Starting phenix.real_space_refine on Sat Aug 23 11:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrd_38603/08_2025/8xrd_38603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrd_38603/08_2025/8xrd_38603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xrd_38603/08_2025/8xrd_38603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrd_38603/08_2025/8xrd_38603.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrd_38603/08_2025/8xrd_38603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrd_38603/08_2025/8xrd_38603.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 72 5.16 5 C 7361 2.51 5 N 2004 2.21 5 O 2355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11792 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3854 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 19, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3840 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 19, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3831 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'NAG': 2, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.29, per 1000 atoms: 0.28 Number of scatterers: 11792 At special positions: 0 Unit cell: (92.46, 86.94, 151.8, 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 72 16.00 O 2355 8.00 N 2004 7.00 C 7361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.02 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.02 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA2-6 " GAL G 1 " - " SIA G 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL H 1 " - " SIA H 2 " NAG-ASN " NAG A1001 " - " ASN A 290 " " NAG A1002 " - " ASN A 16 " " NAG A1003 " - " ASN A 28 " " NAG B 701 " - " ASN B 28 " " NAG B 702 " - " ASN B 290 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 290 " " NAG D 1 " - " ASN A 169 " " NAG E 1 " - " ASN B 169 " " NAG F 1 " - " ASN C 169 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 565.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 28.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.585A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 389 removed outlier: 3.810A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 404 through 456 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 492 through 502 removed outlier: 4.098A pdb=" N SER A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.592A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 76' Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 389 removed outlier: 3.762A pdb=" N THR B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 484 removed outlier: 4.057A pdb=" N MET B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.621A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.567A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 369 through 389 removed outlier: 3.676A pdb=" N LYS C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 404 through 457 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 493 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.514A pdb=" N GLY A 11 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.642A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.664A pdb=" N PHE A 232 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.664A pdb=" N PHE A 232 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.637A pdb=" N ALA A 138 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.746A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB3, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=AB4, first strand: chain 'B' and resid 362 through 366 removed outlier: 3.662A pdb=" N ALA B 365 " --> pdb=" O TYR B 354 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 8 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 468 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.380A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.538A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 280 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.847A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.597A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 100 removed outlier: 8.107A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 113 through 115 removed outlier: 7.364A pdb=" N LYS B 262 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.699A pdb=" N ALA B 138 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N SER B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AC7, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AC9, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.840A pdb=" N LYS C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.866A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.515A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.515A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.535A pdb=" N ALA C 138 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N SER C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AD8, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AD9, first strand: chain 'C' and resid 460 through 462 474 hydrogen bonds defined for protein. 1296 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: 2.11 Time building geometry restraints manager: 1.45 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: 3876 1.34 - 1.46: 2825 1.46 - 1.58: 5231 1.58 - 1.71: 1 1.71 - 1.83: 108 Bond restraints: 12041 Sorted by residual: bond pdb=" C6 GAL H 1 " pdb=" O6 GAL H 1 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C6 GAL G 1 " pdb=" O6 GAL G 1 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C1 NAG A1003 " pdb=" O5 NAG A1003 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 GAL G 1 " pdb=" O5 GAL G 1 " ideal model delta sigma weight residual 1.412 1.440 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C5 GAL H 1 " pdb=" O5 GAL H 1 " ideal model delta sigma weight residual 1.412 1.439 -0.027 2.00e-02 2.50e+03 1.89e+00 ... (remaining 12036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 16230 3.98 - 7.96: 53 7.96 - 11.94: 4 11.94 - 15.93: 1 15.93 - 19.91: 2 Bond angle restraints: 16290 Sorted by residual: angle pdb=" C5 GAL G 1 " pdb=" C6 GAL G 1 " pdb=" O6 GAL G 1 " ideal model delta sigma weight residual 109.08 128.99 -19.91 3.00e+00 1.11e-01 4.40e+01 angle pdb=" C5 GAL H 1 " pdb=" C6 GAL H 1 " pdb=" O6 GAL H 1 " ideal model delta sigma weight residual 109.08 127.66 -18.58 3.00e+00 1.11e-01 3.83e+01 angle pdb=" CB MET B 454 " pdb=" CG MET B 454 " pdb=" SD MET B 454 " ideal model delta sigma weight residual 112.70 124.65 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CB MET C 347 " pdb=" CG MET C 347 " pdb=" SD MET C 347 " ideal model delta sigma weight residual 112.70 123.81 -11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N LYS A 446 " pdb=" CA LYS A 446 " pdb=" CB LYS A 446 " ideal model delta sigma weight residual 110.22 115.61 -5.39 1.54e+00 4.22e-01 1.23e+01 ... (remaining 16285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 6566 23.96 - 47.93: 765 47.93 - 71.89: 130 71.89 - 95.85: 33 95.85 - 119.81: 12 Dihedral angle restraints: 7506 sinusoidal: 3339 harmonic: 4167 Sorted by residual: dihedral pdb=" CB CYS C 474 " pdb=" SG CYS C 474 " pdb=" SG CYS C 478 " pdb=" CB CYS C 478 " ideal model delta sinusoidal sigma weight residual 93.00 25.89 67.11 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 478 " pdb=" CB CYS B 478 " ideal model delta sinusoidal sigma weight residual 93.00 27.62 65.38 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 478 " pdb=" CB CYS A 478 " ideal model delta sinusoidal sigma weight residual 93.00 28.52 64.48 1 1.00e+01 1.00e-02 5.46e+01 ... (remaining 7503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1576 0.067 - 0.134: 217 0.134 - 0.201: 6 0.201 - 0.268: 1 0.268 - 0.335: 1 Chirality restraints: 1801 Sorted by residual: chirality pdb=" C2 SIA H 2 " pdb=" O6 GAL H 1 " pdb=" C1 SIA H 2 " pdb=" O6 SIA H 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-02 2.50e+03 5.72e+01 chirality pdb=" C2 SIA G 2 " pdb=" O6 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.63 0.13 2.00e-02 2.50e+03 4.19e+01 chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 28 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1798 not shown) Planarity restraints: 2109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 492 " -0.013 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR B 492 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 492 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 492 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 492 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 492 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 492 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 492 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 313 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" CD GLU B 313 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 313 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU B 313 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 492 " -0.018 2.00e-02 2.50e+03 1.70e-02 5.79e+00 pdb=" CG TYR A 492 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 492 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 492 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 492 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 492 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 492 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 492 " 0.001 2.00e-02 2.50e+03 ... (remaining 2106 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 425 2.67 - 3.23: 11032 3.23 - 3.79: 18160 3.79 - 4.34: 22507 4.34 - 4.90: 38948 Nonbonded interactions: 91072 Sorted by model distance: nonbonded pdb=" O6 SIA G 2 " pdb=" O8 SIA G 2 " model vdw 2.113 3.040 nonbonded pdb=" O6 SIA C 703 " pdb=" O8 SIA C 703 " model vdw 2.148 3.040 nonbonded pdb=" O6 SIA H 2 " pdb=" O8 SIA H 2 " model vdw 2.152 3.040 nonbonded pdb=" O PHE B 440 " pdb=" OG SER B 443 " model vdw 2.187 3.040 nonbonded pdb=" O LYS A 368 " pdb=" NE2 GLN A 372 " model vdw 2.200 3.120 ... (remaining 91067 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 325 or resid 338 through 501 or resid 1001 throu \ gh 1002)) selection = (chain 'B' and (resid 6 through 501 or resid 701 through 702)) selection = (chain 'C' and resid 6 through 702) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.006 0.062 12074 Z= 0.247 Angle : 0.712 19.907 16371 Z= 0.339 Chirality : 0.044 0.335 1801 Planarity : 0.003 0.048 2099 Dihedral : 20.035 119.814 4792 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.64 % Allowed : 31.54 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.22), residues: 1444 helix: 2.60 (0.27), residues: 366 sheet: -0.18 (0.30), residues: 312 loop : -1.33 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 406 TYR 0.044 0.002 TYR B 492 PHE 0.012 0.001 PHE A 339 TRP 0.008 0.001 TRP A 81 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00551 (12041) covalent geometry : angle 0.68829 (16290) SS BOND : bond 0.00429 ( 18) SS BOND : angle 1.36707 ( 36) hydrogen bonds : bond 0.17817 ( 440) hydrogen bonds : angle 7.26299 ( 1296) glycosidic custom : bond 0.06029 ( 2) glycosidic custom : angle 7.44316 ( 6) link_BETA1-4 : bond 0.00083 ( 3) link_BETA1-4 : angle 1.07231 ( 9) link_NAG-ASN : bond 0.00464 ( 10) link_NAG-ASN : angle 2.38017 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 76 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 LYS cc_start: 0.9131 (mtmp) cc_final: 0.8915 (mppt) REVERT: C 354 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8134 (t80) REVERT: C 414 MET cc_start: 0.8630 (tpt) cc_final: 0.8165 (tpt) outliers start: 85 outliers final: 76 residues processed: 155 average time/residue: 0.4091 time to fit residues: 71.2996 Evaluate side-chains 155 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 78 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 501 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN C 129 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.050253 restraints weight = 31070.099| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 4.19 r_work: 0.2463 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12074 Z= 0.159 Angle : 0.592 9.723 16371 Z= 0.300 Chirality : 0.044 0.353 1801 Planarity : 0.003 0.044 2099 Dihedral : 12.433 131.601 2071 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.93 % Allowed : 29.20 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.22), residues: 1444 helix: 2.69 (0.27), residues: 371 sheet: -0.15 (0.30), residues: 312 loop : -1.29 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 406 TYR 0.024 0.001 TYR A 492 PHE 0.009 0.001 PHE C 440 TRP 0.008 0.001 TRP C 422 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00350 (12041) covalent geometry : angle 0.58158 (16290) SS BOND : bond 0.00410 ( 18) SS BOND : angle 0.95848 ( 36) hydrogen bonds : bond 0.06453 ( 440) hydrogen bonds : angle 5.74198 ( 1296) glycosidic custom : bond 0.00337 ( 2) glycosidic custom : angle 2.36353 ( 6) link_BETA1-4 : bond 0.00497 ( 3) link_BETA1-4 : angle 0.72544 ( 9) link_NAG-ASN : bond 0.00541 ( 10) link_NAG-ASN : angle 2.32668 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 86 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 239 MET cc_start: 0.9259 (mmm) cc_final: 0.9049 (mmt) REVERT: A 255 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: A 284 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9015 (p) REVERT: A 446 LYS cc_start: 0.9016 (mtmp) cc_final: 0.8781 (mtmt) REVERT: A 454 MET cc_start: 0.9119 (mmp) cc_final: 0.8753 (ttt) REVERT: A 465 ASN cc_start: 0.8482 (t0) cc_final: 0.8225 (t0) REVERT: B 47 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7808 (p) REVERT: B 352 TYR cc_start: 0.8206 (m-10) cc_final: 0.7732 (m-10) REVERT: B 457 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7608 (pmt170) REVERT: B 479 MET cc_start: 0.9069 (ppp) cc_final: 0.8777 (pmm) REVERT: C 41 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 306 CYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6640 (m) REVERT: C 354 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8234 (t80) REVERT: C 414 MET cc_start: 0.8696 (tpt) cc_final: 0.8253 (tpt) REVERT: C 435 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8898 (tp30) outliers start: 76 outliers final: 39 residues processed: 151 average time/residue: 0.4989 time to fit residues: 82.4811 Evaluate side-chains 128 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 81 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.049561 restraints weight = 31353.644| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 4.21 r_work: 0.2441 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12074 Z= 0.221 Angle : 0.617 10.042 16371 Z= 0.310 Chirality : 0.044 0.362 1801 Planarity : 0.003 0.043 2099 Dihedral : 10.854 135.139 2023 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.01 % Allowed : 28.49 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1444 helix: 2.67 (0.27), residues: 375 sheet: -0.24 (0.29), residues: 327 loop : -1.38 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.022 0.001 TYR B 471 PHE 0.010 0.001 PHE C 100 TRP 0.009 0.001 TRP A 81 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00506 (12041) covalent geometry : angle 0.60640 (16290) SS BOND : bond 0.00404 ( 18) SS BOND : angle 1.24902 ( 36) hydrogen bonds : bond 0.06489 ( 440) hydrogen bonds : angle 5.46451 ( 1296) glycosidic custom : bond 0.00221 ( 2) glycosidic custom : angle 1.32242 ( 6) link_BETA1-4 : bond 0.00219 ( 3) link_BETA1-4 : angle 0.86893 ( 9) link_NAG-ASN : bond 0.00483 ( 10) link_NAG-ASN : angle 2.34064 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 88 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.9288 (mmm) cc_final: 0.9031 (mmt) REVERT: A 269 MET cc_start: 0.8892 (ttm) cc_final: 0.8642 (ttp) REVERT: A 284 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9058 (p) REVERT: A 354 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: A 450 ASP cc_start: 0.9711 (t0) cc_final: 0.9380 (p0) REVERT: A 454 MET cc_start: 0.9050 (mmp) cc_final: 0.8670 (mmt) REVERT: A 465 ASN cc_start: 0.8487 (t0) cc_final: 0.8236 (t0) REVERT: A 470 PHE cc_start: 0.6127 (t80) cc_final: 0.5523 (t80) REVERT: A 472 HIS cc_start: 0.6274 (OUTLIER) cc_final: 0.5520 (p90) REVERT: B 47 CYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7650 (p) REVERT: B 457 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7703 (pmt170) REVERT: C 354 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8280 (t80) REVERT: C 427 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.9021 (mt-10) REVERT: C 433 GLU cc_start: 0.9358 (tp30) cc_final: 0.9030 (tp30) REVERT: C 435 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9006 (tp30) REVERT: C 479 MET cc_start: 0.8909 (mmp) cc_final: 0.8701 (mmp) outliers start: 77 outliers final: 39 residues processed: 151 average time/residue: 0.5471 time to fit residues: 90.2833 Evaluate side-chains 130 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 472 HIS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS B 210 ASN B 358 ASN C 13 HIS ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.049973 restraints weight = 30907.822| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 4.18 r_work: 0.2446 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12074 Z= 0.176 Angle : 0.573 9.921 16371 Z= 0.291 Chirality : 0.043 0.362 1801 Planarity : 0.003 0.044 2099 Dihedral : 10.141 136.580 2012 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.92 % Allowed : 29.90 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1444 helix: 2.68 (0.27), residues: 375 sheet: -0.17 (0.29), residues: 327 loop : -1.34 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 457 TYR 0.022 0.001 TYR B 471 PHE 0.009 0.001 PHE B 339 TRP 0.008 0.001 TRP C 422 HIS 0.008 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00400 (12041) covalent geometry : angle 0.56255 (16290) SS BOND : bond 0.00348 ( 18) SS BOND : angle 1.22369 ( 36) hydrogen bonds : bond 0.06233 ( 440) hydrogen bonds : angle 5.28375 ( 1296) glycosidic custom : bond 0.00041 ( 2) glycosidic custom : angle 0.94957 ( 6) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 0.86310 ( 9) link_NAG-ASN : bond 0.00484 ( 10) link_NAG-ASN : angle 2.31427 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 88 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 269 MET cc_start: 0.8906 (ttm) cc_final: 0.8615 (ttp) REVERT: A 284 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9054 (p) REVERT: A 354 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8632 (m-80) REVERT: A 450 ASP cc_start: 0.9699 (t0) cc_final: 0.9373 (p0) REVERT: A 454 MET cc_start: 0.9048 (mmp) cc_final: 0.8650 (mmt) REVERT: A 465 ASN cc_start: 0.8483 (t0) cc_final: 0.8257 (t0) REVERT: A 470 PHE cc_start: 0.6110 (t80) cc_final: 0.5885 (t80) REVERT: B 457 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7596 (pmt170) REVERT: C 41 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8936 (p) REVERT: C 354 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8277 (t80) REVERT: C 433 GLU cc_start: 0.9392 (tp30) cc_final: 0.9035 (tp30) REVERT: C 435 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8959 (tp30) REVERT: C 470 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7905 (t80) REVERT: C 479 MET cc_start: 0.8911 (mmp) cc_final: 0.8709 (mmp) outliers start: 63 outliers final: 37 residues processed: 137 average time/residue: 0.4998 time to fit residues: 74.8108 Evaluate side-chains 130 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS B 210 ASN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS ** C 356 HIS ** 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 = 0.3422 r_free = 0.3422 target = 0.084083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.049607 restraints weight = 31134.034| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 4.16 r_work: 0.2428 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 12074 Z= 0.257 Angle : 0.620 10.431 16371 Z= 0.313 Chirality : 0.044 0.370 1801 Planarity : 0.003 0.044 2099 Dihedral : 9.904 137.521 2009 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.78 % Allowed : 29.74 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.22), residues: 1444 helix: 2.62 (0.27), residues: 375 sheet: -0.15 (0.29), residues: 327 loop : -1.42 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.021 0.001 TYR A 492 PHE 0.011 0.001 PHE C 100 TRP 0.009 0.001 TRP A 81 HIS 0.008 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00590 (12041) covalent geometry : angle 0.60899 (16290) SS BOND : bond 0.00550 ( 18) SS BOND : angle 1.29975 ( 36) hydrogen bonds : bond 0.06458 ( 440) hydrogen bonds : angle 5.33070 ( 1296) glycosidic custom : bond 0.00205 ( 2) glycosidic custom : angle 1.03388 ( 6) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 0.95359 ( 9) link_NAG-ASN : bond 0.00500 ( 10) link_NAG-ASN : angle 2.44457 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 86 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: A 269 MET cc_start: 0.8906 (ttm) cc_final: 0.8534 (ttp) REVERT: A 284 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9052 (p) REVERT: A 354 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: A 406 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7100 (mtp180) REVERT: A 450 ASP cc_start: 0.9694 (t0) cc_final: 0.9373 (p0) REVERT: A 454 MET cc_start: 0.9050 (mmp) cc_final: 0.8661 (mmt) REVERT: A 465 ASN cc_start: 0.8542 (t0) cc_final: 0.8293 (t0) REVERT: A 470 PHE cc_start: 0.6177 (t80) cc_final: 0.5859 (t80) REVERT: A 472 HIS cc_start: 0.6066 (OUTLIER) cc_final: 0.5428 (p90) REVERT: A 479 MET cc_start: 0.8826 (mmp) cc_final: 0.8611 (mmp) REVERT: B 457 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7671 (pmt170) REVERT: B 479 MET cc_start: 0.9146 (ppp) cc_final: 0.8842 (pmm) REVERT: C 41 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8935 (p) REVERT: C 354 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8337 (t80) REVERT: C 399 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8574 (mm-30) REVERT: C 433 GLU cc_start: 0.9410 (tp30) cc_final: 0.9039 (tp30) REVERT: C 435 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9018 (tp30) REVERT: C 470 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7929 (t80) outliers start: 74 outliers final: 40 residues processed: 146 average time/residue: 0.4603 time to fit residues: 73.7264 Evaluate side-chains 135 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 472 HIS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.049934 restraints weight = 30745.922| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 4.15 r_work: 0.2436 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12074 Z= 0.232 Angle : 0.613 10.318 16371 Z= 0.310 Chirality : 0.044 0.370 1801 Planarity : 0.003 0.044 2099 Dihedral : 9.654 137.070 2008 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.92 % Allowed : 30.37 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1444 helix: 2.56 (0.27), residues: 375 sheet: -0.15 (0.29), residues: 327 loop : -1.43 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.033 0.001 TYR A 492 PHE 0.011 0.001 PHE B 339 TRP 0.009 0.001 TRP A 81 HIS 0.009 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00532 (12041) covalent geometry : angle 0.60207 (16290) SS BOND : bond 0.00407 ( 18) SS BOND : angle 1.18757 ( 36) hydrogen bonds : bond 0.06424 ( 440) hydrogen bonds : angle 5.26431 ( 1296) glycosidic custom : bond 0.00225 ( 2) glycosidic custom : angle 0.94770 ( 6) link_BETA1-4 : bond 0.00202 ( 3) link_BETA1-4 : angle 0.95359 ( 9) link_NAG-ASN : bond 0.00500 ( 10) link_NAG-ASN : angle 2.43695 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 87 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: A 269 MET cc_start: 0.8880 (ttm) cc_final: 0.8531 (ttp) REVERT: A 284 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9053 (p) REVERT: A 450 ASP cc_start: 0.9692 (t0) cc_final: 0.9365 (p0) REVERT: A 454 MET cc_start: 0.9054 (mmp) cc_final: 0.8661 (mmt) REVERT: A 465 ASN cc_start: 0.8527 (t0) cc_final: 0.8279 (t0) REVERT: A 470 PHE cc_start: 0.6162 (t80) cc_final: 0.5834 (t80) REVERT: A 479 MET cc_start: 0.8918 (mmp) cc_final: 0.8670 (mmp) REVERT: B 47 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7917 (p) REVERT: B 139 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7652 (m) REVERT: B 457 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7623 (pmt170) REVERT: B 479 MET cc_start: 0.9193 (ppp) cc_final: 0.8813 (pmm) REVERT: C 41 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8922 (p) REVERT: C 354 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8321 (t80) REVERT: C 433 GLU cc_start: 0.9419 (tp30) cc_final: 0.9050 (tp30) REVERT: C 435 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9005 (tp30) REVERT: C 470 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7928 (t80) outliers start: 63 outliers final: 40 residues processed: 138 average time/residue: 0.5213 time to fit residues: 78.5770 Evaluate side-chains 131 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 83 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS A 455 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS ** C 356 HIS ** 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 = 0.3431 r_free = 0.3431 target = 0.084815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.049924 restraints weight = 30910.516| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 4.18 r_work: 0.2452 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12074 Z= 0.169 Angle : 0.593 10.198 16371 Z= 0.300 Chirality : 0.043 0.373 1801 Planarity : 0.003 0.044 2099 Dihedral : 9.317 136.343 2004 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.68 % Allowed : 31.30 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1444 helix: 2.50 (0.27), residues: 376 sheet: -0.09 (0.29), residues: 327 loop : -1.37 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 457 TYR 0.021 0.001 TYR B 471 PHE 0.008 0.001 PHE C 393 TRP 0.009 0.001 TRP C 422 HIS 0.009 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00384 (12041) covalent geometry : angle 0.58258 (16290) SS BOND : bond 0.00351 ( 18) SS BOND : angle 1.08410 ( 36) hydrogen bonds : bond 0.06254 ( 440) hydrogen bonds : angle 5.16331 ( 1296) glycosidic custom : bond 0.00114 ( 2) glycosidic custom : angle 0.89395 ( 6) link_BETA1-4 : bond 0.00260 ( 3) link_BETA1-4 : angle 0.90978 ( 9) link_NAG-ASN : bond 0.00491 ( 10) link_NAG-ASN : angle 2.38384 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 83 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: A 284 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9046 (p) REVERT: A 406 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7078 (mtp180) REVERT: A 450 ASP cc_start: 0.9698 (t0) cc_final: 0.9363 (p0) REVERT: A 454 MET cc_start: 0.9052 (mmp) cc_final: 0.8667 (mmt) REVERT: A 465 ASN cc_start: 0.8555 (t0) cc_final: 0.8315 (t0) REVERT: A 479 MET cc_start: 0.8976 (mmp) cc_final: 0.8727 (mmp) REVERT: B 47 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7868 (p) REVERT: B 139 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7607 (m) REVERT: B 457 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7569 (pmt170) REVERT: C 41 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8910 (p) REVERT: C 354 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8389 (t80) REVERT: C 399 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8598 (mm-30) REVERT: C 433 GLU cc_start: 0.9424 (tp30) cc_final: 0.9039 (tp30) REVERT: C 435 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9044 (tp30) REVERT: C 470 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (t80) outliers start: 60 outliers final: 35 residues processed: 134 average time/residue: 0.5255 time to fit residues: 76.6345 Evaluate side-chains 125 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 26 optimal weight: 0.0170 chunk 69 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS A 455 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.050550 restraints weight = 30823.664| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.20 r_work: 0.2459 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12074 Z= 0.135 Angle : 0.580 9.975 16371 Z= 0.295 Chirality : 0.043 0.368 1801 Planarity : 0.003 0.044 2099 Dihedral : 9.048 135.893 2002 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.22 % Allowed : 31.77 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1444 helix: 2.54 (0.27), residues: 376 sheet: 0.11 (0.29), residues: 323 loop : -1.33 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.022 0.001 TYR A 492 PHE 0.012 0.001 PHE B 339 TRP 0.009 0.001 TRP C 422 HIS 0.009 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00303 (12041) covalent geometry : angle 0.56922 (16290) SS BOND : bond 0.00310 ( 18) SS BOND : angle 1.16520 ( 36) hydrogen bonds : bond 0.06046 ( 440) hydrogen bonds : angle 5.05964 ( 1296) glycosidic custom : bond 0.00069 ( 2) glycosidic custom : angle 0.86544 ( 6) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 0.86083 ( 9) link_NAG-ASN : bond 0.00498 ( 10) link_NAG-ASN : angle 2.30856 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 83 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: A 284 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9084 (p) REVERT: A 450 ASP cc_start: 0.9700 (t0) cc_final: 0.9362 (p0) REVERT: A 454 MET cc_start: 0.9021 (mmp) cc_final: 0.8631 (mmt) REVERT: A 465 ASN cc_start: 0.8594 (t0) cc_final: 0.8341 (t0) REVERT: A 479 MET cc_start: 0.9003 (mmp) cc_final: 0.8750 (mmp) REVERT: B 47 CYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7883 (p) REVERT: B 139 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7622 (m) REVERT: B 457 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7498 (pmt170) REVERT: C 41 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8931 (p) REVERT: C 354 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8420 (t80) REVERT: C 433 GLU cc_start: 0.9421 (tp30) cc_final: 0.9024 (tp30) REVERT: C 435 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9055 (tp30) REVERT: C 470 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7919 (t80) outliers start: 54 outliers final: 35 residues processed: 129 average time/residue: 0.5506 time to fit residues: 77.7118 Evaluate side-chains 123 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 492 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 0.0870 chunk 77 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 441 HIS ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS ** C 356 HIS ** 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 = 0.3438 r_free = 0.3438 target = 0.085121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.050034 restraints weight = 30802.836| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 4.20 r_work: 0.2452 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12074 Z= 0.175 Angle : 0.617 11.904 16371 Z= 0.309 Chirality : 0.043 0.365 1801 Planarity : 0.003 0.045 2099 Dihedral : 8.951 136.008 2001 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.29 % Allowed : 31.54 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1444 helix: 2.56 (0.27), residues: 375 sheet: 0.18 (0.29), residues: 323 loop : -1.36 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 457 TYR 0.020 0.001 TYR B 471 PHE 0.008 0.001 PHE C 393 TRP 0.009 0.001 TRP C 422 HIS 0.010 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00402 (12041) covalent geometry : angle 0.60598 (16290) SS BOND : bond 0.00330 ( 18) SS BOND : angle 1.36627 ( 36) hydrogen bonds : bond 0.06094 ( 440) hydrogen bonds : angle 5.07002 ( 1296) glycosidic custom : bond 0.00086 ( 2) glycosidic custom : angle 0.92519 ( 6) link_BETA1-4 : bond 0.00232 ( 3) link_BETA1-4 : angle 0.88625 ( 9) link_NAG-ASN : bond 0.00489 ( 10) link_NAG-ASN : angle 2.32727 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 84 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (mpp80) REVERT: A 255 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: A 284 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9071 (p) REVERT: A 414 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8751 (tpp) REVERT: A 450 ASP cc_start: 0.9696 (t0) cc_final: 0.9357 (p0) REVERT: A 454 MET cc_start: 0.9084 (mmp) cc_final: 0.8709 (mmt) REVERT: A 465 ASN cc_start: 0.8560 (t0) cc_final: 0.8308 (t0) REVERT: A 479 MET cc_start: 0.9005 (mmp) cc_final: 0.8754 (mmp) REVERT: B 47 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7898 (p) REVERT: B 139 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7672 (m) REVERT: B 457 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7435 (pmt170) REVERT: B 479 MET cc_start: 0.9202 (ppp) cc_final: 0.8849 (pmm) REVERT: C 41 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8923 (p) REVERT: C 354 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8409 (t80) REVERT: C 433 GLU cc_start: 0.9420 (tp30) cc_final: 0.9026 (tp30) REVERT: C 435 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8954 (tp30) REVERT: C 470 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (t80) outliers start: 55 outliers final: 41 residues processed: 130 average time/residue: 0.5596 time to fit residues: 79.5204 Evaluate side-chains 131 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 80 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 492 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 455 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.084140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.049186 restraints weight = 31371.275| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 4.20 r_work: 0.2426 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12074 Z= 0.271 Angle : 0.680 10.943 16371 Z= 0.345 Chirality : 0.045 0.364 1801 Planarity : 0.004 0.045 2099 Dihedral : 9.015 136.051 2001 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.53 % Allowed : 31.38 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.22), residues: 1444 helix: 2.40 (0.27), residues: 375 sheet: 0.16 (0.29), residues: 323 loop : -1.50 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 27 TYR 0.025 0.001 TYR B 492 PHE 0.013 0.002 PHE A 339 TRP 0.009 0.001 TRP A 81 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00626 (12041) covalent geometry : angle 0.66952 (16290) SS BOND : bond 0.00402 ( 18) SS BOND : angle 1.49783 ( 36) hydrogen bonds : bond 0.06540 ( 440) hydrogen bonds : angle 5.25652 ( 1296) glycosidic custom : bond 0.00313 ( 2) glycosidic custom : angle 1.04417 ( 6) link_BETA1-4 : bond 0.00139 ( 3) link_BETA1-4 : angle 0.98543 ( 9) link_NAG-ASN : bond 0.00502 ( 10) link_NAG-ASN : angle 2.46456 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 81 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: A 284 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9081 (p) REVERT: A 406 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7163 (mtp180) REVERT: A 450 ASP cc_start: 0.9685 (t0) cc_final: 0.9350 (p0) REVERT: A 454 MET cc_start: 0.9040 (mmp) cc_final: 0.8660 (mmt) REVERT: A 465 ASN cc_start: 0.8610 (t0) cc_final: 0.8372 (t0) REVERT: A 479 MET cc_start: 0.8997 (mmp) cc_final: 0.8746 (mmp) REVERT: B 47 CYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8125 (p) REVERT: B 139 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7671 (m) REVERT: B 457 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7681 (pmt170) REVERT: B 479 MET cc_start: 0.9231 (ppp) cc_final: 0.8877 (pmm) REVERT: C 41 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8913 (p) REVERT: C 354 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8393 (t80) REVERT: C 399 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8641 (mm-30) REVERT: C 433 GLU cc_start: 0.9431 (tp30) cc_final: 0.9045 (tp30) REVERT: C 435 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9043 (tp30) REVERT: C 470 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7821 (t80) outliers start: 58 outliers final: 37 residues processed: 129 average time/residue: 0.5277 time to fit residues: 74.5578 Evaluate side-chains 126 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 139 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 69 optimal weight: 0.0570 chunk 136 optimal weight: 0.7980 chunk 96 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 441 HIS A 455 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** 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 = 0.3453 r_free = 0.3453 target = 0.085903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.050978 restraints weight = 30692.028| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 4.19 r_work: 0.2469 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12074 Z= 0.128 Angle : 0.622 13.656 16371 Z= 0.315 Chirality : 0.044 0.362 1801 Planarity : 0.003 0.045 2099 Dihedral : 8.777 134.872 2001 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.36 % Allowed : 32.32 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1444 helix: 2.50 (0.27), residues: 374 sheet: 0.28 (0.30), residues: 321 loop : -1.36 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 436 TYR 0.019 0.001 TYR B 471 PHE 0.019 0.001 PHE A 470 TRP 0.010 0.001 TRP C 422 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00278 (12041) covalent geometry : angle 0.61231 (16290) SS BOND : bond 0.00286 ( 18) SS BOND : angle 1.14385 ( 36) hydrogen bonds : bond 0.06017 ( 440) hydrogen bonds : angle 5.06058 ( 1296) glycosidic custom : bond 0.00037 ( 2) glycosidic custom : angle 0.85916 ( 6) link_BETA1-4 : bond 0.00362 ( 3) link_BETA1-4 : angle 0.85779 ( 9) link_NAG-ASN : bond 0.00509 ( 10) link_NAG-ASN : angle 2.29837 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.47 seconds wall clock time: 66 minutes 8.41 seconds (3968.41 seconds total)