Starting phenix.real_space_refine on Wed May 14 12:38:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrd_38603/05_2025/8xrd_38603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrd_38603/05_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_38603/05_2025/8xrd_38603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrd_38603/05_2025/8xrd_38603.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrd_38603/05_2025/8xrd_38603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrd_38603/05_2025/8xrd_38603.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.40, per 1000 atoms: 0.71 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: 3.18 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.01 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: 3.85 Time building geometry restraints manager: 3.70 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 501 or resid 701 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: 0.010 Normalize map: mean=0, sd=1: 5.830 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.110 Process input model: 31.380 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- 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 : 11.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 81 HIS 0.005 0.001 HIS A 472 PHE 0.012 0.001 PHE A 339 TYR 0.044 0.002 TYR B 492 ARG 0.010 0.000 ARG B 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 10) link_NAG-ASN : angle 2.38017 ( 30) link_BETA1-4 : bond 0.00083 ( 3) link_BETA1-4 : angle 1.07231 ( 9) hydrogen bonds : bond 0.17817 ( 440) hydrogen bonds : angle 7.26299 ( 1296) SS BOND : bond 0.00429 ( 18) SS BOND : angle 1.36707 ( 36) glycosidic custom : bond 0.06029 ( 2) glycosidic custom : angle 7.44316 ( 6) covalent geometry : bond 0.00551 (12041) covalent geometry : angle 0.68829 (16290) *********************** 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 : 1.400 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: 0.8016 time to fit residues: 140.7475 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 : 1.463 ------------------------------------------------------------------------------- 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 121 optimal weight: 6.9990 chunk 109 optimal weight: 0.0170 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 84 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 overall best weight: 2.3024 ------------------------------------------------------------------------------- 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 = 0.084883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.050209 restraints weight = 30913.000| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 4.19 r_work: 0.2463 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0785 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= 0.163 Angle : 0.595 10.323 16371 Z= 0.300 Chirality : 0.044 0.360 1801 Planarity : 0.003 0.044 2099 Dihedral : 12.312 132.764 2071 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.25 % Allowed : 28.81 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1444 helix: 2.69 (0.27), residues: 371 sheet: -0.10 (0.30), residues: 317 loop : -1.30 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.006 0.001 HIS A 472 PHE 0.009 0.001 PHE C 100 TYR 0.025 0.001 TYR A 492 ARG 0.006 0.000 ARG B 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 10) link_NAG-ASN : angle 2.32835 ( 30) link_BETA1-4 : bond 0.00424 ( 3) link_BETA1-4 : angle 0.72574 ( 9) hydrogen bonds : bond 0.06421 ( 440) hydrogen bonds : angle 5.70774 ( 1296) SS BOND : bond 0.00384 ( 18) SS BOND : angle 0.97656 ( 36) glycosidic custom : bond 0.00317 ( 2) glycosidic custom : angle 2.37773 ( 6) covalent geometry : bond 0.00363 (12041) covalent geometry : angle 0.58380 (16290) *********************** 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 166 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 86 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8617 (p) REVERT: A 239 MET cc_start: 0.9259 (mmm) cc_final: 0.9048 (mmt) REVERT: A 255 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: A 284 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9024 (p) REVERT: A 446 LYS cc_start: 0.9014 (mtmp) cc_final: 0.8781 (mtmt) REVERT: A 454 MET cc_start: 0.9129 (mmp) cc_final: 0.8806 (tpt) REVERT: A 465 ASN cc_start: 0.8464 (t0) cc_final: 0.8204 (t0) REVERT: B 47 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7500 (p) REVERT: B 457 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7591 (pmt170) REVERT: B 479 MET cc_start: 0.9069 (ppp) cc_final: 0.8778 (pmm) REVERT: C 41 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8965 (p) REVERT: C 354 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8237 (t80) REVERT: C 414 MET cc_start: 0.8700 (tpt) cc_final: 0.8251 (tpt) REVERT: C 427 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.9028 (mt-10) REVERT: C 435 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8891 (tp30) outliers start: 80 outliers final: 40 residues processed: 154 average time/residue: 1.1290 time to fit residues: 190.9555 Evaluate side-chains 129 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 81 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 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 306 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 357 SER 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 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 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 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 107 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.085041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050234 restraints weight = 31062.691| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 4.20 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: 0.8551 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12074 Z= 0.152 Angle : 0.584 9.912 16371 Z= 0.294 Chirality : 0.043 0.361 1801 Planarity : 0.003 0.043 2099 Dihedral : 10.732 134.444 2020 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.31 % Allowed : 28.96 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1444 helix: 2.73 (0.27), residues: 375 sheet: -0.21 (0.29), residues: 327 loop : -1.29 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.005 0.001 HIS A 472 PHE 0.008 0.001 PHE C 440 TYR 0.024 0.001 TYR B 471 ARG 0.008 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 10) link_NAG-ASN : angle 2.27556 ( 30) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 0.81707 ( 9) hydrogen bonds : bond 0.06197 ( 440) hydrogen bonds : angle 5.39866 ( 1296) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.08598 ( 36) glycosidic custom : bond 0.00218 ( 2) glycosidic custom : angle 1.35923 ( 6) covalent geometry : bond 0.00341 (12041) covalent geometry : angle 0.57396 (16290) *********************** 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 156 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 88 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8571 (p) REVERT: A 239 MET cc_start: 0.9277 (mmm) cc_final: 0.9031 (mmt) REVERT: A 255 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: A 269 MET cc_start: 0.8878 (ttm) cc_final: 0.8554 (ttp) REVERT: A 284 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9017 (p) REVERT: A 354 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: A 450 ASP cc_start: 0.9707 (t0) cc_final: 0.9363 (p0) REVERT: A 454 MET cc_start: 0.9002 (mmp) cc_final: 0.8642 (mmt) REVERT: A 465 ASN cc_start: 0.8482 (t0) cc_final: 0.8234 (t0) REVERT: B 352 TYR cc_start: 0.8138 (m-10) cc_final: 0.7699 (m-10) REVERT: B 457 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7610 (pmt170) REVERT: C 354 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8278 (t80) REVERT: C 427 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9032 (mt-10) REVERT: C 435 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8933 (tp30) outliers start: 68 outliers final: 35 residues processed: 145 average time/residue: 1.1195 time to fit residues: 177.3171 Evaluate side-chains 123 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 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 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 13 HIS 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 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 401 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 457 ARG 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 51 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 B 358 ASN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 92 ASN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.048044 restraints weight = 31543.835| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 4.17 r_work: 0.2401 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.049 12074 Z= 0.415 Angle : 0.749 11.149 16371 Z= 0.373 Chirality : 0.047 0.365 1801 Planarity : 0.004 0.043 2099 Dihedral : 10.402 138.530 2009 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.93 % Allowed : 28.73 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1444 helix: 2.39 (0.27), residues: 375 sheet: -0.25 (0.28), residues: 325 loop : -1.58 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.008 0.001 HIS C 13 PHE 0.015 0.002 PHE C 100 TYR 0.022 0.002 TYR A 492 ARG 0.006 0.001 ARG B 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 10) link_NAG-ASN : angle 2.54969 ( 30) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 1.04563 ( 9) hydrogen bonds : bond 0.07055 ( 440) hydrogen bonds : angle 5.61486 ( 1296) SS BOND : bond 0.00513 ( 18) SS BOND : angle 2.02514 ( 36) glycosidic custom : bond 0.00581 ( 2) glycosidic custom : angle 1.25204 ( 6) covalent geometry : bond 0.00954 (12041) covalent geometry : angle 0.73543 (16290) *********************** 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 160 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 84 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.9271 (mmm) cc_final: 0.9004 (mmt) REVERT: A 269 MET cc_start: 0.8930 (ttm) cc_final: 0.8622 (ttp) REVERT: A 284 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9062 (p) REVERT: A 406 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7305 (mtp180) REVERT: A 450 ASP cc_start: 0.9700 (t0) cc_final: 0.9373 (p0) REVERT: A 454 MET cc_start: 0.9090 (mmp) cc_final: 0.8705 (mmt) REVERT: A 465 ASN cc_start: 0.8455 (t0) cc_final: 0.8209 (t0) REVERT: A 472 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5686 (p90) REVERT: B 457 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7695 (pmt170) REVERT: B 479 MET cc_start: 0.9142 (ppp) cc_final: 0.8791 (pmm) REVERT: C 41 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 354 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8305 (t80) REVERT: C 399 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8594 (mm-30) REVERT: C 433 GLU cc_start: 0.9333 (tp30) cc_final: 0.9037 (tp30) REVERT: C 435 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8987 (tp30) REVERT: C 470 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7861 (t80) outliers start: 76 outliers final: 41 residues processed: 147 average time/residue: 0.9973 time to fit residues: 162.2575 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 : 1.297 ------------------------------------------------------------------------------- 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 208 THR 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 82 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 ASN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3443 r_free = 0.3443 target = 0.085293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050625 restraints weight = 30782.001| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.17 r_work: 0.2458 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12074 Z= 0.122 Angle : 0.571 10.455 16371 Z= 0.288 Chirality : 0.043 0.366 1801 Planarity : 0.003 0.044 2099 Dihedral : 9.774 135.820 2007 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.61 % Allowed : 30.44 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1444 helix: 2.57 (0.27), residues: 375 sheet: -0.18 (0.29), residues: 327 loop : -1.34 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS B 355 PHE 0.009 0.001 PHE B 470 TYR 0.019 0.001 TYR A 492 ARG 0.005 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 10) link_NAG-ASN : angle 2.34377 ( 30) link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 0.83557 ( 9) hydrogen bonds : bond 0.06164 ( 440) hydrogen bonds : angle 5.23673 ( 1296) SS BOND : bond 0.00318 ( 18) SS BOND : angle 1.55946 ( 36) glycosidic custom : bond 0.00199 ( 2) glycosidic custom : angle 0.92054 ( 6) covalent geometry : bond 0.00262 (12041) covalent geometry : angle 0.55853 (16290) *********************** 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 149 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 90 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: A 269 MET cc_start: 0.8859 (ttm) cc_final: 0.8512 (ttp) REVERT: A 284 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9044 (p) REVERT: A 314 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8574 (pptt) REVERT: A 406 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7108 (mtp180) REVERT: A 450 ASP cc_start: 0.9708 (t0) cc_final: 0.9358 (p0) REVERT: A 454 MET cc_start: 0.9034 (mmp) cc_final: 0.8643 (mmt) REVERT: A 465 ASN cc_start: 0.8537 (t0) cc_final: 0.8295 (t0) REVERT: A 472 HIS cc_start: 0.6134 (OUTLIER) cc_final: 0.5551 (p90) REVERT: A 479 MET cc_start: 0.8841 (mmp) cc_final: 0.8618 (mmp) REVERT: B 139 CYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7541 (m) REVERT: B 457 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7628 (pmt170) REVERT: C 41 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8945 (p) REVERT: C 354 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8357 (t80) REVERT: C 399 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8634 (mm-30) REVERT: C 433 GLU cc_start: 0.9364 (tp30) cc_final: 0.8969 (tp30) REVERT: C 435 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9035 (tp30) REVERT: C 470 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7935 (t80) outliers start: 59 outliers final: 29 residues processed: 137 average time/residue: 1.1315 time to fit residues: 169.4688 Evaluate side-chains 119 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 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 314 LYS 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 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 242 THR Chi-restraints excluded: chain B residue 271 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 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 274 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 407 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 96 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 B 210 ASN ** 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 = 0.3421 r_free = 0.3421 target = 0.084200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.049271 restraints weight = 31346.951| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 4.19 r_work: 0.2436 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12074 Z= 0.229 Angle : 0.619 10.666 16371 Z= 0.311 Chirality : 0.044 0.376 1801 Planarity : 0.003 0.045 2099 Dihedral : 9.497 137.383 2003 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.07 % Allowed : 30.37 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1444 helix: 2.51 (0.27), residues: 375 sheet: -0.14 (0.29), residues: 327 loop : -1.40 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.006 0.001 HIS A 472 PHE 0.011 0.001 PHE A 339 TYR 0.026 0.001 TYR B 492 ARG 0.009 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 10) link_NAG-ASN : angle 2.42786 ( 30) link_BETA1-4 : bond 0.00105 ( 3) link_BETA1-4 : angle 0.92235 ( 9) hydrogen bonds : bond 0.06382 ( 440) hydrogen bonds : angle 5.23383 ( 1296) SS BOND : bond 0.00380 ( 18) SS BOND : angle 1.69682 ( 36) glycosidic custom : bond 0.00164 ( 2) glycosidic custom : angle 1.00812 ( 6) covalent geometry : bond 0.00528 (12041) covalent geometry : angle 0.60602 (16290) *********************** 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 145 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 80 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8861 (ttm) cc_final: 0.8508 (ttp) REVERT: A 284 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9045 (p) REVERT: A 406 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7093 (mtp180) REVERT: A 450 ASP cc_start: 0.9709 (t0) cc_final: 0.9377 (p0) REVERT: A 454 MET cc_start: 0.9062 (mmp) cc_final: 0.8676 (mmt) REVERT: A 465 ASN cc_start: 0.8547 (t0) cc_final: 0.8291 (t0) REVERT: A 472 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5545 (p90) REVERT: A 479 MET cc_start: 0.8883 (mmp) cc_final: 0.8561 (mmp) REVERT: B 457 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7598 (pmt170) REVERT: B 479 MET cc_start: 0.9264 (ppp) cc_final: 0.8895 (pmm) REVERT: C 27 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7116 (mmt-90) REVERT: C 41 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 354 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8341 (t80) REVERT: C 399 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8606 (mm-30) REVERT: C 433 GLU cc_start: 0.9391 (tp30) cc_final: 0.8970 (tp30) REVERT: C 435 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9010 (tp30) REVERT: C 470 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7944 (t80) outliers start: 65 outliers final: 42 residues processed: 133 average time/residue: 1.0803 time to fit residues: 159.0034 Evaluate side-chains 130 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 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 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 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 441 HIS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 27 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 113 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 140 optimal weight: 40.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 B 210 ASN ** 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 = 0.3428 r_free = 0.3428 target = 0.084559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.049697 restraints weight = 31234.055| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 4.20 r_work: 0.2447 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12074 Z= 0.189 Angle : 0.606 10.506 16371 Z= 0.304 Chirality : 0.043 0.373 1801 Planarity : 0.003 0.045 2099 Dihedral : 9.335 136.820 2003 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.45 % Allowed : 30.76 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1444 helix: 2.46 (0.27), residues: 376 sheet: 0.04 (0.29), residues: 317 loop : -1.39 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.007 0.001 HIS A 472 PHE 0.009 0.001 PHE C 100 TYR 0.032 0.001 TYR A 492 ARG 0.007 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 10) link_NAG-ASN : angle 2.39269 ( 30) link_BETA1-4 : bond 0.00235 ( 3) link_BETA1-4 : angle 0.92461 ( 9) hydrogen bonds : bond 0.06290 ( 440) hydrogen bonds : angle 5.17643 ( 1296) SS BOND : bond 0.00339 ( 18) SS BOND : angle 1.79500 ( 36) glycosidic custom : bond 0.00145 ( 2) glycosidic custom : angle 0.93960 ( 6) covalent geometry : bond 0.00434 (12041) covalent geometry : angle 0.59226 (16290) *********************** 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 138 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 81 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9053 (p) REVERT: A 406 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7127 (mtp180) REVERT: A 450 ASP cc_start: 0.9709 (t0) cc_final: 0.9358 (p0) REVERT: A 454 MET cc_start: 0.9105 (mmp) cc_final: 0.8737 (mmt) REVERT: A 465 ASN cc_start: 0.8534 (t0) cc_final: 0.8286 (t0) REVERT: A 472 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5650 (p90) REVERT: B 139 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7651 (m) REVERT: B 457 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7594 (pmt170) REVERT: C 41 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8918 (p) REVERT: C 354 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8412 (t80) REVERT: C 399 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8655 (mm-30) REVERT: C 433 GLU cc_start: 0.9402 (tp30) cc_final: 0.8962 (tp30) REVERT: C 435 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9018 (tp30) REVERT: C 470 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7932 (t80) outliers start: 57 outliers final: 37 residues processed: 128 average time/residue: 1.0894 time to fit residues: 153.1720 Evaluate side-chains 122 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 468 PHE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 472 HIS 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 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 364 TYR 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 428 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 61 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 chunk 25 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 52 optimal weight: 0.0980 chunk 31 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3455 r_free = 0.3455 target = 0.086196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.051289 restraints weight = 30719.414| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 4.21 r_work: 0.2480 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12074 Z= 0.114 Angle : 0.580 9.971 16371 Z= 0.295 Chirality : 0.043 0.365 1801 Planarity : 0.003 0.044 2099 Dihedral : 8.960 135.694 2002 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.83 % Allowed : 31.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1444 helix: 2.49 (0.27), residues: 376 sheet: 0.17 (0.30), residues: 315 loop : -1.25 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 422 HIS 0.005 0.001 HIS A 472 PHE 0.013 0.001 PHE A 470 TYR 0.022 0.001 TYR A 492 ARG 0.006 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 10) link_NAG-ASN : angle 2.24567 ( 30) link_BETA1-4 : bond 0.00277 ( 3) link_BETA1-4 : angle 0.80195 ( 9) hydrogen bonds : bond 0.05797 ( 440) hydrogen bonds : angle 5.01161 ( 1296) SS BOND : bond 0.00230 ( 18) SS BOND : angle 1.57863 ( 36) glycosidic custom : bond 0.00212 ( 2) glycosidic custom : angle 0.75145 ( 6) covalent geometry : bond 0.00240 (12041) covalent geometry : angle 0.56778 (16290) *********************** 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 131 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 82 time to evaluate : 1.394 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: 0.9059 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: A 284 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9091 (p) REVERT: A 406 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6730 (mtp180) REVERT: A 450 ASP cc_start: 0.9710 (t0) cc_final: 0.9372 (p0) REVERT: A 454 MET cc_start: 0.9000 (mmp) cc_final: 0.8611 (mmt) REVERT: A 465 ASN cc_start: 0.8530 (t0) cc_final: 0.8285 (t0) REVERT: A 472 HIS cc_start: 0.6139 (OUTLIER) cc_final: 0.5524 (p90) REVERT: B 139 CYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7577 (m) REVERT: B 457 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7514 (pmt170) REVERT: C 41 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8933 (p) REVERT: C 354 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8420 (t80) REVERT: C 399 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8010 (mm-30) REVERT: C 433 GLU cc_start: 0.9416 (tp30) cc_final: 0.8956 (tp30) REVERT: C 435 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9019 (tp30) REVERT: C 470 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7916 (t80) outliers start: 49 outliers final: 28 residues processed: 122 average time/residue: 1.1141 time to fit residues: 149.2304 Evaluate side-chains 115 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 406 ARG 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 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 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 27 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 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 441 HIS Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 476 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 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 372 GLN A 441 HIS A 455 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3440 r_free = 0.3440 target = 0.085287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.050359 restraints weight = 30915.088| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.18 r_work: 0.2459 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12074 Z= 0.174 Angle : 0.617 11.983 16371 Z= 0.308 Chirality : 0.043 0.362 1801 Planarity : 0.003 0.044 2099 Dihedral : 8.853 136.114 1999 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 31.23 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1444 helix: 2.48 (0.27), residues: 375 sheet: 0.19 (0.29), residues: 323 loop : -1.34 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 422 HIS 0.007 0.001 HIS A 472 PHE 0.013 0.001 PHE A 470 TYR 0.021 0.001 TYR A 492 ARG 0.006 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 10) link_NAG-ASN : angle 2.29779 ( 30) link_BETA1-4 : bond 0.00243 ( 3) link_BETA1-4 : angle 0.89521 ( 9) hydrogen bonds : bond 0.05990 ( 440) hydrogen bonds : angle 5.04931 ( 1296) SS BOND : bond 0.00288 ( 18) SS BOND : angle 1.89795 ( 36) glycosidic custom : bond 0.00140 ( 2) glycosidic custom : angle 0.88145 ( 6) covalent geometry : bond 0.00402 (12041) covalent geometry : angle 0.60349 (16290) *********************** 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 133 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 82 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8591 (mpp80) REVERT: A 255 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: A 269 MET cc_start: 0.8797 (ttm) cc_final: 0.8517 (ttm) REVERT: A 284 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9060 (p) REVERT: A 414 MET cc_start: 0.9121 (mmm) cc_final: 0.8827 (tpt) REVERT: A 450 ASP cc_start: 0.9709 (t0) cc_final: 0.9376 (p0) REVERT: A 454 MET cc_start: 0.9012 (mmp) cc_final: 0.8629 (mmt) REVERT: A 465 ASN cc_start: 0.8554 (t0) cc_final: 0.8304 (t0) REVERT: A 472 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5574 (p90) REVERT: B 139 CYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7685 (m) REVERT: B 457 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7334 (pmt170) REVERT: B 479 MET cc_start: 0.9180 (ppp) cc_final: 0.8832 (pmm) REVERT: C 27 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7057 (mmt180) REVERT: C 41 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8929 (p) REVERT: C 354 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8399 (t80) REVERT: C 433 GLU cc_start: 0.9431 (tp30) cc_final: 0.8963 (tp30) REVERT: C 435 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9064 (tp30) REVERT: C 470 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (t80) outliers start: 51 outliers final: 31 residues processed: 124 average time/residue: 1.2640 time to fit residues: 171.5459 Evaluate side-chains 121 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 27 ARG 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 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 491 LYS Chi-restraints excluded: chain A residue 496 SER 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 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 390 ASN 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 27 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 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 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 72 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 444 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3443 r_free = 0.3443 target = 0.085420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.050419 restraints weight = 30883.491| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.19 r_work: 0.2459 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12074 Z= 0.171 Angle : 0.634 11.069 16371 Z= 0.318 Chirality : 0.043 0.360 1801 Planarity : 0.003 0.043 2099 Dihedral : 8.765 135.842 1998 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.43 % Allowed : 31.93 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1444 helix: 2.41 (0.27), residues: 376 sheet: 0.23 (0.29), residues: 323 loop : -1.35 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 422 HIS 0.007 0.001 HIS A 472 PHE 0.021 0.001 PHE A 470 TYR 0.018 0.001 TYR B 471 ARG 0.005 0.000 ARG B 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 10) link_NAG-ASN : angle 2.29339 ( 30) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 0.89937 ( 9) hydrogen bonds : bond 0.06017 ( 440) hydrogen bonds : angle 5.07476 ( 1296) SS BOND : bond 0.00284 ( 18) SS BOND : angle 1.85512 ( 36) glycosidic custom : bond 0.00116 ( 2) glycosidic custom : angle 0.86944 ( 6) covalent geometry : bond 0.00392 (12041) covalent geometry : angle 0.62100 (16290) ********************** 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 127 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8601 (mpp80) REVERT: A 255 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 269 MET cc_start: 0.8816 (ttm) cc_final: 0.8535 (ttm) REVERT: A 284 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9065 (p) REVERT: A 450 ASP cc_start: 0.9710 (t0) cc_final: 0.9365 (p0) REVERT: A 454 MET cc_start: 0.9080 (mmp) cc_final: 0.8724 (mmt) REVERT: A 465 ASN cc_start: 0.8565 (t0) cc_final: 0.8314 (t0) REVERT: A 496 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8388 (m) REVERT: B 139 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7672 (m) REVERT: B 457 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7405 (pmt170) REVERT: B 479 MET cc_start: 0.9204 (ppp) cc_final: 0.8858 (pmm) REVERT: C 27 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7029 (mmt180) REVERT: C 41 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 354 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8362 (t80) REVERT: C 433 GLU cc_start: 0.9430 (tp30) cc_final: 0.8977 (tp30) REVERT: C 435 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9055 (tp30) REVERT: C 470 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7834 (t80) outliers start: 44 outliers final: 28 residues processed: 120 average time/residue: 1.1914 time to fit residues: 155.9387 Evaluate side-chains 118 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 27 ARG 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 496 SER 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 139 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 27 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 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 441 HIS 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 136 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 99 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.085277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.050496 restraints weight = 30841.087| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 4.16 r_work: 0.2454 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12074 Z= 0.187 Angle : 0.639 13.405 16371 Z= 0.320 Chirality : 0.043 0.359 1801 Planarity : 0.003 0.043 2099 Dihedral : 8.712 135.473 1998 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.43 % Allowed : 31.93 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1444 helix: 2.50 (0.27), residues: 375 sheet: 0.25 (0.29), residues: 323 loop : -1.40 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS B 472 PHE 0.010 0.001 PHE A 470 TYR 0.031 0.001 TYR B 492 ARG 0.005 0.000 ARG B 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 10) link_NAG-ASN : angle 2.31345 ( 30) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 0.93317 ( 9) hydrogen bonds : bond 0.06119 ( 440) hydrogen bonds : angle 5.10537 ( 1296) SS BOND : bond 0.00281 ( 18) SS BOND : angle 1.80287 ( 36) glycosidic custom : bond 0.00080 ( 2) glycosidic custom : angle 0.95978 ( 6) covalent geometry : bond 0.00429 (12041) covalent geometry : angle 0.62605 (16290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8046.80 seconds wall clock time: 139 minutes 38.71 seconds (8378.71 seconds total)