REVERT: A 445 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7667 (p0) REVERT: A 609 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6845 (pp30) REVERT: B 107 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: B 128 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: B 158 LYS cc_start: 0.8925 (mttm) cc_final: 0.8677 (mtpp) REVERT: B 232 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6951 (mtm) REVERT: B 609 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6800 (pp30) REVERT: B 619 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 663 ASP cc_start: 0.7218 (m-30) cc_final: 0.6810 (m-30) REVERT: B 666 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6262 (p) REVERT: C 107 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: C 212 LYS cc_start: 0.7603 (mtpt) cc_final: 0.6978 (mttp) REVERT: C 235 LYS cc_start: 0.7015 (mtmt) cc_final: 0.5883 (mmtm) REVERT: C 304 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6070 (ptt90) REVERT: C 367 THR cc_start: 0.8913 (p) cc_final: 0.8559 (m) REVERT: C 663 ASP cc_start: 0.7257 (m-30) cc_final: 0.6982 (m-30) outliers start: 61 outliers final: 40 residues processed: 202 average time/residue: 0.6803 time to fit residues: 147.2073 Evaluate side-chains 213 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112940 restraints weight = 12971.444| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.10 r_work: 0.3114 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12132 Z= 0.120 Angle : 0.500 5.286 16494 Z= 0.268 Chirality : 0.042 0.200 1800 Planarity : 0.004 0.057 2139 Dihedral : 7.195 56.861 1803 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.70 % Allowed : 21.93 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1431 helix: 0.75 (0.32), residues: 258 sheet: 1.08 (0.25), residues: 414 loop : -0.93 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 406 TYR 0.012 0.001 TYR A 640 PHE 0.013 0.001 PHE C 287 TRP 0.013 0.001 TRP B 354 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00279 (12120) covalent geometry : angle 0.49645 (16464) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.95058 ( 12) hydrogen bonds : bond 0.03646 ( 466) hydrogen bonds : angle 4.63572 ( 1479) link_NAG-ASN : bond 0.00355 ( 6) link_NAG-ASN : angle 1.62963 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: A 128 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: A 136 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.6959 (ttm110) REVERT: A 158 LYS cc_start: 0.8965 (mttm) cc_final: 0.8704 (mtpp) REVERT: A 212 LYS cc_start: 0.7571 (mtpt) cc_final: 0.6962 (mttp) REVERT: A 232 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6873 (mtm) REVERT: A 374 GLU cc_start: 0.8728 (tt0) cc_final: 0.7801 (tp30) REVERT: A 445 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7607 (p0) REVERT: A 609 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6844 (pp30) REVERT: B 107 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: B 128 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: B 158 LYS cc_start: 0.8924 (mttm) cc_final: 0.8673 (mtpp) REVERT: B 232 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6936 (mtm) REVERT: B 505 ARG cc_start: 0.7049 (pmt-80) cc_final: 0.6634 (pmt-80) REVERT: B 609 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6791 (pp30) REVERT: B 619 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: B 663 ASP cc_start: 0.7195 (m-30) cc_final: 0.6787 (m-30) REVERT: B 666 THR cc_start: 0.6534 (OUTLIER) cc_final: 0.6227 (p) REVERT: C 107 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: C 212 LYS cc_start: 0.7620 (mtpt) cc_final: 0.6993 (mttp) REVERT: C 235 LYS cc_start: 0.7024 (mtmt) cc_final: 0.5900 (mmtm) REVERT: C 304 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6077 (ptt90) REVERT: C 367 THR cc_start: 0.8916 (p) cc_final: 0.8564 (m) REVERT: C 663 ASP cc_start: 0.7233 (m-30) cc_final: 0.6966 (m-30) outliers start: 59 outliers final: 39 residues processed: 199 average time/residue: 0.6625 time to fit residues: 141.3287 Evaluate side-chains 212 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 143 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 112 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 512 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112839 restraints weight = 12903.896| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.10 r_work: 0.3112 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12132 Z= 0.125 Angle : 0.504 6.412 16494 Z= 0.270 Chirality : 0.043 0.199 1800 Planarity : 0.004 0.057 2139 Dihedral : 7.192 56.802 1803 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.23 % Allowed : 22.41 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1431 helix: 0.74 (0.32), residues: 258 sheet: 1.06 (0.25), residues: 414 loop : -0.92 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 406 TYR 0.013 0.001 TYR A 640 PHE 0.013 0.001 PHE C 287 TRP 0.013 0.001 TRP B 354 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00293 (12120) covalent geometry : angle 0.50110 (16464) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.96679 ( 12) hydrogen bonds : bond 0.03682 ( 466) hydrogen bonds : angle 4.63752 ( 1479) link_NAG-ASN : bond 0.00351 ( 6) link_NAG-ASN : angle 1.67556 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5310.36 seconds wall clock time: 91 minutes 0.06 seconds (5460.06 seconds total)