Starting phenix.real_space_refine on Sat Aug 23 11:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr8_38598/08_2025/8xr8_38598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr8_38598/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xr8_38598/08_2025/8xr8_38598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr8_38598/08_2025/8xr8_38598.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xr8_38598/08_2025/8xr8_38598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr8_38598/08_2025/8xr8_38598.map" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.21, per 1000 atoms: 0.27 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: 1.06 Conformation dependent library (CDL) restraints added in 522.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 2.21 Time building geometry restraints manager: 1.35 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 702) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (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 ARG 0.007 0.001 ARG C 27 TYR 0.009 0.001 TYR C 364 PHE 0.015 0.002 PHE C 148 TRP 0.011 0.001 TRP C 422 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00474 (12058) covalent geometry : angle 0.67841 (16313) SS BOND : bond 0.00546 ( 18) SS BOND : angle 3.10648 ( 36) hydrogen bonds : bond 0.15226 ( 436) hydrogen bonds : angle 7.05096 ( 1299) link_BETA1-4 : bond 0.00419 ( 3) link_BETA1-4 : angle 0.93059 ( 9) 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) *********************** 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 : 0.518 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: 0.6581 time to fit residues: 266.6396 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 : 0.482 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 283 GLN B 16 ASN B 50 ASN B 196 GLN B 383 ASN C 196 GLN C 358 ASN C 444 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.141497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114781 restraints weight = 15704.637| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.91 r_work: 0.3423 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12091 Z= 0.192 Angle : 0.648 14.549 16394 Z= 0.324 Chirality : 0.046 0.313 1804 Planarity : 0.004 0.058 2102 Dihedral : 13.597 141.726 2112 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 7.09 % Allowed : 27.67 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.22), residues: 1446 helix: 2.09 (0.26), residues: 373 sheet: -0.47 (0.30), residues: 341 loop : -1.74 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.013 0.001 TYR B 103 PHE 0.013 0.002 PHE C 148 TRP 0.011 0.001 TRP C 422 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00458 (12058) covalent geometry : angle 0.61512 (16313) SS BOND : bond 0.00476 ( 18) SS BOND : angle 2.47346 ( 36) hydrogen bonds : bond 0.05803 ( 436) hydrogen bonds : angle 5.25725 ( 1299) link_BETA1-4 : bond 0.00529 ( 3) link_BETA1-4 : angle 0.72668 ( 9) link_BETA2-3 : bond 0.02607 ( 2) link_BETA2-3 : angle 8.04612 ( 6) link_NAG-ASN : bond 0.00306 ( 10) link_NAG-ASN : angle 1.86003 ( 30) *********************** 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 405 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 VAL cc_start: 0.8808 (m) cc_final: 0.8443 (t) REVERT: A 455 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: B 196 GLN cc_start: 0.8575 (tp40) cc_final: 0.8248 (tp40) REVERT: B 454 MET cc_start: 0.6055 (tmm) cc_final: 0.5790 (tmm) REVERT: B 479 MET cc_start: 0.7448 (tmm) cc_final: 0.7081 (ttt) REVERT: C 345 GLN cc_start: 0.7746 (mp10) cc_final: 0.7537 (mp10) outliers start: 91 outliers final: 51 residues processed: 374 average time/residue: 0.6329 time to fit residues: 254.9501 Evaluate side-chains 353 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 340 ILE 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 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 117 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 VAL 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 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 109 LEU 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 279 GLU Chi-restraints excluded: chain C residue 356 HIS 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 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 126 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 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 = 0.3933 r_free = 0.3933 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117194 restraints weight = 15835.765| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.93 r_work: 0.3446 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12091 Z= 0.124 Angle : 0.597 14.812 16394 Z= 0.297 Chirality : 0.043 0.288 1804 Planarity : 0.004 0.051 2102 Dihedral : 11.700 144.314 2035 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.55 % Allowed : 28.06 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1446 helix: 2.40 (0.27), residues: 373 sheet: -0.43 (0.30), residues: 345 loop : -1.65 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 27 TYR 0.021 0.001 TYR A 12 PHE 0.010 0.001 PHE B 339 TRP 0.010 0.001 TRP C 422 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00279 (12058) covalent geometry : angle 0.56231 (16313) SS BOND : bond 0.00466 ( 18) SS BOND : angle 2.53974 ( 36) hydrogen bonds : bond 0.05192 ( 436) hydrogen bonds : angle 4.88809 ( 1299) link_BETA1-4 : bond 0.00391 ( 3) link_BETA1-4 : angle 0.83697 ( 9) link_BETA2-3 : bond 0.02251 ( 2) link_BETA2-3 : angle 7.67677 ( 6) link_NAG-ASN : bond 0.00243 ( 10) link_NAG-ASN : angle 1.68748 ( 30) *********************** 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 392 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 308 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 348 VAL cc_start: 0.8854 (m) cc_final: 0.8488 (t) REVERT: A 389 MET cc_start: 0.8466 (mmm) cc_final: 0.8254 (mmm) REVERT: A 455 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: B 454 MET cc_start: 0.5998 (tmm) cc_final: 0.5712 (tmm) REVERT: B 479 MET cc_start: 0.7400 (tmm) cc_final: 0.7112 (ttp) REVERT: B 500 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6083 (ptm160) REVERT: C 219 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 345 GLN cc_start: 0.7693 (mp10) cc_final: 0.7459 (mp10) outliers start: 84 outliers final: 50 residues processed: 362 average time/residue: 0.6174 time to fit residues: 240.6439 Evaluate side-chains 356 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 248 THR 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 448 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 457 ARG 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 99 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 GLU 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 399 GLU Chi-restraints excluded: chain B residue 410 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 B residue 500 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 194 LEU 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 279 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 496 SER 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 140 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 111 optimal weight: 0.0470 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 16 ASN B 50 ASN B 196 GLN B 383 ASN B 455 GLN C 196 GLN C 402 ASN C 444 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.144378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117419 restraints weight = 15803.603| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.92 r_work: 0.3451 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12091 Z= 0.136 Angle : 0.593 14.617 16394 Z= 0.296 Chirality : 0.043 0.268 1804 Planarity : 0.004 0.050 2102 Dihedral : 10.792 143.260 2019 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.63 % Allowed : 28.76 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.22), residues: 1446 helix: 2.44 (0.27), residues: 373 sheet: -0.36 (0.30), residues: 345 loop : -1.64 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.016 0.001 TYR A 492 PHE 0.010 0.001 PHE B 339 TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00315 (12058) covalent geometry : angle 0.56343 (16313) SS BOND : bond 0.00436 ( 18) SS BOND : angle 2.26474 ( 36) hydrogen bonds : bond 0.05128 ( 436) hydrogen bonds : angle 4.75056 ( 1299) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 0.79460 ( 9) link_BETA2-3 : bond 0.02142 ( 2) link_BETA2-3 : angle 7.18305 ( 6) link_NAG-ASN : bond 0.00256 ( 10) link_NAG-ASN : angle 1.60914 ( 30) *********************** 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 393 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 308 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8114 (t) REVERT: A 246 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: A 348 VAL cc_start: 0.8871 (m) cc_final: 0.8506 (t) REVERT: A 455 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7517 (tp40) REVERT: B 196 GLN cc_start: 0.8556 (tp40) cc_final: 0.8251 (tp40) REVERT: B 454 MET cc_start: 0.5997 (tmm) cc_final: 0.5699 (tmm) REVERT: B 479 MET cc_start: 0.7457 (tmm) cc_final: 0.7203 (ttp) REVERT: B 500 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.6028 (ptm160) REVERT: C 219 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8194 (p) REVERT: C 308 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8337 (mmtp) REVERT: C 455 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7257 (tt0) outliers start: 85 outliers final: 53 residues processed: 367 average time/residue: 0.6452 time to fit residues: 254.7523 Evaluate side-chains 364 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 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 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 99 SER 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 402 ASN 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 13 HIS 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 446 LYS Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 468 PHE 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 2 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116912 restraints weight = 15897.444| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.94 r_work: 0.3444 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.004 0.046 12091 Z= 0.156 Angle : 0.613 14.664 16394 Z= 0.307 Chirality : 0.044 0.256 1804 Planarity : 0.004 0.051 2102 Dihedral : 10.426 142.899 2014 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.63 % Allowed : 29.07 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.22), residues: 1446 helix: 2.47 (0.27), residues: 373 sheet: -0.47 (0.30), residues: 349 loop : -1.62 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.020 0.001 TYR A 12 PHE 0.010 0.001 PHE C 148 TRP 0.009 0.001 TRP C 422 HIS 0.016 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00367 (12058) covalent geometry : angle 0.58114 (16313) SS BOND : bond 0.00578 ( 18) SS BOND : angle 2.74904 ( 36) hydrogen bonds : bond 0.05196 ( 436) hydrogen bonds : angle 4.72570 ( 1299) link_BETA1-4 : bond 0.00382 ( 3) link_BETA1-4 : angle 0.79608 ( 9) link_BETA2-3 : bond 0.02209 ( 2) link_BETA2-3 : angle 6.98102 ( 6) link_NAG-ASN : bond 0.00287 ( 10) link_NAG-ASN : angle 1.69850 ( 30) *********************** 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 394 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 309 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8129 (t) REVERT: A 455 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7551 (tp40) REVERT: B 196 GLN cc_start: 0.8564 (tp40) cc_final: 0.8287 (tp40) REVERT: B 454 MET cc_start: 0.5796 (tmm) cc_final: 0.5480 (tmm) REVERT: B 479 MET cc_start: 0.7351 (tmm) cc_final: 0.7146 (ttp) REVERT: B 500 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6223 (ptm160) REVERT: C 182 VAL cc_start: 0.8918 (p) cc_final: 0.8689 (t) REVERT: C 187 ASP cc_start: 0.7435 (p0) cc_final: 0.7191 (p0) REVERT: C 219 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8191 (p) REVERT: C 345 GLN cc_start: 0.7729 (mp10) cc_final: 0.7520 (mp10) outliers start: 85 outliers final: 54 residues processed: 363 average time/residue: 0.6396 time to fit residues: 249.5646 Evaluate side-chains 372 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 248 THR 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 441 HIS 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 27 ARG Chi-restraints excluded: chain B residue 99 SER 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 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 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 402 ASN Chi-restraints excluded: chain B residue 410 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 392 GLN B 16 ASN B 50 ASN B 383 ASN B 455 GLN 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 = 0.3905 r_free = 0.3905 target = 0.142038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115139 restraints weight = 15938.749| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.94 r_work: 0.3399 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12091 Z= 0.252 Angle : 0.682 14.639 16394 Z= 0.345 Chirality : 0.048 0.227 1804 Planarity : 0.004 0.057 2102 Dihedral : 10.299 141.458 2011 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.47 % Allowed : 29.23 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.22), residues: 1446 helix: 2.21 (0.26), residues: 373 sheet: -0.51 (0.29), residues: 347 loop : -1.69 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.010 0.002 TYR C 364 PHE 0.016 0.002 PHE C 295 TRP 0.012 0.002 TRP C 81 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00615 (12058) covalent geometry : angle 0.64896 (16313) SS BOND : bond 0.00596 ( 18) SS BOND : angle 3.19908 ( 36) hydrogen bonds : bond 0.05851 ( 436) hydrogen bonds : angle 4.86467 ( 1299) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 0.79092 ( 9) link_BETA2-3 : bond 0.02089 ( 2) link_BETA2-3 : angle 6.82987 ( 6) link_NAG-ASN : bond 0.00373 ( 10) link_NAG-ASN : angle 1.84833 ( 30) *********************** 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 389 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 306 time to evaluate : 0.397 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: 0.7832 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: A 389 MET cc_start: 0.8477 (mmm) cc_final: 0.8222 (mmm) REVERT: B 196 GLN cc_start: 0.8567 (tp40) cc_final: 0.8223 (tp40) REVERT: B 454 MET cc_start: 0.5843 (tmm) cc_final: 0.5491 (tmm) REVERT: B 500 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6216 (ptm160) REVERT: C 187 ASP cc_start: 0.7490 (p0) cc_final: 0.7252 (p0) REVERT: C 219 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 345 GLN cc_start: 0.7787 (mp10) cc_final: 0.7545 (mp10) outliers start: 83 outliers final: 52 residues processed: 360 average time/residue: 0.6554 time to fit residues: 253.6143 Evaluate side-chains 351 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 296 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 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 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR 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 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 402 ASN 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 279 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 471 TYR 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 116 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 32 optimal weight: 0.0070 chunk 127 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 392 GLN A 455 GLN B 16 ASN B 50 ASN B 383 ASN B 455 GLN 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 = 0.3933 r_free = 0.3933 target = 0.143927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117012 restraints weight = 15791.628| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.92 r_work: 0.3443 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1090 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= 0.135 Angle : 0.609 14.275 16394 Z= 0.307 Chirality : 0.043 0.215 1804 Planarity : 0.004 0.053 2102 Dihedral : 9.887 144.090 2007 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.14 % Allowed : 31.02 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1446 helix: 2.40 (0.27), residues: 374 sheet: -0.48 (0.30), residues: 349 loop : -1.62 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.018 0.001 TYR A 12 PHE 0.010 0.001 PHE C 148 TRP 0.011 0.001 TRP C 422 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00312 (12058) covalent geometry : angle 0.58060 (16313) SS BOND : bond 0.00504 ( 18) SS BOND : angle 2.58078 ( 36) hydrogen bonds : bond 0.05161 ( 436) hydrogen bonds : angle 4.68449 ( 1299) link_BETA1-4 : bond 0.00349 ( 3) link_BETA1-4 : angle 0.81777 ( 9) link_BETA2-3 : bond 0.01900 ( 2) link_BETA2-3 : angle 6.43125 ( 6) link_NAG-ASN : bond 0.00330 ( 10) link_NAG-ASN : angle 1.70122 ( 30) *********************** 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 372 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 306 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8308 (p) cc_final: 0.8096 (t) REVERT: A 246 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: B 192 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8032 (mtp85) REVERT: B 196 GLN cc_start: 0.8557 (tp40) cc_final: 0.8157 (tp40) REVERT: B 455 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: B 457 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.4974 (mpp-170) REVERT: B 479 MET cc_start: 0.6762 (ttp) cc_final: 0.6551 (ttt) REVERT: B 500 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6057 (ptm160) REVERT: C 182 VAL cc_start: 0.8913 (p) cc_final: 0.8698 (t) REVERT: C 187 ASP cc_start: 0.7414 (p0) cc_final: 0.7181 (p0) REVERT: C 219 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8199 (p) REVERT: C 345 GLN cc_start: 0.7704 (mp10) cc_final: 0.7489 (mp10) outliers start: 66 outliers final: 47 residues processed: 352 average time/residue: 0.6426 time to fit residues: 243.2624 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 : 0.485 ------------------------------------------------------------------------------- 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 174 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 GLU 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 468 PHE 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 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 99 SER 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 163 VAL Chi-restraints excluded: chain B residue 208 THR 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 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 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 356 HIS 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 142 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 455 GLN B 16 ASN B 50 ASN B 383 ASN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.142101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115028 restraints weight = 15874.015| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.94 r_work: 0.3432 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12091 Z= 0.174 Angle : 0.640 14.284 16394 Z= 0.324 Chirality : 0.044 0.189 1804 Planarity : 0.004 0.054 2102 Dihedral : 9.775 143.391 2006 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.38 % Allowed : 30.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.22), residues: 1446 helix: 2.36 (0.27), residues: 374 sheet: -0.49 (0.30), residues: 349 loop : -1.64 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.011 0.001 TYR C 492 PHE 0.012 0.002 PHE C 148 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00417 (12058) covalent geometry : angle 0.60917 (16313) SS BOND : bond 0.00509 ( 18) SS BOND : angle 2.97227 ( 36) hydrogen bonds : bond 0.05326 ( 436) hydrogen bonds : angle 4.68807 ( 1299) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 0.79226 ( 9) link_BETA2-3 : bond 0.01953 ( 2) link_BETA2-3 : angle 6.47116 ( 6) link_NAG-ASN : bond 0.00321 ( 10) link_NAG-ASN : angle 1.71926 ( 30) *********************** 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 360 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 0.478 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: 0.7829 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: B 196 GLN cc_start: 0.8617 (tp40) cc_final: 0.8268 (tp40) REVERT: B 454 MET cc_start: 0.5925 (tmm) cc_final: 0.5538 (tmm) REVERT: B 457 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5239 (mpp-170) REVERT: B 479 MET cc_start: 0.6820 (ttp) cc_final: 0.6596 (ttt) REVERT: B 500 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6106 (ptm160) REVERT: C 182 VAL cc_start: 0.8916 (p) cc_final: 0.8688 (t) REVERT: C 187 ASP cc_start: 0.7435 (p0) cc_final: 0.7218 (p0) REVERT: C 219 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8203 (p) REVERT: C 345 GLN cc_start: 0.7701 (mp10) cc_final: 0.7477 (mp10) REVERT: C 492 TYR cc_start: 0.7358 (t80) cc_final: 0.7100 (t80) outliers start: 69 outliers final: 48 residues processed: 337 average time/residue: 0.6380 time to fit residues: 231.1871 Evaluate side-chains 343 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 165 LYS 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 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 441 HIS 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 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 99 SER 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.142566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115653 restraints weight = 15719.515| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.92 r_work: 0.3440 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1163 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= 0.157 Angle : 0.630 13.944 16394 Z= 0.319 Chirality : 0.044 0.169 1804 Planarity : 0.004 0.053 2102 Dihedral : 9.547 142.439 2005 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.68 % Allowed : 31.41 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.22), residues: 1446 helix: 2.38 (0.27), residues: 374 sheet: -0.50 (0.30), residues: 349 loop : -1.64 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.024 0.001 TYR A 492 PHE 0.011 0.001 PHE C 148 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00373 (12058) covalent geometry : angle 0.59871 (16313) SS BOND : bond 0.00531 ( 18) SS BOND : angle 3.03035 ( 36) hydrogen bonds : bond 0.05232 ( 436) hydrogen bonds : angle 4.64431 ( 1299) link_BETA1-4 : bond 0.00373 ( 3) link_BETA1-4 : angle 0.82264 ( 9) link_BETA2-3 : bond 0.01846 ( 2) link_BETA2-3 : angle 6.31655 ( 6) link_NAG-ASN : bond 0.00312 ( 10) link_NAG-ASN : angle 1.69777 ( 30) *********************** 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 359 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 299 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8128 (t) REVERT: A 246 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: B 457 ARG cc_start: 0.5553 (OUTLIER) cc_final: 0.5138 (mpp-170) REVERT: B 500 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6067 (ptm160) REVERT: C 182 VAL cc_start: 0.8915 (p) cc_final: 0.8692 (t) REVERT: C 187 ASP cc_start: 0.7448 (p0) cc_final: 0.7227 (p0) REVERT: C 219 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 345 GLN cc_start: 0.7694 (mp10) cc_final: 0.7473 (mp10) REVERT: C 455 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7245 (tt0) outliers start: 60 outliers final: 47 residues processed: 339 average time/residue: 0.6550 time to fit residues: 239.0437 Evaluate side-chains 345 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 165 LYS 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 279 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 347 MET 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 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 99 SER 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 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 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 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 356 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 455 GLN 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: 0.0270 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8038 ------------------------------------------------------------------------------- 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 196 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.142688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115687 restraints weight = 15837.834| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.93 r_work: 0.3445 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12091 Z= 0.158 Angle : 0.643 13.506 16394 Z= 0.327 Chirality : 0.044 0.184 1804 Planarity : 0.004 0.052 2102 Dihedral : 9.429 141.607 2005 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.91 % Allowed : 31.18 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1446 helix: 2.36 (0.27), residues: 374 sheet: -0.38 (0.30), residues: 335 loop : -1.64 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.029 0.001 TYR A 492 PHE 0.011 0.002 PHE C 148 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00373 (12058) covalent geometry : angle 0.61441 (16313) SS BOND : bond 0.00507 ( 18) SS BOND : angle 2.91689 ( 36) hydrogen bonds : bond 0.05247 ( 436) hydrogen bonds : angle 4.63199 ( 1299) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 0.83627 ( 9) link_BETA2-3 : bond 0.01785 ( 2) link_BETA2-3 : angle 6.19251 ( 6) link_NAG-ASN : bond 0.00310 ( 10) link_NAG-ASN : angle 1.67418 ( 30) ********************** 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 357 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 294 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 246 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: A 479 MET cc_start: 0.7226 (pp-130) cc_final: 0.6962 (ptp) REVERT: B 192 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.8178 (mtp85) REVERT: B 196 GLN cc_start: 0.8602 (tp40) cc_final: 0.8231 (tp40) REVERT: B 457 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.5131 (mpp-170) REVERT: B 500 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6118 (ptm160) REVERT: C 182 VAL cc_start: 0.8911 (p) cc_final: 0.8688 (t) REVERT: C 219 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 345 GLN cc_start: 0.7732 (mp10) cc_final: 0.7499 (mp10) REVERT: C 455 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7213 (tt0) outliers start: 63 outliers final: 49 residues processed: 335 average time/residue: 0.6693 time to fit residues: 241.2859 Evaluate side-chains 346 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 165 LYS 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 315 LEU Chi-restraints excluded: chain A residue 347 MET 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 26 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 99 SER 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 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 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 497 LYS Chi-restraints excluded: chain B residue 500 ARG 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 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 262 LYS 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 455 GLN 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 122 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 0.0670 chunk 32 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116848 restraints weight = 15800.118| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.94 r_work: 0.3462 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12091 Z= 0.121 Angle : 0.615 12.394 16394 Z= 0.312 Chirality : 0.043 0.153 1804 Planarity : 0.004 0.051 2102 Dihedral : 9.160 140.212 2005 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.29 % Allowed : 32.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1446 helix: 2.43 (0.27), residues: 374 sheet: -0.42 (0.30), residues: 341 loop : -1.57 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.020 0.001 TYR A 492 PHE 0.009 0.001 PHE A 470 TRP 0.013 0.001 TRP C 422 HIS 0.004 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00273 (12058) covalent geometry : angle 0.59132 (16313) SS BOND : bond 0.00404 ( 18) SS BOND : angle 2.39263 ( 36) hydrogen bonds : bond 0.04867 ( 436) hydrogen bonds : angle 4.54552 ( 1299) link_BETA1-4 : bond 0.00396 ( 3) link_BETA1-4 : angle 0.88120 ( 9) link_BETA2-3 : bond 0.01568 ( 2) link_BETA2-3 : angle 5.78936 ( 6) link_NAG-ASN : bond 0.00327 ( 10) link_NAG-ASN : angle 1.56829 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5958.50 seconds wall clock time: 102 minutes 9.06 seconds (6129.06 seconds total)