Starting phenix.real_space_refine on Wed Jul 30 00:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr8_38598/07_2025/8xr8_38598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr8_38598/07_2025/8xr8_38598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xr8_38598/07_2025/8xr8_38598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr8_38598/07_2025/8xr8_38598.map" model { file = "/net/cci-nas-00/data/ceres_data/8xr8_38598/07_2025/8xr8_38598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr8_38598/07_2025/8xr8_38598.cif" } resolution = 2.53 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= 0.001 sd= 0.024 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 7372 2.51 5 N 2006 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11809 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3871 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} 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: 8.72, per 1000 atoms: 0.74 Number of scatterers: 11809 At special positions: 0 Unit cell: (91.8, 87.55, 150.45, 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 2359 8.00 N 2006 7.00 C 7372 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=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 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=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 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=2.02 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=2.02 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 " BETA2-3 " 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 A 701 " - " ASN A 28 " " NAG A 702 " - " ASN A 290 " " NAG A 703 " - " ASN A 16 " " 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 34 sheets defined 27.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.759A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.905A 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 removed outlier: 3.819A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.568A pdb=" N GLN A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 388 removed outlier: 3.507A pdb=" N LYS A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.707A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.882A 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 removed outlier: 3.540A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 369 through 388 removed outlier: 3.695A pdb=" N LYS B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 456 Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 493 through 502 Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.531A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.781A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.512A pdb=" N GLN C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 389 removed outlier: 3.848A pdb=" N THR C 371 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) 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 501 removed outlier: 3.822A pdb=" N ASN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.426A pdb=" N ILE A 8 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 468 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 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 38 through 39 Processing sheet with id=AA6, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.517A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.500A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.949A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.456A pdb=" N ALA A 138 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N SER A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.505A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.731A pdb=" N GLY B 11 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.267A 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 55 through 56 removed outlier: 6.872A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.801A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.801A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.212A pdb=" N ALA B 138 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N SER B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.558A pdb=" N ILE B 289 " --> pdb=" O CYS B 282 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 357 removed outlier: 4.542A pdb=" N ILE C 8 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 468 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.543A pdb=" N GLY C 11 " --> pdb=" O GLY C 353 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.177A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) 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 38 through 39 Processing sheet with id=AD2, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.939A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.348A 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: 5.369A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.000A 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: 7.960A 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: 7.522A pdb=" N ALA C 138 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 10.539A 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 288 through 289 removed outlier: 4.262A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1299 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: 5.38 Time building geometry restraints manager: 3.66 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: 3880 1.34 - 1.46: 2756 1.46 - 1.58: 5314 1.58 - 1.71: 0 1.71 - 1.83: 108 Bond restraints: 12058 Sorted by residual: bond pdb=" CB CYS C 278 " pdb=" SG CYS C 278 " ideal model delta sigma weight residual 1.808 1.746 0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" CB CYS B 278 " pdb=" SG CYS B 278 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" C3 GAL G 1 " pdb=" O3 GAL G 1 " ideal model delta sigma weight residual 1.406 1.375 0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C3 GAL H 1 " pdb=" O3 GAL H 1 " ideal model delta sigma weight residual 1.406 1.375 0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 12053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 16269 4.25 - 8.51: 39 8.51 - 12.76: 3 12.76 - 17.01: 0 17.01 - 21.26: 2 Bond angle restraints: 16313 Sorted by residual: angle pdb=" C2 GAL G 1 " pdb=" C3 GAL G 1 " pdb=" O3 GAL G 1 " ideal model delta sigma weight residual 107.49 128.75 -21.26 3.00e+00 1.11e-01 5.02e+01 angle pdb=" C2 GAL H 1 " pdb=" C3 GAL H 1 " pdb=" O3 GAL H 1 " ideal model delta sigma weight residual 107.49 125.90 -18.41 3.00e+00 1.11e-01 3.77e+01 angle pdb=" CA CYS C 278 " pdb=" CB CYS C 278 " pdb=" SG CYS C 278 " ideal model delta sigma weight residual 114.40 124.99 -10.59 2.30e+00 1.89e-01 2.12e+01 angle pdb=" C CYS C 278 " pdb=" CA CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sigma weight residual 112.44 103.13 9.31 2.07e+00 2.33e-01 2.02e+01 angle pdb=" CA LYS C 368 " pdb=" CB LYS C 368 " pdb=" CG LYS C 368 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 ... (remaining 16308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 6713 27.99 - 55.99: 705 55.99 - 83.98: 80 83.98 - 111.98: 11 111.98 - 139.97: 8 Dihedral angle restraints: 7517 sinusoidal: 3344 harmonic: 4173 Sorted by residual: 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 27.37 65.63 1 1.00e+01 1.00e-02 5.64e+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 37.04 55.96 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS C 282 " pdb=" SG CYS C 282 " pdb=" SG CYS C 306 " pdb=" CB CYS C 306 " ideal model delta sinusoidal sigma weight residual 93.00 37.44 55.56 1 1.00e+01 1.00e-02 4.17e+01 ... (remaining 7514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 1800 0.162 - 0.325: 2 0.325 - 0.487: 0 0.487 - 0.650: 1 0.650 - 0.812: 1 Chirality restraints: 1804 Sorted by residual: chirality pdb=" C2 SIA H 2 " pdb=" O3 GAL H 1 " pdb=" C1 SIA H 2 " pdb=" O6 SIA H 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.69 0.19 2.00e-02 2.50e+03 8.78e+01 chirality pdb=" C2 SIA G 2 " pdb=" O3 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.64 0.14 2.00e-02 2.50e+03 5.00e+01 chirality pdb=" C3 GAL H 1 " pdb=" C2 GAL H 1 " pdb=" C4 GAL H 1 " pdb=" O3 GAL H 1 " both_signs ideal model delta sigma weight residual False 2.41 1.59 0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 1801 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 16 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ASN C 16 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN C 16 " -0.015 2.00e-02 2.50e+03 pdb=" N SER C 17 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 293 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO C 294 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 294 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 294 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 78 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 79 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.023 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1393 2.75 - 3.28: 10505 3.28 - 3.82: 19411 3.82 - 4.36: 22475 4.36 - 4.90: 39215 Nonbonded interactions: 92999 Sorted by model distance: nonbonded pdb=" O ASP B 458 " pdb=" NH2 ARG B 500 " model vdw 2.208 3.120 nonbonded pdb=" O SER B 159 " pdb=" OG SER B 159 " model vdw 2.221 3.040 nonbonded pdb=" O SER C 112 " pdb=" OG SER C 112 " model vdw 2.237 3.040 nonbonded pdb=" O TYR A 492 " pdb=" OG SER A 496 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 112 " pdb=" OG SER A 112 " model vdw 2.250 3.040 ... (remaining 92994 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 701 throug \ h 702)) 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: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.020 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:18.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.005 0.062 12091 Z= 0.208 Angle : 0.829 41.979 16394 Z= 0.372 Chirality : 0.051 0.812 1804 Planarity : 0.004 0.057 2102 Dihedral : 20.794 139.972 4799 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.92 % Allowed : 30.71 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.07 % 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: -0.58 (0.22), residues: 1446 helix: 2.03 (0.27), residues: 366 sheet: -0.30 (0.30), residues: 331 loop : -1.74 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.005 0.001 HIS A 296 PHE 0.015 0.002 PHE C 148 TYR 0.009 0.001 TYR C 364 ARG 0.007 0.001 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.05709 ( 2) link_BETA2-3 : angle 23.45757 ( 6) link_NAG-ASN : bond 0.00221 ( 10) link_NAG-ASN : angle 1.87743 ( 30) link_BETA1-4 : bond 0.00419 ( 3) link_BETA1-4 : angle 0.93059 ( 9) hydrogen bonds : bond 0.15226 ( 436) hydrogen bonds : angle 7.05096 ( 1299) SS BOND : bond 0.00546 ( 18) SS BOND : angle 3.10648 ( 36) covalent geometry : bond 0.00474 (12058) covalent geometry : angle 0.67841 (16313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 1.438 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 348 VAL cc_start: 0.8819 (m) cc_final: 0.8465 (t) outliers start: 76 outliers final: 70 residues processed: 376 average time/residue: 1.5620 time to fit residues: 631.7787 Evaluate side-chains 374 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS 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: 2.9990 chunk 109 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 33 HIS B 50 ASN B 196 GLN B 383 ASN C 196 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.140532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113871 restraints weight = 15643.432| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.89 r_work: 0.3408 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12091 Z= 0.258 Angle : 0.690 14.638 16394 Z= 0.347 Chirality : 0.048 0.333 1804 Planarity : 0.005 0.063 2102 Dihedral : 13.801 141.129 2112 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.17 % Allowed : 27.36 % Favored : 65.47 % 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: -0.69 (0.22), residues: 1446 helix: 1.94 (0.26), residues: 373 sheet: -0.50 (0.29), residues: 341 loop : -1.79 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 81 HIS 0.006 0.001 HIS A 296 PHE 0.016 0.002 PHE C 295 TYR 0.013 0.002 TYR B 103 ARG 0.004 0.001 ARG C 137 Details of bonding type rmsd link_BETA2-3 : bond 0.02903 ( 2) link_BETA2-3 : angle 8.20644 ( 6) link_NAG-ASN : bond 0.00313 ( 10) link_NAG-ASN : angle 1.96524 ( 30) link_BETA1-4 : bond 0.00520 ( 3) link_BETA1-4 : angle 0.72522 ( 9) hydrogen bonds : bond 0.06238 ( 436) hydrogen bonds : angle 5.36897 ( 1299) SS BOND : bond 0.00551 ( 18) SS BOND : angle 2.75146 ( 36) covalent geometry : bond 0.00627 (12058) covalent geometry : angle 0.65559 (16313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 309 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 VAL cc_start: 0.8912 (m) cc_final: 0.8532 (t) REVERT: B 196 GLN cc_start: 0.8568 (tp40) cc_final: 0.8187 (tp40) REVERT: B 454 MET cc_start: 0.6070 (tmm) cc_final: 0.5808 (tmm) REVERT: B 479 MET cc_start: 0.7453 (tmm) cc_final: 0.7075 (ttp) outliers start: 92 outliers final: 57 residues processed: 371 average time/residue: 1.3092 time to fit residues: 523.3174 Evaluate side-chains 352 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0020 chunk 42 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 110 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 16 ASN B 33 HIS B 50 ASN B 323 ASN B 383 ASN B 455 GLN C 196 GLN C 358 ASN C 444 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115415 restraints weight = 15828.051| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.91 r_work: 0.3437 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12091 Z= 0.150 Angle : 0.627 14.907 16394 Z= 0.312 Chirality : 0.044 0.289 1804 Planarity : 0.004 0.055 2102 Dihedral : 12.063 143.430 2038 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.24 % Allowed : 28.99 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.53 (0.22), residues: 1446 helix: 2.22 (0.27), residues: 373 sheet: -0.53 (0.29), residues: 345 loop : -1.71 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 PHE 0.012 0.001 PHE C 148 TYR 0.020 0.001 TYR A 12 ARG 0.005 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.02391 ( 2) link_BETA2-3 : angle 7.76711 ( 6) link_NAG-ASN : bond 0.00219 ( 10) link_NAG-ASN : angle 1.79179 ( 30) link_BETA1-4 : bond 0.00358 ( 3) link_BETA1-4 : angle 0.82421 ( 9) hydrogen bonds : bond 0.05511 ( 436) hydrogen bonds : angle 5.03031 ( 1299) SS BOND : bond 0.00484 ( 18) SS BOND : angle 2.75015 ( 36) covalent geometry : bond 0.00349 (12058) covalent geometry : angle 0.59113 (16313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 302 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: A 348 VAL cc_start: 0.8800 (m) cc_final: 0.8431 (t) REVERT: A 468 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.6098 (p90) REVERT: B 454 MET cc_start: 0.5916 (tmm) cc_final: 0.5626 (tmm) REVERT: B 479 MET cc_start: 0.7388 (tmm) cc_final: 0.7150 (ttp) REVERT: B 500 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6192 (ptm160) REVERT: C 113 VAL cc_start: 0.8043 (t) cc_final: 0.7615 (p) REVERT: C 219 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 345 GLN cc_start: 0.7743 (mp10) cc_final: 0.7528 (mp10) REVERT: C 454 MET cc_start: 0.6769 (tmm) cc_final: 0.6541 (tmm) outliers start: 80 outliers final: 46 residues processed: 354 average time/residue: 1.3010 time to fit residues: 496.0665 Evaluate side-chains 346 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 210 ASN A 283 GLN A 392 GLN B 16 ASN B 50 ASN B 191 GLN B 196 GLN B 383 ASN C 196 GLN C 402 ASN C 444 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.142734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115935 restraints weight = 15629.056| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.90 r_work: 0.3448 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12091 Z= 0.139 Angle : 0.600 14.798 16394 Z= 0.301 Chirality : 0.044 0.272 1804 Planarity : 0.004 0.052 2102 Dihedral : 11.037 143.510 2022 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.39 % Allowed : 28.68 % Favored : 64.93 % 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: -0.41 (0.22), residues: 1446 helix: 2.37 (0.27), residues: 373 sheet: -0.43 (0.30), residues: 345 loop : -1.69 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 422 HIS 0.003 0.001 HIS A 296 PHE 0.010 0.001 PHE C 148 TYR 0.007 0.001 TYR B 471 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.02296 ( 2) link_BETA2-3 : angle 7.33809 ( 6) link_NAG-ASN : bond 0.00222 ( 10) link_NAG-ASN : angle 1.66732 ( 30) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 0.82160 ( 9) hydrogen bonds : bond 0.05271 ( 436) hydrogen bonds : angle 4.85738 ( 1299) SS BOND : bond 0.00423 ( 18) SS BOND : angle 2.25147 ( 36) covalent geometry : bond 0.00321 (12058) covalent geometry : angle 0.57037 (16313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 306 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: A 348 VAL cc_start: 0.8880 (m) cc_final: 0.8510 (t) REVERT: B 196 GLN cc_start: 0.8535 (tp40) cc_final: 0.8189 (tp40) REVERT: B 454 MET cc_start: 0.5939 (tmm) cc_final: 0.5645 (tmm) REVERT: B 479 MET cc_start: 0.7464 (tmm) cc_final: 0.7210 (ttp) REVERT: B 500 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6048 (ptm160) REVERT: C 219 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 345 GLN cc_start: 0.7747 (mp10) cc_final: 0.7501 (mp10) REVERT: C 454 MET cc_start: 0.6749 (tmm) cc_final: 0.6493 (tmm) outliers start: 82 outliers final: 51 residues processed: 359 average time/residue: 1.3025 time to fit residues: 505.5382 Evaluate side-chains 359 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 0.0060 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 455 GLN B 16 ASN B 50 ASN B 383 ASN B 455 GLN C 196 GLN C 444 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.144144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117395 restraints weight = 15688.022| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.90 r_work: 0.3452 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12091 Z= 0.129 Angle : 0.595 14.664 16394 Z= 0.298 Chirality : 0.043 0.260 1804 Planarity : 0.004 0.051 2102 Dihedral : 10.552 143.510 2014 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.47 % Allowed : 29.38 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.36 (0.22), residues: 1446 helix: 2.46 (0.27), residues: 373 sheet: -0.46 (0.30), residues: 347 loop : -1.64 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 422 HIS 0.005 0.001 HIS C 13 PHE 0.010 0.001 PHE B 339 TYR 0.020 0.001 TYR A 12 ARG 0.006 0.000 ARG C 126 Details of bonding type rmsd link_BETA2-3 : bond 0.02154 ( 2) link_BETA2-3 : angle 7.02544 ( 6) link_NAG-ASN : bond 0.00219 ( 10) link_NAG-ASN : angle 1.61744 ( 30) link_BETA1-4 : bond 0.00395 ( 3) link_BETA1-4 : angle 0.80733 ( 9) hydrogen bonds : bond 0.05079 ( 436) hydrogen bonds : angle 4.73438 ( 1299) SS BOND : bond 0.00626 ( 18) SS BOND : angle 2.60527 ( 36) covalent geometry : bond 0.00296 (12058) covalent geometry : angle 0.56333 (16313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8135 (mptp) REVERT: A 111 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8118 (t) REVERT: A 246 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 348 VAL cc_start: 0.8870 (m) cc_final: 0.8501 (t) REVERT: A 389 MET cc_start: 0.8518 (mmm) cc_final: 0.8262 (mmm) REVERT: A 455 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7537 (tp40) REVERT: B 196 GLN cc_start: 0.8579 (tp40) cc_final: 0.8293 (tp40) REVERT: B 479 MET cc_start: 0.7399 (tmm) cc_final: 0.7150 (ttp) REVERT: B 500 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6052 (ptm160) REVERT: C 182 VAL cc_start: 0.8908 (p) cc_final: 0.8686 (t) REVERT: C 219 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8189 (p) REVERT: C 345 GLN cc_start: 0.7727 (mp10) cc_final: 0.7476 (mp10) REVERT: C 454 MET cc_start: 0.6679 (tmm) cc_final: 0.6408 (tmm) outliers start: 83 outliers final: 52 residues processed: 368 average time/residue: 2.1557 time to fit residues: 851.9864 Evaluate side-chains 358 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 300 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 392 GLN A 455 GLN B 16 ASN B 50 ASN B 383 ASN C 196 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.143649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116696 restraints weight = 15777.213| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.93 r_work: 0.3439 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12091 Z= 0.161 Angle : 0.616 14.492 16394 Z= 0.310 Chirality : 0.044 0.244 1804 Planarity : 0.004 0.051 2102 Dihedral : 10.319 144.066 2014 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.31 % Allowed : 29.70 % Favored : 63.99 % 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: -0.38 (0.22), residues: 1446 helix: 2.42 (0.27), residues: 373 sheet: -0.45 (0.30), residues: 346 loop : -1.66 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 PHE 0.010 0.002 PHE C 148 TYR 0.010 0.001 TYR C 492 ARG 0.006 0.000 ARG C 126 Details of bonding type rmsd link_BETA2-3 : bond 0.02034 ( 2) link_BETA2-3 : angle 6.78594 ( 6) link_NAG-ASN : bond 0.00228 ( 10) link_NAG-ASN : angle 1.61096 ( 30) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 0.81831 ( 9) hydrogen bonds : bond 0.05233 ( 436) hydrogen bonds : angle 4.72679 ( 1299) SS BOND : bond 0.00470 ( 18) SS BOND : angle 2.72786 ( 36) covalent geometry : bond 0.00382 (12058) covalent geometry : angle 0.58551 (16313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 303 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 348 VAL cc_start: 0.8864 (m) cc_final: 0.8491 (t) REVERT: A 389 MET cc_start: 0.8489 (mmm) cc_final: 0.8216 (mmm) REVERT: B 454 MET cc_start: 0.5830 (tmm) cc_final: 0.5481 (tmm) REVERT: B 500 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.6141 (ptm160) REVERT: C 182 VAL cc_start: 0.8918 (p) cc_final: 0.8683 (t) REVERT: C 187 ASP cc_start: 0.7449 (p0) cc_final: 0.7205 (p0) REVERT: C 219 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 454 MET cc_start: 0.6717 (tmm) cc_final: 0.6438 (tmm) outliers start: 81 outliers final: 52 residues processed: 358 average time/residue: 1.3045 time to fit residues: 504.3511 Evaluate side-chains 358 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN A 455 GLN B 16 ASN B 50 ASN B 196 GLN B 383 ASN B 499 ASN C 196 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115639 restraints weight = 15913.530| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.93 r_work: 0.3427 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12091 Z= 0.208 Angle : 0.665 14.596 16394 Z= 0.335 Chirality : 0.046 0.219 1804 Planarity : 0.004 0.054 2102 Dihedral : 10.071 143.611 2007 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.69 % Allowed : 30.55 % Favored : 63.76 % 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: -0.46 (0.22), residues: 1446 helix: 2.31 (0.26), residues: 373 sheet: -0.43 (0.30), residues: 340 loop : -1.71 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 81 HIS 0.005 0.001 HIS A 296 PHE 0.014 0.002 PHE B 440 TYR 0.024 0.001 TYR A 12 ARG 0.007 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.02057 ( 2) link_BETA2-3 : angle 6.72450 ( 6) link_NAG-ASN : bond 0.00249 ( 10) link_NAG-ASN : angle 1.70831 ( 30) link_BETA1-4 : bond 0.00382 ( 3) link_BETA1-4 : angle 0.78738 ( 9) hydrogen bonds : bond 0.05562 ( 436) hydrogen bonds : angle 4.75851 ( 1299) SS BOND : bond 0.00581 ( 18) SS BOND : angle 3.27545 ( 36) covalent geometry : bond 0.00504 (12058) covalent geometry : angle 0.63110 (16313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 306 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 348 VAL cc_start: 0.8878 (m) cc_final: 0.8496 (t) REVERT: B 192 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8054 (mtp85) REVERT: B 196 GLN cc_start: 0.8540 (tp40) cc_final: 0.8175 (tp40) REVERT: B 479 MET cc_start: 0.6605 (ttp) cc_final: 0.6372 (ttt) REVERT: B 500 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6220 (ptm160) REVERT: C 125 ASP cc_start: 0.7737 (p0) cc_final: 0.7515 (p0) REVERT: C 182 VAL cc_start: 0.8913 (p) cc_final: 0.8685 (t) REVERT: C 187 ASP cc_start: 0.7479 (p0) cc_final: 0.7225 (p0) REVERT: C 219 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8194 (p) REVERT: C 454 MET cc_start: 0.6792 (tmm) cc_final: 0.6512 (tmm) outliers start: 73 outliers final: 52 residues processed: 354 average time/residue: 1.6190 time to fit residues: 617.2764 Evaluate side-chains 347 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 130 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN A 455 GLN B 16 ASN B 50 ASN B 323 ASN B 383 ASN C 196 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116794 restraints weight = 15803.725| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.93 r_work: 0.3446 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12091 Z= 0.135 Angle : 0.619 14.230 16394 Z= 0.313 Chirality : 0.043 0.204 1804 Planarity : 0.004 0.052 2102 Dihedral : 9.838 143.975 2006 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.99 % Allowed : 31.72 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.22), residues: 1446 helix: 2.39 (0.27), residues: 374 sheet: -0.41 (0.30), residues: 340 loop : -1.68 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.003 0.001 HIS C 355 PHE 0.010 0.001 PHE C 148 TYR 0.011 0.001 TYR A 492 ARG 0.007 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.01881 ( 2) link_BETA2-3 : angle 6.45055 ( 6) link_NAG-ASN : bond 0.00254 ( 10) link_NAG-ASN : angle 1.69438 ( 30) link_BETA1-4 : bond 0.00359 ( 3) link_BETA1-4 : angle 0.79866 ( 9) hydrogen bonds : bond 0.05150 ( 436) hydrogen bonds : angle 4.66499 ( 1299) SS BOND : bond 0.00472 ( 18) SS BOND : angle 2.72187 ( 36) covalent geometry : bond 0.00313 (12058) covalent geometry : angle 0.58979 (16313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8136 (t) REVERT: A 348 VAL cc_start: 0.8882 (m) cc_final: 0.8502 (t) REVERT: B 192 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8145 (mtt-85) REVERT: B 457 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.4934 (mpp-170) REVERT: B 479 MET cc_start: 0.6622 (ttp) cc_final: 0.6404 (ttt) REVERT: B 500 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6215 (ptm160) REVERT: C 125 ASP cc_start: 0.7732 (p0) cc_final: 0.7510 (p0) REVERT: C 182 VAL cc_start: 0.8916 (p) cc_final: 0.8689 (t) REVERT: C 187 ASP cc_start: 0.7450 (p0) cc_final: 0.7201 (p0) REVERT: C 219 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 454 MET cc_start: 0.6714 (tmm) cc_final: 0.6429 (tmm) outliers start: 64 outliers final: 47 residues processed: 341 average time/residue: 1.3181 time to fit residues: 483.9805 Evaluate side-chains 349 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 4 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 210 ASN A 455 GLN B 16 ASN B 50 ASN B 196 GLN B 383 ASN C 196 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116097 restraints weight = 15874.432| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.93 r_work: 0.3452 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12091 Z= 0.136 Angle : 0.616 14.259 16394 Z= 0.311 Chirality : 0.043 0.181 1804 Planarity : 0.004 0.052 2102 Dihedral : 9.720 143.679 2006 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.75 % Allowed : 31.88 % Favored : 63.37 % 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: -0.36 (0.22), residues: 1446 helix: 2.41 (0.27), residues: 374 sheet: -0.41 (0.30), residues: 340 loop : -1.65 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.003 0.001 HIS C 355 PHE 0.009 0.001 PHE C 148 TYR 0.020 0.001 TYR A 12 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.01867 ( 2) link_BETA2-3 : angle 6.43948 ( 6) link_NAG-ASN : bond 0.00244 ( 10) link_NAG-ASN : angle 1.63640 ( 30) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 0.80750 ( 9) hydrogen bonds : bond 0.05084 ( 436) hydrogen bonds : angle 4.61529 ( 1299) SS BOND : bond 0.00493 ( 18) SS BOND : angle 2.67746 ( 36) covalent geometry : bond 0.00318 (12058) covalent geometry : angle 0.58759 (16313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.8142 (t) REVERT: A 246 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 348 VAL cc_start: 0.8877 (m) cc_final: 0.8487 (t) REVERT: B 457 ARG cc_start: 0.5515 (OUTLIER) cc_final: 0.5218 (mpp-170) REVERT: B 479 MET cc_start: 0.6761 (ttp) cc_final: 0.6549 (ttt) REVERT: B 500 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.6125 (ptm160) REVERT: C 125 ASP cc_start: 0.7728 (p0) cc_final: 0.7502 (p0) REVERT: C 182 VAL cc_start: 0.8912 (p) cc_final: 0.8683 (t) REVERT: C 187 ASP cc_start: 0.7441 (p0) cc_final: 0.7207 (p0) REVERT: C 219 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8195 (p) REVERT: C 454 MET cc_start: 0.6676 (tmm) cc_final: 0.6384 (tmm) outliers start: 61 outliers final: 48 residues processed: 343 average time/residue: 1.3085 time to fit residues: 483.4682 Evaluate side-chains 351 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 92 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.0060 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN B 16 ASN B 50 ASN B 226 GLN B 383 ASN C 196 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114955 restraints weight = 15756.851| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.93 r_work: 0.3435 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12091 Z= 0.181 Angle : 0.657 13.934 16394 Z= 0.334 Chirality : 0.045 0.172 1804 Planarity : 0.004 0.053 2102 Dihedral : 9.598 142.333 2005 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.52 % Allowed : 32.11 % Favored : 63.37 % 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: -0.39 (0.22), residues: 1446 helix: 2.35 (0.27), residues: 374 sheet: -0.36 (0.30), residues: 335 loop : -1.67 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.005 0.001 HIS A 296 PHE 0.012 0.002 PHE C 148 TYR 0.012 0.001 TYR A 492 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.01871 ( 2) link_BETA2-3 : angle 6.37426 ( 6) link_NAG-ASN : bond 0.00252 ( 10) link_NAG-ASN : angle 1.69186 ( 30) link_BETA1-4 : bond 0.00387 ( 3) link_BETA1-4 : angle 0.80574 ( 9) hydrogen bonds : bond 0.05389 ( 436) hydrogen bonds : angle 4.65761 ( 1299) SS BOND : bond 0.00576 ( 18) SS BOND : angle 3.05043 ( 36) covalent geometry : bond 0.00434 (12058) covalent geometry : angle 0.62635 (16313) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 296 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 348 VAL cc_start: 0.8853 (m) cc_final: 0.8453 (t) REVERT: B 192 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8181 (mtt-85) REVERT: B 196 GLN cc_start: 0.8606 (tp40) cc_final: 0.8284 (tp40) REVERT: B 457 ARG cc_start: 0.5556 (OUTLIER) cc_final: 0.5138 (mpp-170) REVERT: B 479 MET cc_start: 0.6818 (ttp) cc_final: 0.6617 (ttt) REVERT: B 500 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6082 (ptm160) REVERT: C 125 ASP cc_start: 0.7732 (p0) cc_final: 0.7509 (p0) REVERT: C 182 VAL cc_start: 0.8918 (p) cc_final: 0.8694 (t) REVERT: C 187 ASP cc_start: 0.7460 (p0) cc_final: 0.7242 (p0) REVERT: C 219 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8194 (p) REVERT: C 454 MET cc_start: 0.6699 (tmm) cc_final: 0.6415 (tmm) REVERT: C 471 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.5204 (t80) outliers start: 58 outliers final: 48 residues processed: 334 average time/residue: 1.2940 time to fit residues: 464.4920 Evaluate side-chains 347 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 50 ASN B 383 ASN C 196 GLN ** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114989 restraints weight = 15713.089| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.93 r_work: 0.3438 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 12091 Z= 0.209 Angle : 0.892 59.198 16394 Z= 0.505 Chirality : 0.045 0.392 1804 Planarity : 0.004 0.053 2102 Dihedral : 9.595 142.331 2005 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.75 % Allowed : 31.88 % Favored : 63.37 % Cbeta Deviations : 0.08 % 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: -0.39 (0.22), residues: 1446 helix: 2.36 (0.27), residues: 374 sheet: -0.36 (0.30), residues: 335 loop : -1.68 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 PHE 0.012 0.002 PHE C 470 TYR 0.011 0.001 TYR A 492 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd link_BETA2-3 : bond 0.01426 ( 2) link_BETA2-3 : angle 6.60017 ( 6) link_NAG-ASN : bond 0.00244 ( 10) link_NAG-ASN : angle 1.68896 ( 30) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 0.80843 ( 9) hydrogen bonds : bond 0.05358 ( 436) hydrogen bonds : angle 4.66212 ( 1299) SS BOND : bond 0.00564 ( 18) SS BOND : angle 3.00478 ( 36) covalent geometry : bond 0.00456 (12058) covalent geometry : angle 0.87070 (16313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12917.81 seconds wall clock time: 225 minutes 27.02 seconds (13527.02 seconds total)