Starting phenix.real_space_refine on Fri Jul 3 06:14:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2026/7zj6_14742.map" } resolution = 2.6 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= 0.000 sd= 0.006 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 57 5.16 5 C 7623 2.51 5 N 2088 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12282 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} 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 chiralities: 2 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 chiralities: 2 Restraints were copied for chains: B, C, H, L, I, M, J, N, K, O Time building chain proxies: 2.65, per 1000 atoms: 0.22 Number of scatterers: 12282 At special positions: 0 Unit cell: (95.04, 93.96, 149.04, 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 57 16.00 O 2514 8.00 N 2088 7.00 C 7623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.05 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.05 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.05 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.05 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.04 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.05 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.05 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.05 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.05 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.05 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.05 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG M 1 " - " FUC M 4 " NAG-ASN " NAG A 601 " - " ASN A 483 " " NAG A 602 " - " ASN A 22 " " NAG B 601 " - " ASN B 483 " " NAG B 602 " - " ASN B 22 " " NAG C 601 " - " ASN C 483 " " NAG C 602 " - " ASN C 22 " " NAG D 1 " - " ASN A 38 " " NAG E 1 " - " ASN A 81 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 285 " " NAG H 1 " - " ASN B 38 " " NAG I 1 " - " ASN B 81 " " NAG J 1 " - " ASN B 165 " " NAG K 1 " - " ASN B 285 " " NAG L 1 " - " ASN C 38 " " NAG M 1 " - " ASN C 81 " " NAG N 1 " - " ASN C 165 " " NAG O 1 " - " ASN C 285 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 492.0 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 27.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.711A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.555A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.599A pdb=" N THR A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 490 Processing helix chain 'A' and resid 491 through 501 removed outlier: 3.622A pdb=" N GLN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.712A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 79 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.555A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.982A pdb=" N GLN B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.599A pdb=" N THR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 490 Processing helix chain 'B' and resid 491 through 501 removed outlier: 3.622A pdb=" N GLN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.711A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 79 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.555A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 378 removed outlier: 3.600A pdb=" N THR C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 490 Processing helix chain 'C' and resid 491 through 501 removed outlier: 3.621A pdb=" N GLN C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.565A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.869A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.320A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.174A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 8.115A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 166 through 169 removed outlier: 5.989A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.388A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.678A pdb=" N LYS A 391 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 363 Processing sheet with id=AB5, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.565A pdb=" N THR B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.870A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.320A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.175A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 removed outlier: 8.115A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'B' and resid 166 through 169 removed outlier: 5.991A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.387A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.680A pdb=" N LYS B 391 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 363 Processing sheet with id=AC8, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.565A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.869A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.321A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.175A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 100 through 101 removed outlier: 8.116A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'C' and resid 166 through 169 removed outlier: 5.990A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.389A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.678A pdb=" N LYS C 391 " --> pdb=" O GLY C 303 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1323 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: 2.01 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2417 1.33 - 1.45: 3130 1.45 - 1.57: 6900 1.57 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12525 Sorted by residual: bond pdb=" N VAL B 384 " pdb=" CA VAL B 384 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.39e+01 bond pdb=" N VAL A 384 " pdb=" CA VAL A 384 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" N VAL C 384 " pdb=" CA VAL C 384 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N GLY B 135 " pdb=" CA GLY B 135 " ideal model delta sigma weight residual 1.446 1.481 -0.035 9.50e-03 1.11e+04 1.34e+01 bond pdb=" N GLY A 135 " pdb=" CA GLY A 135 " ideal model delta sigma weight residual 1.446 1.481 -0.035 9.50e-03 1.11e+04 1.34e+01 ... (remaining 12520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11098 1.64 - 3.29: 4763 3.29 - 4.93: 1010 4.93 - 6.58: 100 6.58 - 8.22: 15 Bond angle restraints: 16986 Sorted by residual: angle pdb=" CA ARG C 383 " pdb=" C ARG C 383 " pdb=" O ARG C 383 " ideal model delta sigma weight residual 120.55 114.69 5.86 1.06e+00 8.90e-01 3.05e+01 angle pdb=" CA ARG B 383 " pdb=" C ARG B 383 " pdb=" O ARG B 383 " ideal model delta sigma weight residual 120.55 114.72 5.83 1.06e+00 8.90e-01 3.03e+01 angle pdb=" CA ARG A 383 " pdb=" C ARG A 383 " pdb=" O ARG A 383 " ideal model delta sigma weight residual 120.55 114.76 5.79 1.06e+00 8.90e-01 2.98e+01 angle pdb=" CA GLY C 61 " pdb=" C GLY C 61 " pdb=" O GLY C 61 " ideal model delta sigma weight residual 121.58 116.74 4.84 9.00e-01 1.23e+00 2.89e+01 angle pdb=" CA GLY A 61 " pdb=" C GLY A 61 " pdb=" O GLY A 61 " ideal model delta sigma weight residual 121.58 116.80 4.78 9.00e-01 1.23e+00 2.82e+01 ... (remaining 16981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6408 17.79 - 35.59: 591 35.59 - 53.38: 131 53.38 - 71.17: 22 71.17 - 88.97: 15 Dihedral angle restraints: 7167 sinusoidal: 2910 harmonic: 4257 Sorted by residual: dihedral pdb=" CA ASP B 60 " pdb=" C ASP B 60 " pdb=" N GLY B 61 " pdb=" CA GLY B 61 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP C 60 " pdb=" C ASP C 60 " pdb=" N GLY C 61 " pdb=" CA GLY C 61 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" N GLY A 61 " pdb=" CA GLY A 61 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1397 0.093 - 0.186: 544 0.186 - 0.278: 63 0.278 - 0.371: 3 0.371 - 0.464: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.93e+01 chirality pdb=" C1 FUC I 4 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 4 " pdb=" O5 FUC I 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.76e+01 chirality pdb=" C1 MAN N 5 " pdb=" O6 BMA N 3 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.70e+01 ... (remaining 2007 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.209 2.00e-02 2.50e+03 1.83e-01 4.18e+02 pdb=" C7 NAG H 2 " 0.106 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.291 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.207 2.00e-02 2.50e+03 1.81e-01 4.11e+02 pdb=" C7 NAG D 2 " -0.106 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.288 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " 0.207 2.00e-02 2.50e+03 1.81e-01 4.11e+02 pdb=" C7 NAG L 2 " -0.106 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " -0.288 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.023 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5878 3.00 - 3.47: 10440 3.47 - 3.95: 19940 3.95 - 4.42: 21669 4.42 - 4.90: 35462 Nonbonded interactions: 93389 Sorted by model distance: nonbonded pdb=" N ILE C 34 " pdb=" O ILE C 34 " model vdw 2.524 2.496 nonbonded pdb=" N ILE A 34 " pdb=" O ILE A 34 " model vdw 2.524 2.496 nonbonded pdb=" N ILE B 34 " pdb=" O ILE B 34 " model vdw 2.525 2.496 nonbonded pdb=" N LYS A 391 " pdb=" O LYS A 391 " model vdw 2.574 2.496 nonbonded pdb=" N LYS B 391 " pdb=" O LYS B 391 " model vdw 2.574 2.496 ... (remaining 93384 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.013 0.047 12591 Z= 0.982 Angle : 1.782 8.223 17166 Z= 1.258 Chirality : 0.091 0.464 2010 Planarity : 0.011 0.183 2154 Dihedral : 14.895 88.966 4383 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.46 % Allowed : 11.14 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -1.99 (0.17), residues: 1476 helix: -0.33 (0.25), residues: 330 sheet: -0.07 (0.34), residues: 210 loop : -2.12 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 220 TYR 0.026 0.004 TYR A 161 PHE 0.036 0.004 PHE C 125 TRP 0.026 0.004 TRP B 234 HIS 0.012 0.004 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.01312 / 0.98 (12525) covalent geometry : angle 1.77096 / 1.26 (16986) SS BOND : bond 0.01742 / 1.08 ( 18) SS BOND : angle 2.23570 / 1.56 ( 36) hydrogen bonds : bond 0.28227 / 19.64 ( 447) hydrogen bonds : angle 8.00382 / 5.50 ( 1323) link_ALPHA1-3 : bond 0.01196 / 0.60 ( 3) link_ALPHA1-3 : angle 2.08091 / 1.37 ( 9) link_ALPHA1-6 : bond 0.00679 / 0.34 ( 3) link_ALPHA1-6 : angle 0.33384 / 0.23 ( 9) link_BETA1-4 : bond 0.00705 / 0.44 ( 21) link_BETA1-4 : angle 2.90170 / 1.94 ( 63) link_BETA1-6 : bond 0.00382 / 0.19 ( 3) link_BETA1-6 : angle 0.78406 / 0.57 ( 9) link_NAG-ASN : bond 0.00863 / 0.60 ( 18) link_NAG-ASN : angle 3.00106 / 1.85 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8417 (p0) cc_final: 0.8216 (p0) REVERT: A 119 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7940 (tt0) REVERT: A 137 ASN cc_start: 0.8019 (m-40) cc_final: 0.7810 (m-40) REVERT: A 187 THR cc_start: 0.7691 (p) cc_final: 0.7279 (t) REVERT: A 188 ASN cc_start: 0.7552 (t0) cc_final: 0.7207 (m-40) REVERT: A 189 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7103 (tp40) REVERT: A 275 ASP cc_start: 0.7315 (t0) cc_final: 0.7013 (p0) REVERT: A 341 ASN cc_start: 0.6868 (p0) cc_final: 0.6657 (p0) REVERT: A 382 ASN cc_start: 0.7294 (m-40) cc_final: 0.7021 (m110) REVERT: A 401 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7440 (mp0) REVERT: A 444 MET cc_start: 0.8094 (tpt) cc_final: 0.7787 (tpt) REVERT: A 449 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 452 ARG cc_start: 0.6256 (ttp80) cc_final: 0.5877 (tmt170) REVERT: A 468 LYS cc_start: 0.6776 (tttt) cc_final: 0.6511 (ttmm) REVERT: A 482 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6562 (mtm-85) REVERT: B 14 CYS cc_start: 0.6513 (m) cc_final: 0.6310 (m) REVERT: B 137 ASN cc_start: 0.7884 (m-40) cc_final: 0.7593 (m-40) REVERT: B 188 ASN cc_start: 0.7529 (t0) cc_final: 0.7253 (m-40) REVERT: B 189 GLN cc_start: 0.7472 (tm-30) cc_final: 0.6928 (tp40) REVERT: B 208 ARG cc_start: 0.7030 (ptt180) cc_final: 0.6664 (ptm160) REVERT: B 275 ASP cc_start: 0.6808 (t0) cc_final: 0.6549 (p0) REVERT: B 341 ASN cc_start: 0.6879 (p0) cc_final: 0.6640 (p0) REVERT: B 376 GLN cc_start: 0.7011 (mt0) cc_final: 0.6740 (mt0) REVERT: B 382 ASN cc_start: 0.7449 (m-40) cc_final: 0.7110 (m110) REVERT: B 401 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7540 (mm-30) REVERT: B 449 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 452 ARG cc_start: 0.6485 (ttp80) cc_final: 0.5955 (tmt170) REVERT: B 468 LYS cc_start: 0.6878 (tttt) cc_final: 0.6400 (tptp) REVERT: B 482 ARG cc_start: 0.6800 (mtm-85) cc_final: 0.6481 (mtm180) REVERT: C 78 VAL cc_start: 0.8289 (t) cc_final: 0.7999 (p) REVERT: C 159 SER cc_start: 0.7303 (m) cc_final: 0.7089 (p) REVERT: C 187 THR cc_start: 0.7818 (p) cc_final: 0.7322 (t) REVERT: C 188 ASN cc_start: 0.7418 (t0) cc_final: 0.7049 (m-40) REVERT: C 189 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7163 (tp40) REVERT: C 208 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6816 (ptp-110) REVERT: C 264 LYS cc_start: 0.8612 (pttp) cc_final: 0.8402 (pttt) REVERT: C 275 ASP cc_start: 0.7152 (t0) cc_final: 0.6840 (p0) REVERT: C 371 GLN cc_start: 0.6839 (tp40) cc_final: 0.6300 (tp-100) REVERT: C 382 ASN cc_start: 0.7326 (m-40) cc_final: 0.6948 (m110) REVERT: C 401 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7483 (mm-30) REVERT: C 444 MET cc_start: 0.8039 (tpt) cc_final: 0.7440 (tpt) REVERT: C 446 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7507 (mtmm) REVERT: C 449 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7083 (mm-30) REVERT: C 452 ARG cc_start: 0.6207 (ttp80) cc_final: 0.5922 (tmt170) REVERT: C 468 LYS cc_start: 0.6638 (tttt) cc_final: 0.6164 (tttp) REVERT: C 470 TYR cc_start: 0.7580 (m-80) cc_final: 0.7246 (m-80) outliers start: 6 outliers final: 3 residues processed: 214 average time/residue: 0.5016 time to fit residues: 116.8260 Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 210 GLN A 376 GLN A 475 ASN A 498 ASN B 54 ASN B 210 GLN B 248 ASN B 475 ASN B 497 ASN C 54 ASN C 210 GLN C 295 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112694 restraints weight = 14601.128| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.48 r_work: 0.3115 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12591 Z= 0.141 Angle : 0.619 8.868 17166 Z= 0.317 Chirality : 0.043 0.188 2010 Planarity : 0.004 0.031 2154 Dihedral : 5.133 41.611 1608 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.40 % Allowed : 12.53 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.41 (0.19), residues: 1476 helix: 2.32 (0.26), residues: 333 sheet: -0.04 (0.29), residues: 303 loop : -1.53 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 329 TYR 0.009 0.001 TYR B 486 PHE 0.012 0.001 PHE C 258 TRP 0.008 0.001 TRP B 421 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (12525) covalent geometry : angle 0.59649 / 0.31 (16986) SS BOND : bond 0.00350 / 0.19 ( 18) SS BOND : angle 1.33403 / 0.97 ( 36) hydrogen bonds : bond 0.07457 / 5.15 ( 447) hydrogen bonds : angle 5.04522 / 3.45 ( 1323) link_ALPHA1-3 : bond 0.00333 / 0.17 ( 3) link_ALPHA1-3 : angle 1.45643 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00295 / 0.15 ( 3) link_ALPHA1-6 : angle 1.16460 / 0.72 ( 9) link_BETA1-4 : bond 0.00560 / 0.37 ( 21) link_BETA1-4 : angle 2.03816 / 1.34 ( 63) link_BETA1-6 : bond 0.00400 / 0.20 ( 3) link_BETA1-6 : angle 1.28130 / 0.94 ( 9) link_NAG-ASN : bond 0.00469 / 0.29 ( 18) link_NAG-ASN : angle 1.73554 / 1.12 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7680 (p) cc_final: 0.7426 (t) REVERT: A 188 ASN cc_start: 0.7643 (t0) cc_final: 0.7311 (m-40) REVERT: A 189 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7364 (tp40) REVERT: A 341 ASN cc_start: 0.7122 (p0) cc_final: 0.6891 (p0) REVERT: A 401 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7365 (mp0) REVERT: A 452 ARG cc_start: 0.6336 (ttp80) cc_final: 0.5980 (tmt170) REVERT: A 468 LYS cc_start: 0.6892 (tttt) cc_final: 0.6458 (ttmm) REVERT: A 482 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6548 (mtp180) REVERT: A 487 ASP cc_start: 0.7545 (t0) cc_final: 0.7318 (t0) REVERT: A 497 ASN cc_start: 0.7624 (m-40) cc_final: 0.7280 (m-40) REVERT: B 70 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8651 (tt) REVERT: B 188 ASN cc_start: 0.7726 (t0) cc_final: 0.7471 (m-40) REVERT: B 189 GLN cc_start: 0.7528 (tm-30) cc_final: 0.7155 (tp40) REVERT: B 341 ASN cc_start: 0.7107 (p0) cc_final: 0.6862 (p0) REVERT: B 355 HIS cc_start: 0.6744 (p90) cc_final: 0.6519 (p90) REVERT: B 361 THR cc_start: 0.7499 (t) cc_final: 0.7149 (p) REVERT: B 401 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7484 (mp0) REVERT: B 452 ARG cc_start: 0.6427 (ttp80) cc_final: 0.5807 (tmt170) REVERT: B 468 LYS cc_start: 0.6968 (tttt) cc_final: 0.6591 (tttp) REVERT: B 479 GLU cc_start: 0.6806 (tp30) cc_final: 0.5962 (tp30) REVERT: B 482 ARG cc_start: 0.6969 (mtm-85) cc_final: 0.6643 (mtm-85) REVERT: B 487 ASP cc_start: 0.7477 (t0) cc_final: 0.7184 (t0) REVERT: C 78 VAL cc_start: 0.8587 (t) cc_final: 0.8249 (p) REVERT: C 187 THR cc_start: 0.7804 (p) cc_final: 0.7455 (t) REVERT: C 188 ASN cc_start: 0.7542 (t0) cc_final: 0.7257 (m-40) REVERT: C 189 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7288 (tp40) REVERT: C 371 GLN cc_start: 0.7143 (tp40) cc_final: 0.6465 (tp-100) REVERT: C 401 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7433 (mm-30) REVERT: C 444 MET cc_start: 0.8372 (tpt) cc_final: 0.7835 (tpt) REVERT: C 452 ARG cc_start: 0.6411 (ttp80) cc_final: 0.5991 (tmt170) REVERT: C 468 LYS cc_start: 0.6973 (tttt) cc_final: 0.6460 (tttp) REVERT: C 470 TYR cc_start: 0.7360 (m-80) cc_final: 0.7142 (m-80) REVERT: C 497 ASN cc_start: 0.7511 (m-40) cc_final: 0.7311 (m110) outliers start: 31 outliers final: 11 residues processed: 177 average time/residue: 0.4154 time to fit residues: 81.3479 Evaluate side-chains 138 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 HIS B 18 HIS B 363 GLN B 376 GLN C 295 GLN C 363 GLN C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110319 restraints weight = 14719.159| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.51 r_work: 0.3069 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12591 Z= 0.188 Angle : 0.726 10.511 17166 Z= 0.368 Chirality : 0.046 0.208 2010 Planarity : 0.005 0.035 2154 Dihedral : 5.156 40.081 1604 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.02 % Allowed : 13.92 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.24 (0.20), residues: 1476 helix: 2.40 (0.26), residues: 333 sheet: 0.17 (0.29), residues: 321 loop : -1.46 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.017 0.002 TYR B 308 PHE 0.016 0.002 PHE C 125 TRP 0.009 0.002 TRP A 421 HIS 0.012 0.002 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (12525) covalent geometry : angle 0.67964 / 0.35 (16986) SS BOND : bond 0.00221 / 0.14 ( 18) SS BOND : angle 3.42119 / 2.40 ( 36) hydrogen bonds : bond 0.07677 / 5.31 ( 447) hydrogen bonds : angle 4.82993 / 3.29 ( 1323) link_ALPHA1-3 : bond 0.00626 / 0.31 ( 3) link_ALPHA1-3 : angle 1.38634 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00325 / 0.17 ( 3) link_ALPHA1-6 : angle 1.28250 / 0.88 ( 9) link_BETA1-4 : bond 0.00384 / 0.25 ( 21) link_BETA1-4 : angle 2.01080 / 1.34 ( 63) link_BETA1-6 : bond 0.00436 / 0.22 ( 3) link_BETA1-6 : angle 1.19110 / 0.89 ( 9) link_NAG-ASN : bond 0.00485 / 0.30 ( 18) link_NAG-ASN : angle 3.02154 / 1.71 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7730 (p) cc_final: 0.7462 (t) REVERT: A 188 ASN cc_start: 0.7776 (t0) cc_final: 0.7369 (m-40) REVERT: A 468 LYS cc_start: 0.7115 (tttt) cc_final: 0.6615 (ttmm) REVERT: A 482 ARG cc_start: 0.7046 (mtm-85) cc_final: 0.6708 (mtm-85) REVERT: A 497 ASN cc_start: 0.7813 (m-40) cc_final: 0.7504 (m-40) REVERT: B 70 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8623 (tt) REVERT: B 188 ASN cc_start: 0.7845 (t0) cc_final: 0.7484 (m-40) REVERT: B 208 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6805 (ptm160) REVERT: B 242 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 275 ASP cc_start: 0.7364 (p0) cc_final: 0.6939 (p0) REVERT: B 341 ASN cc_start: 0.7284 (p0) cc_final: 0.6974 (p0) REVERT: B 355 HIS cc_start: 0.6924 (p90) cc_final: 0.6367 (p90) REVERT: B 401 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7611 (mp0) REVERT: B 452 ARG cc_start: 0.6305 (ttp80) cc_final: 0.6095 (tmt170) REVERT: B 468 LYS cc_start: 0.7148 (tttt) cc_final: 0.6879 (tttp) REVERT: C 78 VAL cc_start: 0.8643 (t) cc_final: 0.8329 (p) REVERT: C 187 THR cc_start: 0.7870 (p) cc_final: 0.7521 (t) REVERT: C 188 ASN cc_start: 0.7683 (t0) cc_final: 0.7323 (m-40) REVERT: C 189 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7150 (tp40) REVERT: C 321 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7457 (ptp-170) REVERT: C 371 GLN cc_start: 0.7171 (tp40) cc_final: 0.6527 (tp-100) REVERT: C 401 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7554 (mm-30) REVERT: C 444 MET cc_start: 0.8388 (tpt) cc_final: 0.7981 (tpt) REVERT: C 452 ARG cc_start: 0.6267 (ttp80) cc_final: 0.5820 (tmt170) REVERT: C 468 LYS cc_start: 0.7083 (tttt) cc_final: 0.6588 (tttp) REVERT: C 487 ASP cc_start: 0.7190 (t0) cc_final: 0.6909 (t0) REVERT: C 497 ASN cc_start: 0.7646 (m-40) cc_final: 0.7420 (m110) outliers start: 39 outliers final: 18 residues processed: 152 average time/residue: 0.4161 time to fit residues: 70.0681 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS C 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111487 restraints weight = 14860.156| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.38 r_work: 0.3116 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 12591 Z= 0.222 Angle : 0.765 11.459 17166 Z= 0.385 Chirality : 0.048 0.196 2010 Planarity : 0.005 0.039 2154 Dihedral : 5.319 41.058 1604 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.56 % Allowed : 14.23 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.33 (0.20), residues: 1476 helix: 2.35 (0.26), residues: 333 sheet: -0.10 (0.28), residues: 354 loop : -1.48 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 109 TYR 0.016 0.002 TYR B 308 PHE 0.017 0.002 PHE C 125 TRP 0.010 0.002 TRP A 421 HIS 0.011 0.002 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (12525) covalent geometry : angle 0.72234 / 0.37 (16986) SS BOND : bond 0.00295 / 0.17 ( 18) SS BOND : angle 3.71529 / 2.53 ( 36) hydrogen bonds : bond 0.07881 / 5.46 ( 447) hydrogen bonds : angle 4.85158 / 3.31 ( 1323) link_ALPHA1-3 : bond 0.00700 / 0.35 ( 3) link_ALPHA1-3 : angle 1.31485 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00283 / 0.14 ( 3) link_ALPHA1-6 : angle 1.22414 / 0.86 ( 9) link_BETA1-4 : bond 0.00419 / 0.28 ( 21) link_BETA1-4 : angle 2.07185 / 1.38 ( 63) link_BETA1-6 : bond 0.00337 / 0.17 ( 3) link_BETA1-6 : angle 1.15574 / 0.85 ( 9) link_NAG-ASN : bond 0.00537 / 0.35 ( 18) link_NAG-ASN : angle 2.67445 / 1.70 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7821 (p) cc_final: 0.7482 (t) REVERT: A 208 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6715 (ptm160) REVERT: A 452 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6394 (tmt170) REVERT: A 468 LYS cc_start: 0.7250 (tttt) cc_final: 0.6884 (tttp) REVERT: A 482 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6692 (mtm-85) REVERT: A 497 ASN cc_start: 0.7748 (m-40) cc_final: 0.7510 (m-40) REVERT: B 27 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7472 (ptmt) REVERT: B 70 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8633 (tt) REVERT: B 208 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6820 (ptm160) REVERT: B 355 HIS cc_start: 0.6857 (p90) cc_final: 0.6275 (p90) REVERT: B 371 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6595 (tp40) REVERT: B 401 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7702 (mp0) REVERT: B 468 LYS cc_start: 0.7208 (tttt) cc_final: 0.6869 (tttp) REVERT: C 78 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8454 (p) REVERT: C 187 THR cc_start: 0.7880 (p) cc_final: 0.7572 (t) REVERT: C 188 ASN cc_start: 0.7815 (t0) cc_final: 0.7443 (m-40) REVERT: C 321 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7392 (ptp-170) REVERT: C 371 GLN cc_start: 0.7028 (tp40) cc_final: 0.6376 (tp40) REVERT: C 401 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7637 (mm-30) REVERT: C 444 MET cc_start: 0.8311 (tpt) cc_final: 0.7844 (tpt) REVERT: C 452 ARG cc_start: 0.6211 (ttp80) cc_final: 0.5961 (tmt170) REVERT: C 468 LYS cc_start: 0.6987 (tttt) cc_final: 0.6537 (tttp) REVERT: C 497 ASN cc_start: 0.7782 (m-40) cc_final: 0.7531 (m-40) outliers start: 46 outliers final: 25 residues processed: 147 average time/residue: 0.4102 time to fit residues: 66.8857 Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 355 HIS C 216 ASN C 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111395 restraints weight = 15017.942| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.05 r_work: 0.3151 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12591 Z= 0.155 Angle : 0.672 12.341 17166 Z= 0.336 Chirality : 0.044 0.271 2010 Planarity : 0.004 0.035 2154 Dihedral : 5.065 38.513 1604 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.25 % Allowed : 15.39 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.09 (0.20), residues: 1476 helix: 2.72 (0.26), residues: 333 sheet: -0.05 (0.28), residues: 354 loop : -1.36 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.010 0.002 TYR A 257 PHE 0.012 0.001 PHE C 125 TRP 0.009 0.001 TRP B 222 HIS 0.010 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (12525) covalent geometry : angle 0.63234 / 0.32 (16986) SS BOND : bond 0.00492 / 0.28 ( 18) SS BOND : angle 3.43955 / 2.26 ( 36) hydrogen bonds : bond 0.06907 / 4.77 ( 447) hydrogen bonds : angle 4.67007 / 3.17 ( 1323) link_ALPHA1-3 : bond 0.00679 / 0.34 ( 3) link_ALPHA1-3 : angle 1.31524 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00299 / 0.15 ( 3) link_ALPHA1-6 : angle 1.24302 / 0.85 ( 9) link_BETA1-4 : bond 0.00409 / 0.26 ( 21) link_BETA1-4 : angle 1.83191 / 1.22 ( 63) link_BETA1-6 : bond 0.00303 / 0.15 ( 3) link_BETA1-6 : angle 1.11952 / 0.81 ( 9) link_NAG-ASN : bond 0.00517 / 0.33 ( 18) link_NAG-ASN : angle 2.24805 / 1.20 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7781 (p) cc_final: 0.7490 (t) REVERT: A 468 LYS cc_start: 0.7219 (tttt) cc_final: 0.6871 (tttp) REVERT: A 482 ARG cc_start: 0.7068 (mtm-85) cc_final: 0.6752 (mtm-85) REVERT: A 497 ASN cc_start: 0.7710 (m-40) cc_final: 0.7476 (m-40) REVERT: B 14 CYS cc_start: 0.6600 (t) cc_final: 0.6308 (m) REVERT: B 70 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8529 (tt) REVERT: B 341 ASN cc_start: 0.7468 (p0) cc_final: 0.7225 (p0) REVERT: B 355 HIS cc_start: 0.6913 (p90) cc_final: 0.6290 (p90) REVERT: B 371 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6657 (tp40) REVERT: B 385 ILE cc_start: 0.6338 (tt) cc_final: 0.6122 (tp) REVERT: B 401 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7656 (mp0) REVERT: B 445 ASN cc_start: 0.7417 (t0) cc_final: 0.6847 (m-40) REVERT: B 452 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6374 (tmt170) REVERT: B 468 LYS cc_start: 0.7219 (tttt) cc_final: 0.6881 (ttmm) REVERT: C 52 CYS cc_start: 0.7430 (m) cc_final: 0.7080 (m) REVERT: C 78 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8494 (p) REVERT: C 187 THR cc_start: 0.7783 (p) cc_final: 0.7516 (t) REVERT: C 188 ASN cc_start: 0.7843 (t0) cc_final: 0.7414 (m-40) REVERT: C 371 GLN cc_start: 0.6974 (tp40) cc_final: 0.6263 (tp40) REVERT: C 401 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7601 (mm-30) REVERT: C 444 MET cc_start: 0.8316 (tpt) cc_final: 0.7909 (tpt) REVERT: C 468 LYS cc_start: 0.6989 (tttt) cc_final: 0.6520 (tttp) REVERT: C 497 ASN cc_start: 0.7783 (m-40) cc_final: 0.7550 (m-40) outliers start: 42 outliers final: 21 residues processed: 139 average time/residue: 0.4065 time to fit residues: 62.7570 Evaluate side-chains 129 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN A 355 HIS C 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113175 restraints weight = 14887.840| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.05 r_work: 0.3174 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12591 Z= 0.115 Angle : 0.581 8.757 17166 Z= 0.291 Chirality : 0.042 0.212 2010 Planarity : 0.004 0.035 2154 Dihedral : 4.699 33.981 1604 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.63 % Allowed : 16.16 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: 0.24 (0.21), residues: 1476 helix: 3.13 (0.27), residues: 333 sheet: 0.06 (0.28), residues: 354 loop : -1.16 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 201 TYR 0.008 0.001 TYR C 257 PHE 0.008 0.001 PHE A 258 TRP 0.010 0.001 TRP B 222 HIS 0.009 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12525) covalent geometry : angle 0.54515 / 0.28 (16986) SS BOND : bond 0.00497 / 0.29 ( 18) SS BOND : angle 2.66135 / 1.73 ( 36) hydrogen bonds : bond 0.06078 / 4.19 ( 447) hydrogen bonds : angle 4.47392 / 3.04 ( 1323) link_ALPHA1-3 : bond 0.00643 / 0.32 ( 3) link_ALPHA1-3 : angle 1.32813 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00339 / 0.17 ( 3) link_ALPHA1-6 : angle 1.29573 / 0.88 ( 9) link_BETA1-4 : bond 0.00389 / 0.24 ( 21) link_BETA1-4 : angle 1.66296 / 1.10 ( 63) link_BETA1-6 : bond 0.00295 / 0.15 ( 3) link_BETA1-6 : angle 1.12483 / 0.81 ( 9) link_NAG-ASN : bond 0.00311 / 0.20 ( 18) link_NAG-ASN : angle 2.28489 / 1.50 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 187 THR cc_start: 0.7782 (p) cc_final: 0.7501 (t) REVERT: A 452 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5888 (tmt170) REVERT: A 468 LYS cc_start: 0.7334 (tttt) cc_final: 0.6957 (tttp) REVERT: A 497 ASN cc_start: 0.7667 (m-40) cc_final: 0.7453 (m-40) REVERT: B 52 CYS cc_start: 0.7505 (m) cc_final: 0.7089 (m) REVERT: B 341 ASN cc_start: 0.7472 (p0) cc_final: 0.7246 (p0) REVERT: B 355 HIS cc_start: 0.7028 (p90) cc_final: 0.6412 (p90) REVERT: B 371 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6652 (tp40) REVERT: B 385 ILE cc_start: 0.6460 (tt) cc_final: 0.6227 (tp) REVERT: B 401 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7545 (mp0) REVERT: B 445 ASN cc_start: 0.7321 (t0) cc_final: 0.6803 (m-40) REVERT: B 468 LYS cc_start: 0.7121 (tttt) cc_final: 0.6753 (ttmm) REVERT: C 78 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 187 THR cc_start: 0.7818 (p) cc_final: 0.7573 (t) REVERT: C 188 ASN cc_start: 0.7865 (t0) cc_final: 0.7375 (m-40) REVERT: C 371 GLN cc_start: 0.6946 (tp40) cc_final: 0.6231 (tp40) REVERT: C 401 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7524 (mm-30) REVERT: C 444 MET cc_start: 0.8363 (tpt) cc_final: 0.7959 (tpt) REVERT: C 468 LYS cc_start: 0.7014 (tttt) cc_final: 0.6571 (tttp) outliers start: 34 outliers final: 19 residues processed: 137 average time/residue: 0.3870 time to fit residues: 58.7917 Evaluate side-chains 124 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 0.0370 chunk 120 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 295 GLN C 363 GLN C 497 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109982 restraints weight = 14978.524| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 12591 Z= 0.260 Angle : 0.812 13.782 17166 Z= 0.411 Chirality : 0.051 0.188 2010 Planarity : 0.006 0.040 2154 Dihedral : 5.284 35.583 1602 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.25 % Allowed : 15.78 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1476 helix: 2.34 (0.26), residues: 333 sheet: -0.19 (0.28), residues: 339 loop : -1.48 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 109 TYR 0.019 0.003 TYR B 308 PHE 0.021 0.003 PHE C 125 TRP 0.013 0.002 TRP B 222 HIS 0.007 0.002 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 (12525) covalent geometry : angle 0.76956 / 0.40 (16986) SS BOND : bond 0.00631 / 0.42 ( 18) SS BOND : angle 4.17820 / 3.41 ( 36) hydrogen bonds : bond 0.08131 / 5.64 ( 447) hydrogen bonds : angle 4.92415 / 3.36 ( 1323) link_ALPHA1-3 : bond 0.00754 / 0.38 ( 3) link_ALPHA1-3 : angle 1.22259 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00198 / 0.10 ( 3) link_ALPHA1-6 : angle 1.29579 / 0.93 ( 9) link_BETA1-4 : bond 0.00411 / 0.26 ( 21) link_BETA1-4 : angle 2.09163 / 1.40 ( 63) link_BETA1-6 : bond 0.00191 / 0.10 ( 3) link_BETA1-6 : angle 1.21922 / 0.89 ( 9) link_NAG-ASN : bond 0.00444 / 0.28 ( 18) link_NAG-ASN : angle 2.44253 / 1.38 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6100 (tmt170) REVERT: A 468 LYS cc_start: 0.7569 (tttt) cc_final: 0.7040 (ttmm) REVERT: B 27 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7553 (ptmt) REVERT: B 52 CYS cc_start: 0.7678 (m) cc_final: 0.7256 (m) REVERT: B 70 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 355 HIS cc_start: 0.6926 (p90) cc_final: 0.6369 (p90) REVERT: B 371 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6667 (tp40) REVERT: B 401 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7766 (mp0) REVERT: B 452 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6597 (tmt170) REVERT: C 78 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8387 (p) REVERT: C 187 THR cc_start: 0.7929 (p) cc_final: 0.7645 (t) REVERT: C 371 GLN cc_start: 0.7031 (tp40) cc_final: 0.6366 (tp40) REVERT: C 401 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7693 (mm-30) REVERT: C 444 MET cc_start: 0.8313 (tpt) cc_final: 0.7908 (tpt) outliers start: 42 outliers final: 26 residues processed: 134 average time/residue: 0.4233 time to fit residues: 62.8232 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 329 ARG Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 473 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 49 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN C 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119474 restraints weight = 14934.492| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.75 r_work: 0.3154 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12591 Z= 0.126 Angle : 0.610 11.334 17166 Z= 0.309 Chirality : 0.042 0.228 2010 Planarity : 0.004 0.034 2154 Dihedral : 4.885 35.496 1602 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.09 % Allowed : 17.63 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1476 helix: 2.83 (0.27), residues: 333 sheet: 0.12 (0.28), residues: 339 loop : -1.21 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.008 0.001 TYR C 257 PHE 0.008 0.001 PHE A 258 TRP 0.010 0.001 TRP B 222 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12525) covalent geometry : angle 0.56895 / 0.30 (16986) SS BOND : bond 0.00569 / 0.39 ( 18) SS BOND : angle 3.52500 / 2.78 ( 36) hydrogen bonds : bond 0.06391 / 4.40 ( 447) hydrogen bonds : angle 4.65413 / 3.18 ( 1323) link_ALPHA1-3 : bond 0.00697 / 0.35 ( 3) link_ALPHA1-3 : angle 1.30360 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00284 / 0.14 ( 3) link_ALPHA1-6 : angle 1.32140 / 0.90 ( 9) link_BETA1-4 : bond 0.00383 / 0.24 ( 21) link_BETA1-4 : angle 1.66891 / 1.11 ( 63) link_BETA1-6 : bond 0.00227 / 0.11 ( 3) link_BETA1-6 : angle 1.14394 / 0.83 ( 9) link_NAG-ASN : bond 0.00313 / 0.19 ( 18) link_NAG-ASN : angle 2.03425 / 1.09 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5920 (tmt170) REVERT: B 52 CYS cc_start: 0.7555 (m) cc_final: 0.7187 (m) REVERT: B 355 HIS cc_start: 0.6973 (p90) cc_final: 0.6446 (p90) REVERT: B 371 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6613 (tp40) REVERT: B 401 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7604 (mp0) REVERT: B 445 ASN cc_start: 0.7367 (t0) cc_final: 0.6801 (m-40) REVERT: B 464 ASN cc_start: 0.7349 (m-40) cc_final: 0.7033 (t0) REVERT: C 78 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (p) REVERT: C 187 THR cc_start: 0.7850 (p) cc_final: 0.7644 (t) REVERT: C 371 GLN cc_start: 0.7028 (tp40) cc_final: 0.6361 (tp40) REVERT: C 401 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7579 (mm-30) REVERT: C 444 MET cc_start: 0.8318 (tpt) cc_final: 0.7959 (tpt) outliers start: 27 outliers final: 20 residues processed: 120 average time/residue: 0.4222 time to fit residues: 56.1500 Evaluate side-chains 118 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 473 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 0.0000 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110785 restraints weight = 14872.923| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.04 r_work: 0.3136 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12591 Z= 0.209 Angle : 0.734 12.678 17166 Z= 0.372 Chirality : 0.047 0.240 2010 Planarity : 0.005 0.038 2154 Dihedral : 5.224 33.833 1602 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.17 % Allowed : 17.32 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 are not related in a simple way. whole: -0.26 (0.20), residues: 1476 helix: 2.49 (0.26), residues: 333 sheet: -0.16 (0.28), residues: 339 loop : -1.40 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 109 TYR 0.016 0.002 TYR B 308 PHE 0.019 0.002 PHE C 125 TRP 0.015 0.002 TRP B 222 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (12525) covalent geometry : angle 0.69678 / 0.36 (16986) SS BOND : bond 0.00519 / 0.34 ( 18) SS BOND : angle 3.76148 / 2.83 ( 36) hydrogen bonds : bond 0.07596 / 5.25 ( 447) hydrogen bonds : angle 4.81493 / 3.29 ( 1323) link_ALPHA1-3 : bond 0.00697 / 0.35 ( 3) link_ALPHA1-3 : angle 1.29721 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00242 / 0.12 ( 3) link_ALPHA1-6 : angle 1.27098 / 0.90 ( 9) link_BETA1-4 : bond 0.00403 / 0.25 ( 21) link_BETA1-4 : angle 1.92011 / 1.29 ( 63) link_BETA1-6 : bond 0.00152 / 0.08 ( 3) link_BETA1-6 : angle 1.20082 / 0.88 ( 9) link_NAG-ASN : bond 0.00366 / 0.23 ( 18) link_NAG-ASN : angle 1.99578 / 1.18 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.5980 (tmt170) REVERT: B 52 CYS cc_start: 0.7560 (m) cc_final: 0.7171 (m) REVERT: B 355 HIS cc_start: 0.6739 (p90) cc_final: 0.6289 (p90) REVERT: B 371 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6661 (tp40) REVERT: B 445 ASN cc_start: 0.7400 (t0) cc_final: 0.6814 (m-40) REVERT: B 464 ASN cc_start: 0.7335 (m-40) cc_final: 0.6910 (t0) REVERT: C 78 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8405 (p) REVERT: C 187 THR cc_start: 0.7932 (p) cc_final: 0.7647 (t) REVERT: C 359 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5363 (mt-10) REVERT: C 371 GLN cc_start: 0.7043 (tp40) cc_final: 0.6326 (tp40) REVERT: C 401 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7667 (mm-30) REVERT: C 444 MET cc_start: 0.8304 (tpt) cc_final: 0.7937 (tpt) outliers start: 28 outliers final: 20 residues processed: 118 average time/residue: 0.3958 time to fit residues: 52.1190 Evaluate side-chains 117 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119808 restraints weight = 14861.642| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.89 r_work: 0.3146 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12591 Z= 0.121 Angle : 0.598 10.938 17166 Z= 0.304 Chirality : 0.042 0.171 2010 Planarity : 0.004 0.034 2154 Dihedral : 4.885 34.246 1602 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.70 % Allowed : 18.10 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 are not related in a simple way. whole: 0.19 (0.21), residues: 1476 helix: 3.02 (0.26), residues: 333 sheet: 0.12 (0.28), residues: 339 loop : -1.19 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.008 0.001 TYR A 257 PHE 0.009 0.001 PHE A 258 TRP 0.013 0.001 TRP B 222 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12525) covalent geometry : angle 0.56321 / 0.29 (16986) SS BOND : bond 0.00463 / 0.30 ( 18) SS BOND : angle 3.36156 / 2.61 ( 36) hydrogen bonds : bond 0.06235 / 4.30 ( 447) hydrogen bonds : angle 4.57559 / 3.13 ( 1323) link_ALPHA1-3 : bond 0.00678 / 0.34 ( 3) link_ALPHA1-3 : angle 1.32492 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00300 / 0.15 ( 3) link_ALPHA1-6 : angle 1.30262 / 0.89 ( 9) link_BETA1-4 : bond 0.00382 / 0.24 ( 21) link_BETA1-4 : angle 1.64784 / 1.10 ( 63) link_BETA1-6 : bond 0.00243 / 0.12 ( 3) link_BETA1-6 : angle 1.13118 / 0.82 ( 9) link_NAG-ASN : bond 0.00308 / 0.19 ( 18) link_NAG-ASN : angle 1.55929 / 0.91 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5876 (tmt170) REVERT: A 464 ASN cc_start: 0.7190 (t0) cc_final: 0.6685 (t0) REVERT: B 52 CYS cc_start: 0.7569 (m) cc_final: 0.7221 (m) REVERT: B 355 HIS cc_start: 0.6835 (p90) cc_final: 0.6340 (p90) REVERT: B 371 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6664 (tp40) REVERT: B 445 ASN cc_start: 0.7334 (t0) cc_final: 0.6801 (m-40) REVERT: B 462 MET cc_start: 0.7781 (mtp) cc_final: 0.7382 (mtm) REVERT: C 78 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8292 (p) REVERT: C 371 GLN cc_start: 0.7027 (tp40) cc_final: 0.6354 (tp40) REVERT: C 401 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7559 (mm-30) REVERT: C 444 MET cc_start: 0.8325 (tpt) cc_final: 0.7968 (tpt) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.3894 time to fit residues: 52.0506 Evaluate side-chains 114 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN C 295 GLN ** C 454 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 = 0.3766 r_free = 0.3766 target = 0.149428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117574 restraints weight = 14903.683| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.91 r_work: 0.3114 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12591 Z= 0.208 Angle : 0.736 12.469 17166 Z= 0.375 Chirality : 0.048 0.202 2010 Planarity : 0.005 0.038 2154 Dihedral : 5.178 33.508 1602 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 18.33 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -0.20 (0.20), residues: 1476 helix: 2.69 (0.26), residues: 333 sheet: -0.17 (0.28), residues: 339 loop : -1.40 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 109 TYR 0.017 0.002 TYR B 308 PHE 0.019 0.002 PHE C 125 TRP 0.019 0.002 TRP B 222 HIS 0.012 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (12525) covalent geometry : angle 0.70008 / 0.36 (16986) SS BOND : bond 0.00577 / 0.39 ( 18) SS BOND : angle 3.71314 / 2.80 ( 36) hydrogen bonds : bond 0.07460 / 5.17 ( 447) hydrogen bonds : angle 4.73953 / 3.25 ( 1323) link_ALPHA1-3 : bond 0.00699 / 0.35 ( 3) link_ALPHA1-3 : angle 1.30927 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00205 / 0.10 ( 3) link_ALPHA1-6 : angle 1.29699 / 0.92 ( 9) link_BETA1-4 : bond 0.00379 / 0.23 ( 21) link_BETA1-4 : angle 1.89058 / 1.26 ( 63) link_BETA1-6 : bond 0.00146 / 0.07 ( 3) link_BETA1-6 : angle 1.16994 / 0.85 ( 9) link_NAG-ASN : bond 0.00369 / 0.24 ( 18) link_NAG-ASN : angle 1.90887 / 1.09 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3904.51 seconds wall clock time: 67 minutes 13.18 seconds (4033.18 seconds total)