Starting phenix.real_space_refine on Wed May 14 12:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrc_38602/05_2025/8xrc_38602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrc_38602/05_2025/8xrc_38602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xrc_38602/05_2025/8xrc_38602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrc_38602/05_2025/8xrc_38602.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrc_38602/05_2025/8xrc_38602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrc_38602/05_2025/8xrc_38602.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 7375 2.51 5 N 2009 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 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11815 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3873 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3842 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 19, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3833 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'NAG': 2, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.05, per 1000 atoms: 0.68 Number of scatterers: 11815 At special positions: 0 Unit cell: (91.8, 87.55, 149.6, 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 2009 7.00 C 7375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.02 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.02 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA2-3 " GAL G 1 " - " SIA G 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL H 1 " - " SIA H 2 " NAG-ASN " NAG A 701 " - " ASN A 28 " " NAG A 702 " - " ASN A 290 " " NAG A 703 " - " ASN A 16 " " NAG B 701 " - " ASN B 28 " " NAG B 702 " - " ASN B 290 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 290 " " NAG D 1 " - " ASN A 169 " " NAG E 1 " - " ASN B 169 " " NAG F 1 " - " ASN C 169 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 35 sheets defined 27.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.726A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.885A 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: 3.587A pdb=" N ARG A 126 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 368 through 389 removed outlier: 3.575A pdb=" N LYS A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 389 " --> pdb=" O VAL A 385 " (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 493 through 502 removed outlier: 3.681A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.687A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 4.024A 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 187 through 196 Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.751A pdb=" N MET B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.939A pdb=" N SER B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.701A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.729A 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 112 removed outlier: 4.024A pdb=" N SER C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 369 through 388 removed outlier: 3.777A pdb=" N LYS C 373 " --> pdb=" O GLU C 369 " (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 488 through 492 Processing helix chain 'C' and resid 493 through 501 removed outlier: 3.880A pdb=" N ASN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.537A pdb=" N HIS A 356 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.710A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.510A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.977A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.306A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AA9, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.647A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB2, first strand: chain 'A' and resid 460 through 462 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: 3.811A 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: 4.150A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.314A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 48 " --> pdb=" O CYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.797A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.378A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 100 removed outlier: 8.047A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.229A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=AC7, first strand: chain 'C' and resid 7 through 8 removed outlier: 3.960A pdb=" N ILE C 8 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 468 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.319A 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 55 through 56 removed outlier: 6.826A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.698A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.698A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.348A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.501A pdb=" N ILE C 289 " --> pdb=" O CYS C 282 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 357 466 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 3.68 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: 3888 1.34 - 1.46: 2846 1.46 - 1.59: 5222 1.59 - 1.71: 0 1.71 - 1.83: 108 Bond restraints: 12064 Sorted by residual: bond pdb=" C CYS B 306 " pdb=" N PRO B 307 " ideal model delta sigma weight residual 1.331 1.361 -0.030 1.21e-02 6.83e+03 6.08e+00 bond pdb=" CB CYS C 278 " pdb=" SG CYS C 278 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.26e+00 bond pdb=" C TYR B 489 " pdb=" N PRO B 490 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.15e+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=" 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 2.44e+00 ... (remaining 12059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 16296 5.07 - 10.13: 24 10.13 - 15.20: 0 15.20 - 20.26: 0 20.26 - 25.33: 2 Bond angle restraints: 16322 Sorted by residual: angle pdb=" C2 GAL H 1 " pdb=" C3 GAL H 1 " pdb=" O3 GAL H 1 " ideal model delta sigma weight residual 107.49 132.82 -25.33 3.00e+00 1.11e-01 7.13e+01 angle pdb=" C2 GAL G 1 " pdb=" C3 GAL G 1 " pdb=" O3 GAL G 1 " ideal model delta sigma weight residual 107.49 132.80 -25.31 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C CYS C 278 " pdb=" CA CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sigma weight residual 114.41 105.76 8.65 2.30e+00 1.89e-01 1.42e+01 angle pdb=" N PRO B 307 " pdb=" CA PRO B 307 " pdb=" C PRO B 307 " ideal model delta sigma weight residual 111.33 116.48 -5.15 1.43e+00 4.89e-01 1.30e+01 angle pdb=" N CYS C 306 " pdb=" CA CYS C 306 " pdb=" C CYS C 306 " ideal model delta sigma weight residual 108.07 111.02 -2.95 8.90e-01 1.26e+00 1.10e+01 ... (remaining 16317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6451 23.42 - 46.84: 828 46.84 - 70.27: 194 70.27 - 93.69: 37 93.69 - 117.11: 10 Dihedral angle restraints: 7520 sinusoidal: 3347 harmonic: 4173 Sorted by residual: dihedral pdb=" CB CYS B 282 " pdb=" SG CYS B 282 " pdb=" SG CYS B 306 " pdb=" CB CYS B 306 " ideal model delta sinusoidal sigma weight residual 93.00 22.22 70.78 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 72 " pdb=" CB CYS C 72 " ideal model delta sinusoidal sigma weight residual 93.00 142.08 -49.08 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CA CYS C 47 " pdb=" C CYS C 47 " pdb=" N LYS C 48 " pdb=" CA LYS C 48 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 7517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 1801 0.157 - 0.314: 1 0.314 - 0.471: 0 0.471 - 0.628: 0 0.628 - 0.785: 2 Chirality restraints: 1804 Sorted by residual: 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 5.13e+01 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 -2.64 0.14 2.00e-02 2.50e+03 5.02e+01 chirality pdb=" C3 GAL G 1 " pdb=" C2 GAL G 1 " pdb=" C4 GAL G 1 " pdb=" O3 GAL G 1 " both_signs ideal model delta sigma weight residual False 2.41 1.62 0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 1801 not shown) Planarity restraints: 2115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 39 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" CD GLU A 39 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 39 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 39 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 306 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO C 307 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 284 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 285 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.022 5.00e-02 4.00e+02 ... (remaining 2112 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 314 2.68 - 3.23: 10305 3.23 - 3.79: 17788 3.79 - 4.34: 23727 4.34 - 4.90: 40193 Nonbonded interactions: 92327 Sorted by model distance: nonbonded pdb=" O6 SIA H 2 " pdb=" O8 SIA H 2 " model vdw 2.123 3.040 nonbonded pdb=" O6 SIA G 2 " pdb=" O8 SIA G 2 " model vdw 2.123 3.040 nonbonded pdb=" O6 SIA C 703 " pdb=" O8 SIA C 703 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" O9 SIA G 2 " model vdw 2.196 3.040 nonbonded pdb=" O SER B 142 " pdb=" OG SER B 142 " model vdw 2.207 3.040 ... (remaining 92322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 325 or resid 338 through 501 or resid 701 throug \ h 702)) selection = (chain 'B' and (resid 6 through 501 or resid 701 through 702)) selection = (chain 'C' and (resid 6 through 501 or resid 701 through 702)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.140 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 0.060 12097 Z= 0.218 Angle : 0.860 42.704 16403 Z= 0.382 Chirality : 0.052 0.785 1804 Planarity : 0.004 0.046 2105 Dihedral : 21.042 117.108 4802 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.05 % Allowed : 34.29 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1446 helix: 2.55 (0.27), residues: 369 sheet: -0.07 (0.33), residues: 296 loop : -1.54 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 81 HIS 0.005 0.001 HIS A 296 PHE 0.014 0.002 PHE B 148 TYR 0.025 0.002 TYR A 12 ARG 0.009 0.000 ARG C 192 Details of bonding type rmsd link_BETA2-3 : bond 0.05784 ( 2) link_BETA2-3 : angle 24.87494 ( 6) link_NAG-ASN : bond 0.00236 ( 10) link_NAG-ASN : angle 2.06843 ( 30) link_BETA1-4 : bond 0.00401 ( 3) link_BETA1-4 : angle 1.00673 ( 9) hydrogen bonds : bond 0.15733 ( 432) hydrogen bonds : angle 6.59100 ( 1296) SS BOND : bond 0.00614 ( 18) SS BOND : angle 2.60965 ( 36) covalent geometry : bond 0.00496 (12064) covalent geometry : angle 0.70109 (16322) *********************** 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 388 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 336 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7601 (p90) cc_final: 0.7327 (p90) REVERT: A 351 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7846 (m-10) REVERT: A 370 SER cc_start: 0.8463 (p) cc_final: 0.8130 (t) REVERT: B 468 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.4489 (p90) outliers start: 52 outliers final: 45 residues processed: 379 average time/residue: 1.2094 time to fit residues: 495.2084 Evaluate side-chains 374 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 327 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 443 SER 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 24 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 THR 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 497 LYS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 109 LEU 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 219 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 501 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 402 ASN B 455 GLN C 160 ASN C 210 ASN C 345 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111991 restraints weight = 15474.335| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.92 r_work: 0.3426 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 12097 Z= 0.311 Angle : 0.728 16.425 16403 Z= 0.364 Chirality : 0.049 0.277 1804 Planarity : 0.005 0.042 2105 Dihedral : 12.790 135.126 2064 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.48 % Allowed : 28.37 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1446 helix: 2.48 (0.27), residues: 375 sheet: -0.14 (0.32), residues: 301 loop : -1.60 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 81 HIS 0.010 0.002 HIS A 355 PHE 0.021 0.003 PHE B 148 TYR 0.026 0.002 TYR A 492 ARG 0.007 0.001 ARG C 192 Details of bonding type rmsd link_BETA2-3 : bond 0.03284 ( 2) link_BETA2-3 : angle 9.38798 ( 6) link_NAG-ASN : bond 0.00334 ( 10) link_NAG-ASN : angle 2.08755 ( 30) link_BETA1-4 : bond 0.00374 ( 3) link_BETA1-4 : angle 0.75522 ( 9) hydrogen bonds : bond 0.06245 ( 432) hydrogen bonds : angle 4.95108 ( 1296) SS BOND : bond 0.00668 ( 18) SS BOND : angle 2.54756 ( 36) covalent geometry : bond 0.00753 (12064) covalent geometry : angle 0.69104 (16322) *********************** 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 427 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 331 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7772 (mpp-170) REVERT: A 324 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8207 (m) REVERT: A 351 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: A 370 SER cc_start: 0.8397 (p) cc_final: 0.8107 (t) REVERT: A 376 ASP cc_start: 0.7707 (m-30) cc_final: 0.7471 (m-30) REVERT: B 27 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7745 (mtm-85) REVERT: B 468 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.4680 (p90) REVERT: B 479 MET cc_start: 0.6935 (ttm) cc_final: 0.6636 (mmm) REVERT: C 222 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8325 (mtmt) REVERT: C 399 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7758 (mp0) outliers start: 96 outliers final: 50 residues processed: 376 average time/residue: 1.2732 time to fit residues: 517.6307 Evaluate side-chains 379 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 499 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.0670 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 355 HIS B 480 ASN C 160 ASN C 210 ASN C 345 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.134349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114152 restraints weight = 15649.455| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.94 r_work: 0.3458 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12097 Z= 0.140 Angle : 0.629 15.065 16403 Z= 0.313 Chirality : 0.043 0.183 1804 Planarity : 0.004 0.035 2105 Dihedral : 11.137 138.393 2030 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.24 % Allowed : 29.54 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1446 helix: 2.77 (0.27), residues: 374 sheet: -0.09 (0.32), residues: 301 loop : -1.54 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.005 0.001 HIS B 355 PHE 0.018 0.001 PHE C 468 TYR 0.028 0.001 TYR A 492 ARG 0.004 0.000 ARG B 436 Details of bonding type rmsd link_BETA2-3 : bond 0.02841 ( 2) link_BETA2-3 : angle 8.76063 ( 6) link_NAG-ASN : bond 0.00304 ( 10) link_NAG-ASN : angle 2.07771 ( 30) link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 0.79638 ( 9) hydrogen bonds : bond 0.05353 ( 432) hydrogen bonds : angle 4.60886 ( 1296) SS BOND : bond 0.00574 ( 18) SS BOND : angle 2.09122 ( 36) covalent geometry : bond 0.00321 (12064) covalent geometry : angle 0.59271 (16322) *********************** 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 412 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 332 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7575 (p90) cc_final: 0.7336 (p90) REVERT: A 27 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7779 (mpp-170) REVERT: A 174 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 351 TRP cc_start: 0.8432 (OUTLIER) cc_final: 0.7716 (m-10) REVERT: A 354 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6577 (t80) REVERT: A 370 SER cc_start: 0.8333 (p) cc_final: 0.8028 (t) REVERT: A 376 ASP cc_start: 0.7655 (m-30) cc_final: 0.7402 (m-30) REVERT: A 435 GLU cc_start: 0.7940 (tp30) cc_final: 0.7704 (tp30) REVERT: B 27 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7677 (mtm-85) REVERT: B 165 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8524 (mtpm) REVERT: B 355 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6470 (t-90) REVERT: B 468 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.4732 (p90) REVERT: B 499 ASN cc_start: 0.8430 (m-40) cc_final: 0.8202 (m110) REVERT: C 399 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: C 435 GLU cc_start: 0.7896 (tp30) cc_final: 0.7653 (tp30) outliers start: 80 outliers final: 41 residues processed: 367 average time/residue: 1.2116 time to fit residues: 479.8870 Evaluate side-chains 384 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 499 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 129 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 196 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN C 345 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112495 restraints weight = 15521.350| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.92 r_work: 0.3437 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12097 Z= 0.241 Angle : 0.666 14.950 16403 Z= 0.335 Chirality : 0.046 0.194 1804 Planarity : 0.004 0.039 2105 Dihedral : 10.486 141.974 2012 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.70 % Allowed : 29.15 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1446 helix: 2.71 (0.26), residues: 375 sheet: -0.22 (0.31), residues: 312 loop : -1.52 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 81 HIS 0.010 0.002 HIS B 355 PHE 0.017 0.002 PHE B 148 TYR 0.024 0.002 TYR A 364 ARG 0.004 0.000 ARG C 192 Details of bonding type rmsd link_BETA2-3 : bond 0.02527 ( 2) link_BETA2-3 : angle 8.82859 ( 6) link_NAG-ASN : bond 0.00253 ( 10) link_NAG-ASN : angle 1.96537 ( 30) link_BETA1-4 : bond 0.00418 ( 3) link_BETA1-4 : angle 0.81537 ( 9) hydrogen bonds : bond 0.05740 ( 432) hydrogen bonds : angle 4.56032 ( 1296) SS BOND : bond 0.00634 ( 18) SS BOND : angle 2.19574 ( 36) covalent geometry : bond 0.00582 (12064) covalent geometry : angle 0.63186 (16322) *********************** 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 425 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 339 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7603 (p90) cc_final: 0.7367 (p90) REVERT: A 27 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7808 (mpp-170) REVERT: A 324 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8184 (m) REVERT: A 351 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: A 354 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6646 (t80) REVERT: A 370 SER cc_start: 0.8349 (p) cc_final: 0.8070 (t) REVERT: A 376 ASP cc_start: 0.7688 (m-30) cc_final: 0.7435 (m-30) REVERT: A 435 GLU cc_start: 0.7944 (tp30) cc_final: 0.7707 (tp30) REVERT: A 492 TYR cc_start: 0.6996 (t80) cc_final: 0.6774 (t80) REVERT: B 27 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: B 165 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8548 (mtpm) REVERT: B 402 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8183 (t0) REVERT: B 433 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: B 457 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: B 468 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.4730 (p90) REVERT: B 499 ASN cc_start: 0.8518 (m-40) cc_final: 0.8254 (m110) REVERT: C 222 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8303 (mtmt) REVERT: C 399 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7739 (mp0) outliers start: 86 outliers final: 48 residues processed: 376 average time/residue: 1.1906 time to fit residues: 484.2290 Evaluate side-chains 387 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 327 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 499 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 196 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 160 ASN C 210 ASN C 345 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.133600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113472 restraints weight = 15538.918| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.94 r_work: 0.3451 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12097 Z= 0.183 Angle : 0.633 14.194 16403 Z= 0.320 Chirality : 0.044 0.164 1804 Planarity : 0.004 0.037 2105 Dihedral : 10.019 141.770 2011 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.31 % Allowed : 29.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1446 helix: 2.75 (0.27), residues: 375 sheet: -0.09 (0.32), residues: 301 loop : -1.54 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 81 HIS 0.005 0.001 HIS A 355 PHE 0.019 0.002 PHE C 468 TYR 0.023 0.001 TYR A 364 ARG 0.003 0.000 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.01998 ( 2) link_BETA2-3 : angle 8.31466 ( 6) link_NAG-ASN : bond 0.00249 ( 10) link_NAG-ASN : angle 1.88799 ( 30) link_BETA1-4 : bond 0.00420 ( 3) link_BETA1-4 : angle 0.86567 ( 9) hydrogen bonds : bond 0.05469 ( 432) hydrogen bonds : angle 4.47400 ( 1296) SS BOND : bond 0.00625 ( 18) SS BOND : angle 2.41026 ( 36) covalent geometry : bond 0.00439 (12064) covalent geometry : angle 0.59767 (16322) *********************** 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 413 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 332 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7787 (mpp-170) REVERT: A 324 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8177 (m) REVERT: A 351 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: A 354 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 370 SER cc_start: 0.8352 (p) cc_final: 0.8066 (t) REVERT: A 376 ASP cc_start: 0.7691 (m-30) cc_final: 0.7421 (m-30) REVERT: A 489 TYR cc_start: 0.7542 (t80) cc_final: 0.7254 (t80) REVERT: B 27 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: B 165 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8541 (mtpm) REVERT: B 389 MET cc_start: 0.8623 (mmm) cc_final: 0.8385 (tpp) REVERT: B 402 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8162 (t0) REVERT: B 457 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7370 (ttm170) REVERT: B 468 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.4687 (p90) REVERT: B 499 ASN cc_start: 0.8558 (m-40) cc_final: 0.8295 (m110) REVERT: C 222 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8327 (mtmt) REVERT: C 399 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7706 (mp0) outliers start: 81 outliers final: 48 residues processed: 366 average time/residue: 1.2619 time to fit residues: 498.2178 Evaluate side-chains 389 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 499 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 160 ASN B 196 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 160 ASN C 210 ASN C 345 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111299 restraints weight = 15744.290| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.95 r_work: 0.3420 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12097 Z= 0.344 Angle : 0.735 13.811 16403 Z= 0.375 Chirality : 0.050 0.233 1804 Planarity : 0.004 0.043 2105 Dihedral : 10.033 142.874 2009 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.78 % Allowed : 29.07 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1446 helix: 2.52 (0.26), residues: 375 sheet: -0.14 (0.32), residues: 296 loop : -1.66 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 81 HIS 0.010 0.002 HIS A 355 PHE 0.025 0.003 PHE B 339 TYR 0.033 0.002 TYR A 364 ARG 0.004 0.001 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.01825 ( 2) link_BETA2-3 : angle 8.18498 ( 6) link_NAG-ASN : bond 0.00317 ( 10) link_NAG-ASN : angle 1.99835 ( 30) link_BETA1-4 : bond 0.00405 ( 3) link_BETA1-4 : angle 0.85840 ( 9) hydrogen bonds : bond 0.06259 ( 432) hydrogen bonds : angle 4.62905 ( 1296) SS BOND : bond 0.00789 ( 18) SS BOND : angle 2.92329 ( 36) covalent geometry : bond 0.00838 (12064) covalent geometry : angle 0.70085 (16322) *********************** 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 422 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 335 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7644 (p90) cc_final: 0.7435 (p90) REVERT: A 27 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7797 (mpp-170) REVERT: A 351 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: A 354 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6673 (t80) REVERT: A 370 SER cc_start: 0.8459 (p) cc_final: 0.8198 (t) REVERT: A 376 ASP cc_start: 0.7729 (m-30) cc_final: 0.7491 (m-30) REVERT: B 27 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7775 (mtm-85) REVERT: B 165 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8566 (mtpm) REVERT: B 389 MET cc_start: 0.8602 (mmm) cc_final: 0.8338 (mmm) REVERT: B 402 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 457 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: B 468 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5030 (p90) REVERT: B 499 ASN cc_start: 0.8616 (m-40) cc_final: 0.8337 (m110) REVERT: C 222 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8341 (mtmt) REVERT: C 399 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 462 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6436 (tm-30) REVERT: C 473 LYS cc_start: 0.8072 (tppt) cc_final: 0.7747 (tppt) outliers start: 87 outliers final: 52 residues processed: 370 average time/residue: 1.2507 time to fit residues: 498.9658 Evaluate side-chains 387 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER 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 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 196 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 160 ASN C 210 ASN C 345 GLN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.132922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112888 restraints weight = 15804.548| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.96 r_work: 0.3442 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12097 Z= 0.185 Angle : 0.646 12.284 16403 Z= 0.331 Chirality : 0.044 0.202 1804 Planarity : 0.004 0.040 2105 Dihedral : 9.595 139.215 2005 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.77 % Allowed : 30.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1446 helix: 2.70 (0.27), residues: 375 sheet: -0.11 (0.32), residues: 303 loop : -1.59 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 81 HIS 0.004 0.001 HIS B 296 PHE 0.014 0.002 PHE B 468 TYR 0.025 0.001 TYR A 492 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.01640 ( 2) link_BETA2-3 : angle 7.05552 ( 6) link_NAG-ASN : bond 0.00226 ( 10) link_NAG-ASN : angle 2.30694 ( 30) link_BETA1-4 : bond 0.00350 ( 3) link_BETA1-4 : angle 0.87571 ( 9) hydrogen bonds : bond 0.05508 ( 432) hydrogen bonds : angle 4.50560 ( 1296) SS BOND : bond 0.00612 ( 18) SS BOND : angle 2.50156 ( 36) covalent geometry : bond 0.00443 (12064) covalent geometry : angle 0.61456 (16322) *********************** 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 400 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 326 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7718 (mpp-170) REVERT: A 28 ASN cc_start: 0.7956 (m-40) cc_final: 0.7742 (m-40) REVERT: A 351 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: A 354 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 370 SER cc_start: 0.8421 (p) cc_final: 0.8145 (t) REVERT: A 376 ASP cc_start: 0.7684 (m-30) cc_final: 0.7444 (m-30) REVERT: B 27 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7730 (mtm-85) REVERT: B 457 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7368 (ttm170) REVERT: B 468 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.4963 (p90) REVERT: B 499 ASN cc_start: 0.8593 (m-40) cc_final: 0.8331 (m110) REVERT: C 399 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 473 LYS cc_start: 0.7982 (tppt) cc_final: 0.7645 (tppt) outliers start: 74 outliers final: 44 residues processed: 360 average time/residue: 1.2806 time to fit residues: 496.9446 Evaluate side-chains 385 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 50 ASN B 160 ASN B 196 GLN B 226 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 160 ASN C 210 ASN C 499 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.134394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114398 restraints weight = 15671.650| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.95 r_work: 0.3466 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12097 Z= 0.132 Angle : 0.599 10.241 16403 Z= 0.309 Chirality : 0.043 0.165 1804 Planarity : 0.004 0.036 2105 Dihedral : 9.277 138.879 2001 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.36 % Allowed : 32.03 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.22), residues: 1446 helix: 2.85 (0.27), residues: 374 sheet: -0.11 (0.32), residues: 305 loop : -1.51 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.007 0.001 HIS C 356 PHE 0.024 0.001 PHE C 468 TYR 0.023 0.001 TYR A 12 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.01335 ( 2) link_BETA2-3 : angle 5.96841 ( 6) link_NAG-ASN : bond 0.00256 ( 10) link_NAG-ASN : angle 1.99471 ( 30) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 0.88890 ( 9) hydrogen bonds : bond 0.05044 ( 432) hydrogen bonds : angle 4.38633 ( 1296) SS BOND : bond 0.00564 ( 18) SS BOND : angle 2.21980 ( 36) covalent geometry : bond 0.00305 (12064) covalent geometry : angle 0.57375 (16322) *********************** 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 389 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 333 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7609 (p90) cc_final: 0.7387 (p90) REVERT: A 174 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 354 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 370 SER cc_start: 0.8337 (p) cc_final: 0.8040 (t) REVERT: A 376 ASP cc_start: 0.7645 (m-30) cc_final: 0.7411 (m-30) REVERT: B 27 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7730 (mtm-85) REVERT: B 457 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7314 (ttm170) REVERT: B 468 PHE cc_start: 0.5885 (OUTLIER) cc_final: 0.4935 (p90) REVERT: B 499 ASN cc_start: 0.8610 (m-40) cc_final: 0.8346 (m110) REVERT: C 279 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7099 (tm-30) REVERT: C 399 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: C 473 LYS cc_start: 0.7942 (tppt) cc_final: 0.7562 (tppt) outliers start: 56 outliers final: 36 residues processed: 354 average time/residue: 1.2941 time to fit residues: 492.7775 Evaluate side-chains 374 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 196 GLN B 226 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN C 499 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113752 restraints weight = 15729.483| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.95 r_work: 0.3458 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12097 Z= 0.163 Angle : 0.621 8.774 16403 Z= 0.322 Chirality : 0.043 0.204 1804 Planarity : 0.004 0.036 2105 Dihedral : 9.120 140.811 1997 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.82 % Allowed : 33.20 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1446 helix: 2.85 (0.27), residues: 374 sheet: -0.15 (0.32), residues: 313 loop : -1.51 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 127 HIS 0.005 0.001 HIS C 356 PHE 0.019 0.002 PHE C 468 TYR 0.022 0.001 TYR A 12 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.01113 ( 2) link_BETA2-3 : angle 5.33240 ( 6) link_NAG-ASN : bond 0.00238 ( 10) link_NAG-ASN : angle 1.95961 ( 30) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 0.89820 ( 9) hydrogen bonds : bond 0.05224 ( 432) hydrogen bonds : angle 4.40627 ( 1296) SS BOND : bond 0.00583 ( 18) SS BOND : angle 2.37507 ( 36) covalent geometry : bond 0.00389 (12064) covalent geometry : angle 0.59766 (16322) *********************** 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 376 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7622 (p90) cc_final: 0.7381 (p90) REVERT: A 174 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 354 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6745 (t80) REVERT: A 370 SER cc_start: 0.8342 (p) cc_final: 0.8053 (t) REVERT: A 376 ASP cc_start: 0.7653 (m-30) cc_final: 0.7417 (m-30) REVERT: B 27 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7731 (mtm-85) REVERT: B 433 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: B 457 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7281 (ttm170) REVERT: B 468 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.4954 (p90) REVERT: B 499 ASN cc_start: 0.8638 (m-40) cc_final: 0.8362 (m110) REVERT: C 279 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7071 (tm-30) REVERT: C 399 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: C 473 LYS cc_start: 0.7981 (tppt) cc_final: 0.7558 (tppt) outliers start: 49 outliers final: 35 residues processed: 348 average time/residue: 1.2883 time to fit residues: 482.2266 Evaluate side-chains 371 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 160 ASN B 196 GLN B 226 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 210 ASN C 499 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114604 restraints weight = 15571.316| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3473 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12097 Z= 0.131 Angle : 0.601 7.437 16403 Z= 0.313 Chirality : 0.042 0.204 1804 Planarity : 0.003 0.036 2105 Dihedral : 8.958 141.848 1997 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.43 % Allowed : 33.28 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1446 helix: 2.90 (0.27), residues: 374 sheet: -0.07 (0.32), residues: 307 loop : -1.49 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 127 HIS 0.003 0.001 HIS C 355 PHE 0.019 0.001 PHE C 468 TYR 0.021 0.001 TYR A 492 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.00951 ( 2) link_BETA2-3 : angle 4.35191 ( 6) link_NAG-ASN : bond 0.00246 ( 10) link_NAG-ASN : angle 1.88516 ( 30) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 0.90557 ( 9) hydrogen bonds : bond 0.04940 ( 432) hydrogen bonds : angle 4.35032 ( 1296) SS BOND : bond 0.00520 ( 18) SS BOND : angle 2.03370 ( 36) covalent geometry : bond 0.00303 (12064) covalent geometry : angle 0.58261 (16322) ********************** 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 372 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7617 (p90) cc_final: 0.7361 (p90) REVERT: A 174 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 354 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6746 (t80) REVERT: A 370 SER cc_start: 0.8328 (p) cc_final: 0.8031 (t) REVERT: A 376 ASP cc_start: 0.7633 (m-30) cc_final: 0.7387 (m-30) REVERT: B 27 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7702 (mtm-85) REVERT: B 457 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7289 (ttm170) REVERT: B 468 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.4875 (p90) REVERT: B 499 ASN cc_start: 0.8613 (m-40) cc_final: 0.8346 (m110) REVERT: C 91 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7277 (ttp80) REVERT: C 399 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7694 (mp0) outliers start: 44 outliers final: 32 residues processed: 345 average time/residue: 1.2728 time to fit residues: 472.7019 Evaluate side-chains 364 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 327 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 196 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN C 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112599 restraints weight = 15541.633| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.94 r_work: 0.3446 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12097 Z= 0.219 Angle : 0.663 8.203 16403 Z= 0.345 Chirality : 0.045 0.245 1804 Planarity : 0.004 0.038 2105 Dihedral : 9.087 143.658 1997 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.35 % Allowed : 33.59 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1446 helix: 2.71 (0.27), residues: 375 sheet: -0.17 (0.31), residues: 317 loop : -1.55 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 127 HIS 0.006 0.001 HIS A 355 PHE 0.020 0.002 PHE C 468 TYR 0.023 0.002 TYR A 12 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.00789 ( 2) link_BETA2-3 : angle 4.29777 ( 6) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 1.98872 ( 30) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 0.89527 ( 9) hydrogen bonds : bond 0.05538 ( 432) hydrogen bonds : angle 4.42255 ( 1296) SS BOND : bond 0.00671 ( 18) SS BOND : angle 2.69786 ( 36) covalent geometry : bond 0.00529 (12064) covalent geometry : angle 0.64107 (16322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11379.27 seconds wall clock time: 196 minutes 4.57 seconds (11764.57 seconds total)