Starting phenix.real_space_refine on Wed Mar 4 09:29:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj6_14742/03_2026/7zj6_14742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj6_14742/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zj6_14742/03_2026/7zj6_14742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj6_14742/03_2026/7zj6_14742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zj6_14742/03_2026/7zj6_14742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj6_14742/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, H, L, I, M, J, N, K, O Time building chain proxies: 2.67, 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: 1.21 Conformation dependent library (CDL) restraints added in 526.1 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: 0.31 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: 1.73 Time building geometry restraints manager: 1.54 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 - 23.07: 7494 23.07 - 46.15: 468 46.15 - 69.22: 75 69.22 - 92.29: 60 92.29 - 115.36: 36 Dihedral angle restraints: 8133 sinusoidal: 3876 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 8130 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: 1.870 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 18.227 115.364 5349 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 covalent geometry : bond 0.01312 (12525) covalent geometry : angle 1.77096 (16986) SS BOND : bond 0.01742 ( 18) SS BOND : angle 2.23570 ( 36) hydrogen bonds : bond 0.28227 ( 447) hydrogen bonds : angle 8.00382 ( 1323) link_ALPHA1-3 : bond 0.01196 ( 3) link_ALPHA1-3 : angle 2.08091 ( 9) link_ALPHA1-6 : bond 0.00679 ( 3) link_ALPHA1-6 : angle 0.33384 ( 9) link_BETA1-4 : bond 0.00705 ( 21) link_BETA1-4 : angle 2.90170 ( 63) link_BETA1-6 : bond 0.00382 ( 3) link_BETA1-6 : angle 0.78406 ( 9) link_NAG-ASN : bond 0.00863 ( 18) link_NAG-ASN : angle 3.00106 ( 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 : 0.452 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: 0.5767 time to fit residues: 133.9008 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 : 0.448 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3807 r_free = 0.3807 target = 0.152512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114013 restraints weight = 14965.917| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.07 r_work: 0.3182 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12591 Z= 0.137 Angle : 0.642 8.789 17166 Z= 0.320 Chirality : 0.045 0.194 2010 Planarity : 0.004 0.031 2154 Dihedral : 12.729 85.482 2574 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.55 % Allowed : 12.30 % Favored : 85.15 % 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: -0.38 (0.20), residues: 1476 helix: 2.35 (0.26), residues: 333 sheet: -0.05 (0.29), residues: 303 loop : -1.49 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.011 0.001 TYR B 486 PHE 0.013 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 covalent geometry : bond 0.00272 (12525) covalent geometry : angle 0.61283 (16986) SS BOND : bond 0.00395 ( 18) SS BOND : angle 1.28538 ( 36) hydrogen bonds : bond 0.07153 ( 447) hydrogen bonds : angle 5.01517 ( 1323) link_ALPHA1-3 : bond 0.00827 ( 3) link_ALPHA1-3 : angle 1.96621 ( 9) link_ALPHA1-6 : bond 0.00459 ( 3) link_ALPHA1-6 : angle 1.78578 ( 9) link_BETA1-4 : bond 0.00419 ( 21) link_BETA1-4 : angle 2.50800 ( 63) link_BETA1-6 : bond 0.00492 ( 3) link_BETA1-6 : angle 1.28165 ( 9) link_NAG-ASN : bond 0.00454 ( 18) link_NAG-ASN : angle 1.72784 ( 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 191 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7501 (t) REVERT: A 187 THR cc_start: 0.7685 (p) cc_final: 0.7462 (t) REVERT: A 188 ASN cc_start: 0.7638 (t0) cc_final: 0.7325 (m-40) REVERT: A 189 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7393 (tp40) REVERT: A 341 ASN cc_start: 0.7126 (p0) cc_final: 0.6922 (p0) REVERT: A 401 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7358 (mp0) REVERT: A 452 ARG cc_start: 0.6309 (ttp80) cc_final: 0.5993 (tmt170) REVERT: A 468 LYS cc_start: 0.6974 (tttt) cc_final: 0.6558 (ttmm) REVERT: A 482 ARG cc_start: 0.7113 (mtm-85) cc_final: 0.6620 (mtp180) REVERT: A 487 ASP cc_start: 0.7560 (t0) cc_final: 0.7323 (t0) REVERT: A 497 ASN cc_start: 0.7523 (m-40) cc_final: 0.7168 (m-40) REVERT: B 188 ASN cc_start: 0.7727 (t0) cc_final: 0.7476 (m-40) REVERT: B 189 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7066 (tp40) REVERT: B 341 ASN cc_start: 0.7168 (p0) cc_final: 0.6930 (p0) REVERT: B 355 HIS cc_start: 0.6665 (p90) cc_final: 0.6458 (p90) REVERT: B 361 THR cc_start: 0.7465 (t) cc_final: 0.7132 (p) REVERT: B 401 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7474 (mp0) REVERT: B 452 ARG cc_start: 0.6447 (ttp80) cc_final: 0.6155 (tmt170) REVERT: B 468 LYS cc_start: 0.6995 (tttt) cc_final: 0.6642 (tttp) REVERT: B 479 GLU cc_start: 0.6765 (tp30) cc_final: 0.5952 (tp30) REVERT: B 482 ARG cc_start: 0.6969 (mtm-85) cc_final: 0.6659 (mtm-85) REVERT: B 487 ASP cc_start: 0.7483 (t0) cc_final: 0.7194 (t0) REVERT: C 78 VAL cc_start: 0.8626 (t) cc_final: 0.8307 (p) REVERT: C 187 THR cc_start: 0.7767 (p) cc_final: 0.7445 (t) REVERT: C 188 ASN cc_start: 0.7542 (t0) cc_final: 0.7276 (m-40) REVERT: C 189 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7283 (tp40) REVERT: C 371 GLN cc_start: 0.7104 (tp40) cc_final: 0.6446 (tp-100) REVERT: C 401 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7473 (mm-30) REVERT: C 444 MET cc_start: 0.8409 (tpt) cc_final: 0.7904 (tpt) REVERT: C 452 ARG cc_start: 0.6371 (ttp80) cc_final: 0.5966 (tmt170) REVERT: C 468 LYS cc_start: 0.6954 (tttt) cc_final: 0.6489 (tttp) REVERT: C 487 ASP cc_start: 0.7317 (t0) cc_final: 0.7057 (t0) outliers start: 33 outliers final: 11 residues processed: 182 average time/residue: 0.4638 time to fit residues: 93.0778 Evaluate side-chains 135 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 195 TYR 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 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: 1.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3754 r_free = 0.3754 target = 0.148598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109411 restraints weight = 14919.397| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.08 r_work: 0.3110 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 12591 Z= 0.236 Angle : 0.804 11.218 17166 Z= 0.403 Chirality : 0.051 0.201 2010 Planarity : 0.005 0.040 2154 Dihedral : 11.959 86.795 2568 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.78 % Allowed : 14.39 % Favored : 82.83 % 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: -0.37 (0.20), residues: 1476 helix: 2.20 (0.26), residues: 333 sheet: 0.11 (0.29), residues: 321 loop : -1.52 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 109 TYR 0.020 0.003 TYR B 308 PHE 0.020 0.002 PHE C 125 TRP 0.010 0.002 TRP A 421 HIS 0.012 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00563 (12525) covalent geometry : angle 0.76067 (16986) SS BOND : bond 0.00244 ( 18) SS BOND : angle 3.10875 ( 36) hydrogen bonds : bond 0.08301 ( 447) hydrogen bonds : angle 4.92049 ( 1323) link_ALPHA1-3 : bond 0.01042 ( 3) link_ALPHA1-3 : angle 1.36067 ( 9) link_ALPHA1-6 : bond 0.00251 ( 3) link_ALPHA1-6 : angle 1.64071 ( 9) link_BETA1-4 : bond 0.00325 ( 21) link_BETA1-4 : angle 2.65365 ( 63) link_BETA1-6 : bond 0.00491 ( 3) link_BETA1-6 : angle 1.21153 ( 9) link_NAG-ASN : bond 0.00469 ( 18) link_NAG-ASN : angle 2.83990 ( 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 156 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7718 (p) cc_final: 0.7452 (t) REVERT: A 188 ASN cc_start: 0.7847 (t0) cc_final: 0.7425 (m-40) REVERT: A 468 LYS cc_start: 0.7184 (tttt) cc_final: 0.6695 (ttmm) REVERT: A 482 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6736 (mtp180) REVERT: A 497 ASN cc_start: 0.7642 (m-40) cc_final: 0.7347 (m-40) REVERT: B 70 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8555 (tt) REVERT: B 208 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6831 (ptm160) REVERT: B 275 ASP cc_start: 0.7317 (p0) cc_final: 0.6803 (p0) REVERT: B 341 ASN cc_start: 0.7338 (p0) cc_final: 0.7047 (p0) REVERT: B 355 HIS cc_start: 0.6941 (p90) cc_final: 0.6371 (p90) REVERT: B 401 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7638 (mp0) REVERT: B 468 LYS cc_start: 0.7200 (tttt) cc_final: 0.6810 (tttp) REVERT: C 78 VAL cc_start: 0.8730 (t) cc_final: 0.8411 (p) REVERT: C 187 THR cc_start: 0.7779 (p) cc_final: 0.7438 (t) REVERT: C 188 ASN cc_start: 0.7684 (t0) cc_final: 0.7328 (m-40) REVERT: C 189 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7168 (tp40) REVERT: C 321 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7349 (ptp-170) REVERT: C 371 GLN cc_start: 0.7199 (tp40) cc_final: 0.6597 (tp-100) REVERT: C 401 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7628 (mm-30) REVERT: C 444 MET cc_start: 0.8370 (tpt) cc_final: 0.7947 (tpt) REVERT: C 452 ARG cc_start: 0.6376 (ttp80) cc_final: 0.6087 (tmt170) REVERT: C 468 LYS cc_start: 0.6972 (tttt) cc_final: 0.6508 (tttp) REVERT: C 487 ASP cc_start: 0.7251 (t0) cc_final: 0.6977 (t0) outliers start: 36 outliers final: 17 residues processed: 146 average time/residue: 0.4895 time to fit residues: 78.5378 Evaluate side-chains 131 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 208 ARG Chi-restraints excluded: chain B residue 318 THR 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 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: 9.9990 chunk 45 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3776 r_free = 0.3776 target = 0.150335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111792 restraints weight = 14861.665| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.08 r_work: 0.3142 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12591 Z= 0.149 Angle : 0.653 10.669 17166 Z= 0.327 Chirality : 0.045 0.205 2010 Planarity : 0.004 0.041 2154 Dihedral : 10.363 78.977 2568 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.33 % Allowed : 14.39 % Favored : 82.29 % 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: -0.05 (0.20), residues: 1476 helix: 2.72 (0.26), residues: 333 sheet: -0.06 (0.28), residues: 354 loop : -1.30 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.009 0.002 TYR A 257 PHE 0.011 0.001 PHE C 125 TRP 0.008 0.001 TRP A 421 HIS 0.011 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00337 (12525) covalent geometry : angle 0.60671 (16986) SS BOND : bond 0.00307 ( 18) SS BOND : angle 3.65131 ( 36) hydrogen bonds : bond 0.06850 ( 447) hydrogen bonds : angle 4.65850 ( 1323) link_ALPHA1-3 : bond 0.01120 ( 3) link_ALPHA1-3 : angle 1.56596 ( 9) link_ALPHA1-6 : bond 0.00467 ( 3) link_ALPHA1-6 : angle 1.79583 ( 9) link_BETA1-4 : bond 0.00378 ( 21) link_BETA1-4 : angle 2.28927 ( 63) link_BETA1-6 : bond 0.00425 ( 3) link_BETA1-6 : angle 1.19846 ( 9) link_NAG-ASN : bond 0.00499 ( 18) link_NAG-ASN : angle 1.93578 ( 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: 43 poor density : 116 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7401 (t) REVERT: A 187 THR cc_start: 0.7821 (p) cc_final: 0.7514 (t) REVERT: A 188 ASN cc_start: 0.7710 (t0) cc_final: 0.7352 (m-40) REVERT: A 468 LYS cc_start: 0.7107 (tttt) cc_final: 0.6659 (ttmm) REVERT: A 482 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6737 (mtp180) REVERT: A 497 ASN cc_start: 0.7539 (m-40) cc_final: 0.7293 (m-40) REVERT: B 70 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8784 (tp) REVERT: B 341 ASN cc_start: 0.7335 (p0) cc_final: 0.7084 (p0) REVERT: B 355 HIS cc_start: 0.6855 (p90) cc_final: 0.6268 (p90) REVERT: B 371 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6679 (tp40) REVERT: B 401 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7550 (mp0) REVERT: B 468 LYS cc_start: 0.7065 (tttt) cc_final: 0.6681 (tttp) REVERT: C 78 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8446 (p) REVERT: C 187 THR cc_start: 0.7818 (p) cc_final: 0.7536 (t) REVERT: C 188 ASN cc_start: 0.7729 (t0) cc_final: 0.7348 (m-40) REVERT: C 189 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7181 (tp40) REVERT: C 371 GLN cc_start: 0.7028 (tp40) cc_final: 0.6353 (tp40) REVERT: C 401 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7510 (mm-30) REVERT: C 444 MET cc_start: 0.8340 (tpt) cc_final: 0.7848 (tpt) REVERT: C 468 LYS cc_start: 0.7094 (tttt) cc_final: 0.6625 (tttp) outliers start: 43 outliers final: 16 residues processed: 151 average time/residue: 0.4718 time to fit residues: 78.9121 Evaluate side-chains 126 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 0.0670 chunk 98 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3791 r_free = 0.3791 target = 0.151664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113233 restraints weight = 15058.733| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.09 r_work: 0.3161 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12591 Z= 0.117 Angle : 0.603 9.319 17166 Z= 0.301 Chirality : 0.044 0.274 2010 Planarity : 0.004 0.042 2154 Dihedral : 9.226 72.303 2568 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 15.55 % Favored : 81.67 % 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: 0.29 (0.21), residues: 1476 helix: 3.19 (0.27), residues: 333 sheet: 0.06 (0.27), residues: 354 loop : -1.13 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.008 0.001 TYR A 257 PHE 0.010 0.001 PHE B 353 TRP 0.008 0.001 TRP B 222 HIS 0.009 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00253 (12525) covalent geometry : angle 0.55854 (16986) SS BOND : bond 0.00415 ( 18) SS BOND : angle 3.33282 ( 36) hydrogen bonds : bond 0.06114 ( 447) hydrogen bonds : angle 4.45068 ( 1323) link_ALPHA1-3 : bond 0.01187 ( 3) link_ALPHA1-3 : angle 1.83234 ( 9) link_ALPHA1-6 : bond 0.00640 ( 3) link_ALPHA1-6 : angle 1.80806 ( 9) link_BETA1-4 : bond 0.00378 ( 21) link_BETA1-4 : angle 2.03418 ( 63) link_BETA1-6 : bond 0.00390 ( 3) link_BETA1-6 : angle 1.16114 ( 9) link_NAG-ASN : bond 0.00278 ( 18) link_NAG-ASN : angle 1.97874 ( 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 154 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7348 (t) REVERT: A 187 THR cc_start: 0.7819 (p) cc_final: 0.7536 (t) REVERT: A 361 THR cc_start: 0.7284 (m) cc_final: 0.6728 (p) REVERT: A 452 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6005 (tmt170) REVERT: A 468 LYS cc_start: 0.7138 (tttt) cc_final: 0.6661 (ttmm) REVERT: A 497 ASN cc_start: 0.7645 (m-40) cc_final: 0.7420 (m-40) REVERT: B 70 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 341 ASN cc_start: 0.7365 (p0) cc_final: 0.7130 (p0) REVERT: B 355 HIS cc_start: 0.6891 (p90) cc_final: 0.6293 (p90) REVERT: B 371 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6713 (tp40) REVERT: B 401 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7516 (mp0) REVERT: B 445 ASN cc_start: 0.7299 (t0) cc_final: 0.6733 (m-40) REVERT: B 468 LYS cc_start: 0.7079 (tttt) cc_final: 0.6694 (tttp) REVERT: C 52 CYS cc_start: 0.7474 (m) cc_final: 0.7059 (m) REVERT: C 70 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8869 (tp) REVERT: C 78 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8459 (p) REVERT: C 187 THR cc_start: 0.7814 (p) cc_final: 0.7545 (t) REVERT: C 188 ASN cc_start: 0.7809 (t0) cc_final: 0.7355 (m-40) REVERT: C 371 GLN cc_start: 0.7129 (tp40) cc_final: 0.6455 (tp40) REVERT: C 401 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7453 (mm-30) REVERT: C 444 MET cc_start: 0.8348 (tpt) cc_final: 0.7895 (tpt) REVERT: C 468 LYS cc_start: 0.7010 (tttt) cc_final: 0.6523 (tttp) outliers start: 36 outliers final: 20 residues processed: 144 average time/residue: 0.4869 time to fit residues: 77.5069 Evaluate side-chains 131 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain A residue 173 ASN 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 439 LEU Chi-restraints excluded: chain A residue 452 ARG 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 C residue 70 LEU 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: 6.9990 chunk 111 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3794 r_free = 0.3794 target = 0.151959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114935 restraints weight = 14907.643| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.46 r_work: 0.3162 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12591 Z= 0.117 Angle : 0.586 11.697 17166 Z= 0.292 Chirality : 0.044 0.238 2010 Planarity : 0.004 0.042 2154 Dihedral : 8.553 65.795 2568 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.78 % Allowed : 16.09 % Favored : 81.13 % 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: 0.39 (0.21), residues: 1476 helix: 3.32 (0.27), residues: 333 sheet: 0.10 (0.27), residues: 354 loop : -1.07 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.008 0.001 TYR A 257 PHE 0.008 0.001 PHE A 258 TRP 0.011 0.001 TRP B 222 HIS 0.008 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00254 (12525) covalent geometry : angle 0.54944 (16986) SS BOND : bond 0.00419 ( 18) SS BOND : angle 2.99587 ( 36) hydrogen bonds : bond 0.05973 ( 447) hydrogen bonds : angle 4.39031 ( 1323) link_ALPHA1-3 : bond 0.01218 ( 3) link_ALPHA1-3 : angle 1.96736 ( 9) link_ALPHA1-6 : bond 0.00739 ( 3) link_ALPHA1-6 : angle 1.89113 ( 9) link_BETA1-4 : bond 0.00356 ( 21) link_BETA1-4 : angle 1.85293 ( 63) link_BETA1-6 : bond 0.00389 ( 3) link_BETA1-6 : angle 1.12525 ( 9) link_NAG-ASN : bond 0.00511 ( 18) link_NAG-ASN : angle 1.61464 ( 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 151 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7332 (t) REVERT: A 187 THR cc_start: 0.7784 (p) cc_final: 0.7491 (t) REVERT: A 361 THR cc_start: 0.7311 (m) cc_final: 0.6754 (p) REVERT: A 452 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.5705 (tmt170) REVERT: A 468 LYS cc_start: 0.7116 (tttt) cc_final: 0.6732 (tttp) REVERT: B 27 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7665 (ptmt) REVERT: B 70 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 341 ASN cc_start: 0.7402 (p0) cc_final: 0.7157 (p0) REVERT: B 355 HIS cc_start: 0.6895 (p90) cc_final: 0.6282 (p90) REVERT: B 371 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6634 (tp40) REVERT: B 385 ILE cc_start: 0.6376 (tt) cc_final: 0.6131 (tp) REVERT: B 401 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7509 (mp0) REVERT: B 445 ASN cc_start: 0.7280 (t0) cc_final: 0.6660 (m110) REVERT: B 468 LYS cc_start: 0.7060 (tttt) cc_final: 0.6671 (ttmm) REVERT: C 52 CYS cc_start: 0.7453 (m) cc_final: 0.7069 (m) REVERT: C 70 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8877 (tp) REVERT: C 78 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 187 THR cc_start: 0.7830 (p) cc_final: 0.7570 (t) REVERT: C 188 ASN cc_start: 0.7831 (t0) cc_final: 0.7347 (m-40) REVERT: C 371 GLN cc_start: 0.7036 (tp40) cc_final: 0.6368 (tp40) REVERT: C 401 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7434 (mm-30) REVERT: C 444 MET cc_start: 0.8372 (tpt) cc_final: 0.7913 (tpt) REVERT: C 468 LYS cc_start: 0.6959 (tttt) cc_final: 0.6488 (tttp) outliers start: 36 outliers final: 20 residues processed: 141 average time/residue: 0.4848 time to fit residues: 75.4099 Evaluate side-chains 132 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 131 THR 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 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 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 70 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: 6.9990 chunk 120 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 295 GLN C 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111645 restraints weight = 14857.217| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.07 r_work: 0.3145 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12591 Z= 0.171 Angle : 0.672 11.723 17166 Z= 0.338 Chirality : 0.047 0.326 2010 Planarity : 0.005 0.042 2154 Dihedral : 8.776 65.939 2568 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.86 % Allowed : 16.55 % Favored : 80.59 % 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: 0.08 (0.20), residues: 1476 helix: 2.91 (0.26), residues: 333 sheet: -0.03 (0.28), residues: 354 loop : -1.23 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 109 TYR 0.013 0.002 TYR B 308 PHE 0.015 0.002 PHE C 125 TRP 0.012 0.001 TRP B 222 HIS 0.007 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (12525) covalent geometry : angle 0.63449 (16986) SS BOND : bond 0.00785 ( 18) SS BOND : angle 3.42577 ( 36) hydrogen bonds : bond 0.06903 ( 447) hydrogen bonds : angle 4.68179 ( 1323) link_ALPHA1-3 : bond 0.01209 ( 3) link_ALPHA1-3 : angle 1.94715 ( 9) link_ALPHA1-6 : bond 0.00625 ( 3) link_ALPHA1-6 : angle 1.84620 ( 9) link_BETA1-4 : bond 0.00337 ( 21) link_BETA1-4 : angle 1.92729 ( 63) link_BETA1-6 : bond 0.00423 ( 3) link_BETA1-6 : angle 1.09065 ( 9) link_NAG-ASN : bond 0.00295 ( 18) link_NAG-ASN : angle 1.79021 ( 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 147 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7361 (t) REVERT: A 187 THR cc_start: 0.7708 (p) cc_final: 0.7443 (t) REVERT: A 361 THR cc_start: 0.7238 (m) cc_final: 0.6650 (p) REVERT: A 452 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6005 (tmt170) REVERT: A 468 LYS cc_start: 0.7218 (tttt) cc_final: 0.6719 (ttmm) REVERT: B 70 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8742 (tp) REVERT: B 355 HIS cc_start: 0.6866 (p90) cc_final: 0.6311 (p90) REVERT: B 371 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6640 (tp40) REVERT: B 401 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7605 (mp0) REVERT: B 445 ASN cc_start: 0.7300 (t0) cc_final: 0.6736 (m-40) REVERT: B 452 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6357 (tmt170) REVERT: C 52 CYS cc_start: 0.7482 (m) cc_final: 0.7101 (m) REVERT: C 78 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8443 (p) REVERT: C 187 THR cc_start: 0.7913 (p) cc_final: 0.7615 (t) REVERT: C 188 ASN cc_start: 0.7877 (t0) cc_final: 0.7371 (m-40) REVERT: C 371 GLN cc_start: 0.6975 (tp40) cc_final: 0.6295 (tp40) REVERT: C 401 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7562 (mm-30) REVERT: C 444 MET cc_start: 0.8357 (tpt) cc_final: 0.7935 (tpt) REVERT: C 468 LYS cc_start: 0.7083 (tttt) cc_final: 0.6618 (tttp) outliers start: 37 outliers final: 24 residues processed: 136 average time/residue: 0.4931 time to fit residues: 73.9689 Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 339 ILE 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 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 419 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 49 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112387 restraints weight = 14939.159| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.45 r_work: 0.3125 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12591 Z= 0.183 Angle : 0.682 12.019 17166 Z= 0.345 Chirality : 0.047 0.253 2010 Planarity : 0.005 0.042 2154 Dihedral : 9.011 66.129 2568 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.17 % Allowed : 16.16 % Favored : 80.67 % 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: -0.17 (0.20), residues: 1476 helix: 2.64 (0.26), residues: 333 sheet: -0.17 (0.28), residues: 339 loop : -1.34 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.013 0.002 TYR B 308 PHE 0.014 0.002 PHE C 125 TRP 0.015 0.002 TRP B 222 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00433 (12525) covalent geometry : angle 0.65133 (16986) SS BOND : bond 0.00554 ( 18) SS BOND : angle 2.90847 ( 36) hydrogen bonds : bond 0.07249 ( 447) hydrogen bonds : angle 4.77870 ( 1323) link_ALPHA1-3 : bond 0.01212 ( 3) link_ALPHA1-3 : angle 1.88723 ( 9) link_ALPHA1-6 : bond 0.00577 ( 3) link_ALPHA1-6 : angle 1.81524 ( 9) link_BETA1-4 : bond 0.00348 ( 21) link_BETA1-4 : angle 1.95713 ( 63) link_BETA1-6 : bond 0.00339 ( 3) link_BETA1-6 : angle 1.16808 ( 9) link_NAG-ASN : bond 0.00304 ( 18) link_NAG-ASN : angle 1.70802 ( 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 148 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6778 (ptm160) REVERT: A 326 LYS cc_start: 0.4453 (OUTLIER) cc_final: 0.4222 (ptpp) REVERT: A 452 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.5991 (tmt170) REVERT: A 468 LYS cc_start: 0.7483 (tttt) cc_final: 0.6972 (ttmm) REVERT: B 52 CYS cc_start: 0.7664 (m) cc_final: 0.7223 (m) REVERT: B 70 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8754 (tp) REVERT: B 355 HIS cc_start: 0.6817 (p90) cc_final: 0.6311 (p90) REVERT: B 371 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6642 (tp40) REVERT: B 383 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7432 (mtm-85) REVERT: B 445 ASN cc_start: 0.7381 (t0) cc_final: 0.6796 (m-40) REVERT: B 452 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6439 (tmt170) REVERT: B 464 ASN cc_start: 0.7303 (m-40) cc_final: 0.6892 (t0) REVERT: C 52 CYS cc_start: 0.7436 (m) cc_final: 0.7068 (m) REVERT: C 78 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8403 (p) REVERT: C 187 THR cc_start: 0.7939 (p) cc_final: 0.7655 (t) REVERT: C 371 GLN cc_start: 0.6970 (tp40) cc_final: 0.6287 (tp40) REVERT: C 401 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7601 (mm-30) REVERT: C 464 ASN cc_start: 0.7513 (m-40) cc_final: 0.7068 (t0) REVERT: C 468 LYS cc_start: 0.7043 (tttt) cc_final: 0.6551 (tttp) outliers start: 41 outliers final: 25 residues processed: 137 average time/residue: 0.5087 time to fit residues: 76.6679 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 339 ILE 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 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 419 ASP 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 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 320 MET 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: 2.9990 chunk 126 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS 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 = 0.3786 r_free = 0.3786 target = 0.151213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112466 restraints weight = 14846.843| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.08 r_work: 0.3154 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3007 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= 0.133 Angle : 0.608 10.931 17166 Z= 0.307 Chirality : 0.045 0.241 2010 Planarity : 0.004 0.041 2154 Dihedral : 8.656 63.861 2568 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.40 % Allowed : 17.25 % Favored : 80.36 % 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: 0.02 (0.21), residues: 1476 helix: 2.95 (0.26), residues: 333 sheet: -0.14 (0.28), residues: 339 loop : -1.25 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 482 TYR 0.009 0.001 TYR A 257 PHE 0.009 0.001 PHE A 258 TRP 0.014 0.001 TRP B 222 HIS 0.011 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00302 (12525) covalent geometry : angle 0.57779 (16986) SS BOND : bond 0.00530 ( 18) SS BOND : angle 2.72363 ( 36) hydrogen bonds : bond 0.06499 ( 447) hydrogen bonds : angle 4.59244 ( 1323) link_ALPHA1-3 : bond 0.01191 ( 3) link_ALPHA1-3 : angle 1.96635 ( 9) link_ALPHA1-6 : bond 0.00707 ( 3) link_ALPHA1-6 : angle 1.86279 ( 9) link_BETA1-4 : bond 0.00370 ( 21) link_BETA1-4 : angle 1.82063 ( 63) link_BETA1-6 : bond 0.00331 ( 3) link_BETA1-6 : angle 1.16384 ( 9) link_NAG-ASN : bond 0.00280 ( 18) link_NAG-ASN : angle 1.49980 ( 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 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5921 (tmt170) REVERT: A 464 ASN cc_start: 0.7202 (t0) cc_final: 0.6642 (t0) REVERT: A 468 LYS cc_start: 0.7443 (tttt) cc_final: 0.6946 (ttmm) REVERT: B 52 CYS cc_start: 0.7523 (m) cc_final: 0.7119 (m) REVERT: B 70 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8751 (tp) REVERT: B 355 HIS cc_start: 0.6815 (p90) cc_final: 0.6320 (p90) REVERT: B 371 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6689 (tp40) REVERT: B 445 ASN cc_start: 0.7297 (t0) cc_final: 0.6725 (m-40) REVERT: B 464 ASN cc_start: 0.7308 (m-40) cc_final: 0.6967 (t0) REVERT: C 52 CYS cc_start: 0.7292 (m) cc_final: 0.6931 (m) REVERT: C 78 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8306 (p) REVERT: C 187 THR cc_start: 0.7884 (p) cc_final: 0.7620 (t) REVERT: C 371 GLN cc_start: 0.6971 (tp40) cc_final: 0.6298 (tp40) REVERT: C 401 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7535 (mm-30) REVERT: C 464 ASN cc_start: 0.7559 (m-40) cc_final: 0.7163 (t0) REVERT: C 468 LYS cc_start: 0.7013 (tttt) cc_final: 0.6518 (tttp) outliers start: 31 outliers final: 23 residues processed: 126 average time/residue: 0.4724 time to fit residues: 65.6749 Evaluate side-chains 125 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 371 GLN 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 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 419 ASP 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 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: 3.9990 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 130 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 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 = 0.3810 r_free = 0.3810 target = 0.153160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120705 restraints weight = 14887.443| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.92 r_work: 0.3159 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12591 Z= 0.108 Angle : 0.555 10.029 17166 Z= 0.279 Chirality : 0.043 0.237 2010 Planarity : 0.004 0.043 2154 Dihedral : 8.073 59.711 2568 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.01 % Allowed : 17.87 % Favored : 80.12 % 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: 0.37 (0.21), residues: 1476 helix: 3.26 (0.27), residues: 333 sheet: 0.18 (0.28), residues: 339 loop : -1.10 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 482 TYR 0.007 0.001 TYR A 257 PHE 0.008 0.001 PHE A 258 TRP 0.014 0.001 TRP B 222 HIS 0.010 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00229 (12525) covalent geometry : angle 0.52932 (16986) SS BOND : bond 0.00493 ( 18) SS BOND : angle 2.17730 ( 36) hydrogen bonds : bond 0.05759 ( 447) hydrogen bonds : angle 4.41117 ( 1323) link_ALPHA1-3 : bond 0.01133 ( 3) link_ALPHA1-3 : angle 1.97891 ( 9) link_ALPHA1-6 : bond 0.00776 ( 3) link_ALPHA1-6 : angle 1.89369 ( 9) link_BETA1-4 : bond 0.00394 ( 21) link_BETA1-4 : angle 1.72036 ( 63) link_BETA1-6 : bond 0.00372 ( 3) link_BETA1-6 : angle 1.14712 ( 9) link_NAG-ASN : bond 0.00259 ( 18) link_NAG-ASN : angle 1.33024 ( 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 128 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 THR cc_start: 0.7204 (m) cc_final: 0.6648 (p) REVERT: A 452 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5690 (tmt170) REVERT: A 464 ASN cc_start: 0.7220 (t0) cc_final: 0.6702 (t0) REVERT: B 52 CYS cc_start: 0.7462 (m) cc_final: 0.7072 (m) REVERT: B 70 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8753 (tp) REVERT: B 355 HIS cc_start: 0.6844 (p90) cc_final: 0.6375 (p90) REVERT: B 371 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6692 (tp40) REVERT: B 401 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7522 (mp0) REVERT: B 445 ASN cc_start: 0.7285 (t0) cc_final: 0.6822 (m-40) REVERT: C 52 CYS cc_start: 0.7421 (m) cc_final: 0.7055 (m) REVERT: C 77 ASP cc_start: 0.7579 (m-30) cc_final: 0.7377 (m-30) REVERT: C 187 THR cc_start: 0.7888 (p) cc_final: 0.7664 (t) REVERT: C 371 GLN cc_start: 0.7016 (tp40) cc_final: 0.6344 (tp40) REVERT: C 401 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7474 (mm-30) REVERT: C 464 ASN cc_start: 0.7526 (m-40) cc_final: 0.7278 (t0) REVERT: C 468 LYS cc_start: 0.6990 (tttt) cc_final: 0.6497 (tttp) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 0.4843 time to fit residues: 64.3723 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 : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 371 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 6 optimal weight: 0.0570 chunk 2 optimal weight: 0.0970 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 118 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 464 ASN C 295 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121130 restraints weight = 14849.371| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.95 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12591 Z= 0.106 Angle : 0.563 9.982 17166 Z= 0.284 Chirality : 0.043 0.235 2010 Planarity : 0.004 0.035 2154 Dihedral : 7.829 58.631 2568 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.70 % Allowed : 18.25 % Favored : 80.05 % 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: 0.48 (0.21), residues: 1476 helix: 3.35 (0.26), residues: 333 sheet: 0.26 (0.28), residues: 339 loop : -1.03 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 482 TYR 0.008 0.001 TYR A 257 PHE 0.008 0.001 PHE A 258 TRP 0.014 0.001 TRP B 222 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00226 (12525) covalent geometry : angle 0.53079 (16986) SS BOND : bond 0.00445 ( 18) SS BOND : angle 2.96455 ( 36) hydrogen bonds : bond 0.05640 ( 447) hydrogen bonds : angle 4.33552 ( 1323) link_ALPHA1-3 : bond 0.01132 ( 3) link_ALPHA1-3 : angle 2.01775 ( 9) link_ALPHA1-6 : bond 0.00784 ( 3) link_ALPHA1-6 : angle 1.86054 ( 9) link_BETA1-4 : bond 0.00389 ( 21) link_BETA1-4 : angle 1.69327 ( 63) link_BETA1-6 : bond 0.00371 ( 3) link_BETA1-6 : angle 1.13604 ( 9) link_NAG-ASN : bond 0.00254 ( 18) link_NAG-ASN : angle 1.28185 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.63 seconds wall clock time: 79 minutes 44.02 seconds (4784.02 seconds total)