Starting phenix.real_space_refine on Sat Aug 23 11:38:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrc_38602/08_2025/8xrc_38602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrc_38602/08_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_38602/08_2025/8xrc_38602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrc_38602/08_2025/8xrc_38602.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrc_38602/08_2025/8xrc_38602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrc_38602/08_2025/8xrc_38602.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.91, per 1000 atoms: 0.33 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: 1.27 Conformation dependent library (CDL) restraints added in 619.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 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: 0.52 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: 2.22 Time building geometry restraints manager: 1.48 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 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (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 ARG 0.009 0.000 ARG C 192 TYR 0.025 0.002 TYR A 12 PHE 0.014 0.002 PHE B 148 TRP 0.011 0.001 TRP C 81 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00496 (12064) covalent geometry : angle 0.70109 (16322) SS BOND : bond 0.00614 ( 18) SS BOND : angle 2.60965 ( 36) hydrogen bonds : bond 0.15733 ( 432) hydrogen bonds : angle 6.59100 ( 1296) link_BETA1-4 : bond 0.00401 ( 3) link_BETA1-4 : angle 1.00673 ( 9) 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) *********************** 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 : 0.633 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: 0.6286 time to fit residues: 256.6907 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 : 0.486 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0870 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113717 restraints weight = 15569.415| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.95 r_work: 0.3455 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12097 Z= 0.177 Angle : 0.643 15.520 16403 Z= 0.320 Chirality : 0.045 0.285 1804 Planarity : 0.004 0.042 2105 Dihedral : 12.872 134.220 2064 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.70 % Allowed : 29.62 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1446 helix: 2.72 (0.27), residues: 373 sheet: -0.06 (0.32), residues: 301 loop : -1.51 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 192 TYR 0.030 0.001 TYR A 492 PHE 0.013 0.002 PHE B 148 TRP 0.010 0.001 TRP B 81 HIS 0.006 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00418 (12064) covalent geometry : angle 0.60810 (16322) SS BOND : bond 0.00504 ( 18) SS BOND : angle 1.98441 ( 36) hydrogen bonds : bond 0.05682 ( 432) hydrogen bonds : angle 4.92678 ( 1296) link_BETA1-4 : bond 0.00480 ( 3) link_BETA1-4 : angle 0.80518 ( 9) link_BETA2-3 : bond 0.03122 ( 2) link_BETA2-3 : angle 9.06103 ( 6) link_NAG-ASN : bond 0.00293 ( 10) link_NAG-ASN : angle 1.95153 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 335 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8230 (m) REVERT: A 351 TRP cc_start: 0.8408 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: A 370 SER cc_start: 0.8360 (p) cc_final: 0.8039 (t) REVERT: A 376 ASP cc_start: 0.7702 (m-30) cc_final: 0.7471 (m-30) REVERT: B 27 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7704 (mtm-85) REVERT: B 468 PHE cc_start: 0.5484 (OUTLIER) cc_final: 0.4776 (p90) REVERT: B 479 MET cc_start: 0.6862 (ttm) cc_final: 0.6566 (mmm) REVERT: C 222 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8333 (mtmt) REVERT: C 399 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: C 454 MET cc_start: 0.7157 (tmm) cc_final: 0.6912 (tmm) REVERT: C 489 TYR cc_start: 0.7706 (t80) cc_final: 0.7436 (t80) outliers start: 86 outliers final: 41 residues processed: 378 average time/residue: 0.5967 time to fit residues: 243.3173 Evaluate side-chains 375 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 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 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 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 146 SER 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 313 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 497 LYS Chi-restraints excluded: chain C residue 39 GLU 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS B 392 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.134585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114305 restraints weight = 15610.792| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.94 r_work: 0.3462 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12097 Z= 0.147 Angle : 0.621 14.580 16403 Z= 0.308 Chirality : 0.043 0.168 1804 Planarity : 0.004 0.037 2105 Dihedral : 10.882 140.125 2015 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.24 % Allowed : 29.07 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1446 helix: 2.87 (0.27), residues: 374 sheet: 0.01 (0.32), residues: 301 loop : -1.51 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 192 TYR 0.024 0.001 TYR A 492 PHE 0.013 0.001 PHE A 470 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00339 (12064) covalent geometry : angle 0.58676 (16322) SS BOND : bond 0.00576 ( 18) SS BOND : angle 2.00745 ( 36) hydrogen bonds : bond 0.05283 ( 432) hydrogen bonds : angle 4.59743 ( 1296) link_BETA1-4 : bond 0.00533 ( 3) link_BETA1-4 : angle 0.87220 ( 9) link_BETA2-3 : bond 0.02837 ( 2) link_BETA2-3 : angle 8.64577 ( 6) link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 1.85996 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 331 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7689 (mpp-170) REVERT: A 174 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 370 SER cc_start: 0.8337 (p) cc_final: 0.8005 (t) REVERT: A 376 ASP cc_start: 0.7715 (m-30) cc_final: 0.7462 (m-30) REVERT: A 435 GLU cc_start: 0.7929 (tp30) cc_final: 0.7684 (tp30) REVERT: B 27 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7675 (mtm-85) REVERT: B 165 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8515 (mtpm) REVERT: B 355 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6401 (t-90) REVERT: B 402 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 468 PHE cc_start: 0.5548 (OUTLIER) cc_final: 0.4764 (p90) REVERT: C 399 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: C 445 VAL cc_start: 0.8294 (t) cc_final: 0.8058 (p) REVERT: C 489 TYR cc_start: 0.7738 (t80) cc_final: 0.7528 (t80) REVERT: C 499 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8107 (m-40) outliers start: 80 outliers final: 43 residues processed: 364 average time/residue: 0.6380 time to fit residues: 250.0435 Evaluate side-chains 370 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 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 27 ARG Chi-restraints excluded: chain B residue 40 LYS 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 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 355 HIS Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 402 ASN 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 39 GLU 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 209 VAL 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 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 72 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS ** B 358 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.134556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114180 restraints weight = 15690.736| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.96 r_work: 0.3464 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12097 Z= 0.154 Angle : 0.615 14.257 16403 Z= 0.308 Chirality : 0.043 0.174 1804 Planarity : 0.004 0.041 2105 Dihedral : 10.140 142.173 2005 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.16 % Allowed : 28.84 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.22), residues: 1446 helix: 2.89 (0.27), residues: 374 sheet: -0.11 (0.32), residues: 314 loop : -1.46 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 192 TYR 0.018 0.001 TYR A 364 PHE 0.011 0.002 PHE B 148 TRP 0.010 0.001 TRP C 422 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00362 (12064) covalent geometry : angle 0.58032 (16322) SS BOND : bond 0.00563 ( 18) SS BOND : angle 2.01109 ( 36) hydrogen bonds : bond 0.05217 ( 432) hydrogen bonds : angle 4.47812 ( 1296) link_BETA1-4 : bond 0.00379 ( 3) link_BETA1-4 : angle 0.86375 ( 9) link_BETA2-3 : bond 0.02429 ( 2) link_BETA2-3 : angle 8.51166 ( 6) link_NAG-ASN : bond 0.00238 ( 10) link_NAG-ASN : angle 2.00060 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 323 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7792 (mpp-170) REVERT: A 174 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 324 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 351 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.7777 (m-10) REVERT: A 354 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6708 (t80) REVERT: A 370 SER cc_start: 0.8343 (p) cc_final: 0.8028 (t) REVERT: A 376 ASP cc_start: 0.7671 (m-30) cc_final: 0.7417 (m-30) REVERT: B 27 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7701 (mtm-85) REVERT: B 355 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6615 (t-90) REVERT: B 402 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8098 (t0) REVERT: B 468 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.4744 (p90) REVERT: B 499 ASN cc_start: 0.8547 (m-40) cc_final: 0.8286 (m110) REVERT: C 222 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8344 (mtmt) REVERT: C 399 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: C 445 VAL cc_start: 0.8276 (t) cc_final: 0.8038 (p) REVERT: C 473 LYS cc_start: 0.7943 (tppt) cc_final: 0.7697 (tppt) outliers start: 79 outliers final: 45 residues processed: 358 average time/residue: 0.6502 time to fit residues: 250.5230 Evaluate side-chains 381 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 116 PHE 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 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 27 ARG Chi-restraints excluded: chain B residue 40 LYS 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 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 269 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 433 GLU 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 39 GLU Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 SER 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 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 53 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS B 480 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.134499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114150 restraints weight = 15673.267| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.95 r_work: 0.3461 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12097 Z= 0.165 Angle : 0.611 13.257 16403 Z= 0.309 Chirality : 0.043 0.161 1804 Planarity : 0.004 0.052 2105 Dihedral : 9.740 141.506 2003 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.47 % Allowed : 28.92 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1446 helix: 2.87 (0.27), residues: 374 sheet: -0.05 (0.32), residues: 312 loop : -1.44 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 436 TYR 0.023 0.001 TYR A 12 PHE 0.012 0.002 PHE B 148 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00391 (12064) covalent geometry : angle 0.57843 (16322) SS BOND : bond 0.00569 ( 18) SS BOND : angle 2.11780 ( 36) hydrogen bonds : bond 0.05219 ( 432) hydrogen bonds : angle 4.42944 ( 1296) link_BETA1-4 : bond 0.00357 ( 3) link_BETA1-4 : angle 0.87176 ( 9) link_BETA2-3 : bond 0.02039 ( 2) link_BETA2-3 : angle 8.09869 ( 6) link_NAG-ASN : bond 0.00237 ( 10) link_NAG-ASN : angle 1.83726 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 324 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7767 (mpp-170) REVERT: A 174 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 324 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8188 (m) REVERT: A 351 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.7725 (m-10) REVERT: A 354 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6690 (t80) REVERT: A 370 SER cc_start: 0.8336 (p) cc_final: 0.8028 (t) REVERT: A 376 ASP cc_start: 0.7706 (m-30) cc_final: 0.7453 (m-30) REVERT: A 457 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7032 (mtm180) REVERT: B 27 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7721 (mtm-85) REVERT: B 402 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8121 (t0) REVERT: B 468 PHE cc_start: 0.5626 (OUTLIER) cc_final: 0.4787 (p90) REVERT: B 499 ASN cc_start: 0.8522 (m-40) cc_final: 0.8259 (m110) REVERT: C 222 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8341 (mtmt) REVERT: C 399 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: C 445 VAL cc_start: 0.8290 (t) cc_final: 0.8072 (p) REVERT: C 473 LYS cc_start: 0.7991 (tppt) cc_final: 0.7690 (tppt) REVERT: C 479 MET cc_start: 0.5636 (ttp) cc_final: 0.5402 (ttp) outliers start: 83 outliers final: 50 residues processed: 361 average time/residue: 0.6489 time to fit residues: 252.1891 Evaluate side-chains 382 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 40 LYS 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 157 LYS 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 457 ARG Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS 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 125 ASP Chi-restraints excluded: chain B residue 139 CYS 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 269 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 402 ASN 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 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 8 ILE Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 SER 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 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 25 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 392 GLN B 480 ASN C 210 ASN C 345 GLN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113922 restraints weight = 15739.031| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.96 r_work: 0.3461 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12097 Z= 0.160 Angle : 0.595 11.471 16403 Z= 0.305 Chirality : 0.043 0.163 1804 Planarity : 0.004 0.036 2105 Dihedral : 9.404 140.636 2003 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.70 % Allowed : 28.68 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1446 helix: 2.88 (0.27), residues: 374 sheet: -0.12 (0.31), residues: 316 loop : -1.47 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.019 0.001 TYR A 364 PHE 0.021 0.002 PHE C 440 TRP 0.010 0.001 TRP B 127 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00380 (12064) covalent geometry : angle 0.56599 (16322) SS BOND : bond 0.00555 ( 18) SS BOND : angle 2.15550 ( 36) hydrogen bonds : bond 0.05220 ( 432) hydrogen bonds : angle 4.40352 ( 1296) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 0.89313 ( 9) link_BETA2-3 : bond 0.01653 ( 2) link_BETA2-3 : angle 7.17752 ( 6) link_NAG-ASN : bond 0.00242 ( 10) link_NAG-ASN : angle 1.78539 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 326 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7750 (mpp-170) REVERT: A 174 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 324 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8193 (m) REVERT: A 351 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: A 354 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6681 (t80) REVERT: A 370 SER cc_start: 0.8335 (p) cc_final: 0.8031 (t) REVERT: A 376 ASP cc_start: 0.7686 (m-30) cc_final: 0.7428 (m-30) REVERT: B 27 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7725 (mtm-85) REVERT: B 165 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8620 (mtpp) REVERT: B 246 GLU cc_start: 0.8135 (tt0) cc_final: 0.7859 (tt0) REVERT: B 402 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 468 PHE cc_start: 0.5561 (OUTLIER) cc_final: 0.4817 (p90) REVERT: B 499 ASN cc_start: 0.8544 (m-40) cc_final: 0.8279 (m110) REVERT: C 222 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (mtmt) REVERT: C 399 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7729 (mp0) outliers start: 86 outliers final: 45 residues processed: 362 average time/residue: 0.6408 time to fit residues: 250.1796 Evaluate side-chains 376 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 40 LYS 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 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 378 ILE 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 27 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 174 GLU 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 389 MET Chi-restraints excluded: chain B residue 402 ASN 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 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 39 GLU 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 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 499 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 0.0980 chunk 15 optimal weight: 0.0000 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 196 GLN B 277 ASN B 480 ASN C 210 ASN C 345 GLN ** 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 = 0.3861 r_free = 0.3861 target = 0.135333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114955 restraints weight = 15668.177| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.96 r_work: 0.3473 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1165 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= 0.134 Angle : 0.588 10.004 16403 Z= 0.302 Chirality : 0.042 0.172 1804 Planarity : 0.003 0.034 2105 Dihedral : 9.048 140.207 1995 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.53 % Allowed : 30.79 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.23), residues: 1446 helix: 2.92 (0.27), residues: 374 sheet: -0.12 (0.32), residues: 318 loop : -1.44 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.022 0.001 TYR A 12 PHE 0.021 0.001 PHE C 440 TRP 0.010 0.001 TRP C 422 HIS 0.005 0.001 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00312 (12064) covalent geometry : angle 0.56299 (16322) SS BOND : bond 0.00530 ( 18) SS BOND : angle 2.15181 ( 36) hydrogen bonds : bond 0.04996 ( 432) hydrogen bonds : angle 4.36987 ( 1296) link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 0.89640 ( 9) link_BETA2-3 : bond 0.01378 ( 2) link_BETA2-3 : angle 6.27207 ( 6) link_NAG-ASN : bond 0.00238 ( 10) link_NAG-ASN : angle 1.70620 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 329 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8180 (m) REVERT: A 351 TRP cc_start: 0.8435 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: A 354 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6756 (t80) REVERT: A 370 SER cc_start: 0.8319 (p) cc_final: 0.7999 (t) REVERT: A 376 ASP cc_start: 0.7669 (m-30) cc_final: 0.7407 (m-30) REVERT: B 27 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7713 (mtm-85) REVERT: B 175 GLN cc_start: 0.8733 (mt0) cc_final: 0.8528 (mt0) REVERT: B 468 PHE cc_start: 0.5529 (OUTLIER) cc_final: 0.4794 (p90) REVERT: B 499 ASN cc_start: 0.8566 (m-40) cc_final: 0.8294 (m110) REVERT: C 91 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7296 (ttp80) REVERT: C 399 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: C 445 VAL cc_start: 0.8249 (t) cc_final: 0.8016 (p) outliers start: 71 outliers final: 47 residues processed: 357 average time/residue: 0.6572 time to fit residues: 252.4210 Evaluate side-chains 377 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 277 ASN Chi-restraints excluded: chain A residue 292 THR 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 368 LYS 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 27 ARG Chi-restraints excluded: chain B residue 40 LYS 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 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 269 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU 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 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 39 GLU Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 196 GLN B 226 GLN B 455 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114803 restraints weight = 15585.919| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.96 r_work: 0.3471 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12097 Z= 0.145 Angle : 0.593 8.590 16403 Z= 0.308 Chirality : 0.043 0.180 1804 Planarity : 0.003 0.033 2105 Dihedral : 8.944 141.002 1995 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.22 % Allowed : 31.25 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.22), residues: 1446 helix: 2.92 (0.27), residues: 374 sheet: -0.13 (0.31), residues: 318 loop : -1.44 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.014 0.001 TYR A 364 PHE 0.021 0.002 PHE C 440 TRP 0.013 0.001 TRP B 127 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00341 (12064) covalent geometry : angle 0.57090 (16322) SS BOND : bond 0.00587 ( 18) SS BOND : angle 2.12477 ( 36) hydrogen bonds : bond 0.05022 ( 432) hydrogen bonds : angle 4.33767 ( 1296) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 0.89990 ( 9) link_BETA2-3 : bond 0.01127 ( 2) link_BETA2-3 : angle 5.55822 ( 6) link_NAG-ASN : bond 0.00248 ( 10) link_NAG-ASN : angle 1.69988 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7614 (mpp-170) REVERT: A 324 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8182 (m) REVERT: A 351 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7725 (m-10) REVERT: A 354 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6742 (t80) REVERT: A 370 SER cc_start: 0.8321 (p) cc_final: 0.8019 (t) REVERT: A 376 ASP cc_start: 0.7668 (m-30) cc_final: 0.7402 (m-30) REVERT: A 489 TYR cc_start: 0.7694 (t80) cc_final: 0.7404 (t80) REVERT: B 27 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7709 (mtm-85) REVERT: B 175 GLN cc_start: 0.8733 (mt0) cc_final: 0.8526 (mt0) REVERT: B 389 MET cc_start: 0.8691 (mmm) cc_final: 0.8398 (mmm) REVERT: B 468 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.4808 (p90) REVERT: B 499 ASN cc_start: 0.8578 (m-40) cc_final: 0.8301 (m110) REVERT: C 91 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7283 (ttp80) REVERT: C 399 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 445 VAL cc_start: 0.8263 (t) cc_final: 0.8031 (p) outliers start: 67 outliers final: 44 residues processed: 352 average time/residue: 0.6300 time to fit residues: 238.9691 Evaluate side-chains 373 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 40 LYS Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 125 ASP 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 497 LYS 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 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 247 SER 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 416 ASP Chi-restraints excluded: chain B residue 433 GLU 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 39 GLU Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 111 SER 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 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 454 MET 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 14 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 196 GLN B 226 GLN B 455 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 210 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.135937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115407 restraints weight = 15563.262| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.98 r_work: 0.3482 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1329 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= 0.120 Angle : 0.575 6.668 16403 Z= 0.300 Chirality : 0.042 0.188 1804 Planarity : 0.003 0.033 2105 Dihedral : 8.808 141.508 1995 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.90 % Allowed : 32.74 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.23), residues: 1446 helix: 2.96 (0.27), residues: 374 sheet: -0.09 (0.31), residues: 320 loop : -1.38 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.021 0.001 TYR A 12 PHE 0.020 0.001 PHE C 440 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00271 (12064) covalent geometry : angle 0.55500 (16322) SS BOND : bond 0.00509 ( 18) SS BOND : angle 1.91501 ( 36) hydrogen bonds : bond 0.04759 ( 432) hydrogen bonds : angle 4.27997 ( 1296) link_BETA1-4 : bond 0.00358 ( 3) link_BETA1-4 : angle 0.90248 ( 9) link_BETA2-3 : bond 0.00921 ( 2) link_BETA2-3 : angle 4.44394 ( 6) link_NAG-ASN : bond 0.00249 ( 10) link_NAG-ASN : angle 2.17804 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7651 (mpp-170) REVERT: A 28 ASN cc_start: 0.7922 (m-40) cc_final: 0.7619 (m-40) REVERT: A 324 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 351 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: A 354 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6828 (t80) REVERT: A 370 SER cc_start: 0.8306 (p) cc_final: 0.7994 (t) REVERT: A 376 ASP cc_start: 0.7662 (m-30) cc_final: 0.7397 (m-30) REVERT: A 489 TYR cc_start: 0.7694 (t80) cc_final: 0.7410 (t80) REVERT: B 27 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7702 (mtm-85) REVERT: B 413 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8440 (mttm) REVERT: B 468 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.4795 (p90) REVERT: B 499 ASN cc_start: 0.8550 (m-40) cc_final: 0.8283 (m110) REVERT: C 91 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7312 (ttp80) REVERT: C 399 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7745 (mp0) outliers start: 50 outliers final: 36 residues processed: 354 average time/residue: 0.6607 time to fit residues: 251.5488 Evaluate side-chains 363 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE 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 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 438 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS 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 174 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 247 SER 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 416 ASP Chi-restraints excluded: chain B residue 433 GLU 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 C residue 60 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 SER 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 399 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 454 MET 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 32 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 226 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115544 restraints weight = 15719.574| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.96 r_work: 0.3485 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12097 Z= 0.124 Angle : 0.585 7.369 16403 Z= 0.304 Chirality : 0.042 0.194 1804 Planarity : 0.003 0.034 2105 Dihedral : 8.598 143.048 1991 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.59 % Allowed : 33.59 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.23), residues: 1446 helix: 2.95 (0.27), residues: 374 sheet: -0.08 (0.32), residues: 320 loop : -1.37 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.010 0.001 TYR C 492 PHE 0.024 0.001 PHE A 440 TRP 0.010 0.001 TRP C 422 HIS 0.004 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00284 (12064) covalent geometry : angle 0.56674 (16322) SS BOND : bond 0.00491 ( 18) SS BOND : angle 2.04739 ( 36) hydrogen bonds : bond 0.04736 ( 432) hydrogen bonds : angle 4.26329 ( 1296) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 0.88507 ( 9) link_BETA2-3 : bond 0.00787 ( 2) link_BETA2-3 : angle 3.77893 ( 6) link_NAG-ASN : bond 0.00277 ( 10) link_NAG-ASN : angle 1.98335 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8203 (m) REVERT: A 351 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: A 354 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6797 (t80) REVERT: A 370 SER cc_start: 0.8296 (p) cc_final: 0.7987 (t) REVERT: A 376 ASP cc_start: 0.7643 (m-30) cc_final: 0.7377 (m-30) REVERT: A 489 TYR cc_start: 0.7722 (t80) cc_final: 0.7430 (t80) REVERT: B 389 MET cc_start: 0.8604 (mmm) cc_final: 0.8330 (tpp) REVERT: B 413 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8433 (mttm) REVERT: B 468 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.4774 (p90) REVERT: B 499 ASN cc_start: 0.8562 (m-40) cc_final: 0.8298 (m110) REVERT: C 91 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7313 (ttp80) REVERT: C 399 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7731 (mp0) outliers start: 46 outliers final: 32 residues processed: 343 average time/residue: 0.5587 time to fit residues: 206.8420 Evaluate side-chains 352 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 315 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 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 438 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS 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 174 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 433 GLU 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 C residue 60 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 SER 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 399 GLU Chi-restraints excluded: chain C residue 454 MET 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 82 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 455 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115581 restraints weight = 15716.959| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.96 r_work: 0.3485 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1472 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= 0.125 Angle : 0.581 6.735 16403 Z= 0.304 Chirality : 0.042 0.191 1804 Planarity : 0.003 0.034 2105 Dihedral : 8.533 143.666 1991 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.12 % Allowed : 33.75 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.23), residues: 1446 helix: 2.97 (0.27), residues: 374 sheet: -0.11 (0.31), residues: 322 loop : -1.38 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.021 0.001 TYR A 12 PHE 0.020 0.001 PHE C 440 TRP 0.010 0.001 TRP C 422 HIS 0.003 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00289 (12064) covalent geometry : angle 0.56459 (16322) SS BOND : bond 0.00491 ( 18) SS BOND : angle 1.96088 ( 36) hydrogen bonds : bond 0.04707 ( 432) hydrogen bonds : angle 4.25444 ( 1296) link_BETA1-4 : bond 0.00350 ( 3) link_BETA1-4 : angle 0.89068 ( 9) link_BETA2-3 : bond 0.00658 ( 2) link_BETA2-3 : angle 3.24865 ( 6) link_NAG-ASN : bond 0.00259 ( 10) link_NAG-ASN : angle 1.97041 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5768.21 seconds wall clock time: 98 minutes 56.94 seconds (5936.94 seconds total)