Starting phenix.real_space_refine on Wed Jul 30 15:52:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj6_14742/07_2025/7zj6_14742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj6_14742/07_2025/7zj6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2025/7zj6_14742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2025/7zj6_14742.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2025/7zj6_14742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj6_14742/07_2025/7zj6_14742.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: I, M, J, N, H, L, C, B, K, O Time building chain proxies: 8.39, per 1000 atoms: 0.68 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 C 14 " - pdb=" SG CYS C 466 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.05 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.05 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.05 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.05 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.05 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.05 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 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: 3.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.55 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: 3.99 Time building geometry restraints manager: 3.79 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: 0.08 Found NCS groups: 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 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.004 TRP B 234 HIS 0.012 0.004 HIS C 488 PHE 0.036 0.004 PHE C 125 TYR 0.026 0.004 TYR A 161 ARG 0.006 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00863 ( 18) link_NAG-ASN : angle 3.00106 ( 54) 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_ALPHA1-3 : bond 0.01196 ( 3) link_ALPHA1-3 : angle 2.08091 ( 9) hydrogen bonds : bond 0.28227 ( 447) hydrogen bonds : angle 8.00382 ( 1323) link_BETA1-6 : bond 0.00382 ( 3) link_BETA1-6 : angle 0.78406 ( 9) SS BOND : bond 0.01742 ( 18) SS BOND : angle 2.23570 ( 36) covalent geometry : bond 0.01312 (12525) covalent geometry : angle 1.77096 (16986) *********************** 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 : 1.576 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: 1.2690 time to fit residues: 295.9743 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 : 1.384 ------------------------------------------------------------------------------- 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 124 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.152042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113480 restraints weight = 14910.733| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.07 r_work: 0.3158 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1761 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= 0.140 Angle : 0.646 9.137 17166 Z= 0.323 Chirality : 0.045 0.192 2010 Planarity : 0.004 0.031 2154 Dihedral : 13.127 87.043 2574 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.47 % Allowed : 12.30 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1476 helix: 2.36 (0.26), residues: 333 sheet: -0.03 (0.29), residues: 303 loop : -1.53 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 421 HIS 0.007 0.002 HIS B 75 PHE 0.012 0.001 PHE C 258 TYR 0.010 0.001 TYR B 486 ARG 0.003 0.000 ARG C 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 18) link_NAG-ASN : angle 1.83428 ( 54) link_ALPHA1-6 : bond 0.00478 ( 3) link_ALPHA1-6 : angle 1.82944 ( 9) link_BETA1-4 : bond 0.00542 ( 21) link_BETA1-4 : angle 2.54858 ( 63) link_ALPHA1-3 : bond 0.00754 ( 3) link_ALPHA1-3 : angle 1.92430 ( 9) hydrogen bonds : bond 0.07243 ( 447) hydrogen bonds : angle 5.02375 ( 1323) link_BETA1-6 : bond 0.00525 ( 3) link_BETA1-6 : angle 1.29377 ( 9) SS BOND : bond 0.00776 ( 18) SS BOND : angle 1.15884 ( 36) covalent geometry : bond 0.00281 (12525) covalent geometry : angle 0.61639 (16986) *********************** 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 188 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7688 (p) cc_final: 0.7454 (t) REVERT: A 188 ASN cc_start: 0.7639 (t0) cc_final: 0.7328 (m-40) REVERT: A 189 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7399 (tp40) REVERT: A 401 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7375 (mp0) REVERT: A 452 ARG cc_start: 0.6343 (ttp80) cc_final: 0.5995 (tmt170) REVERT: A 468 LYS cc_start: 0.6981 (tttt) cc_final: 0.6545 (ttmm) REVERT: A 482 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6624 (mtp180) REVERT: A 487 ASP cc_start: 0.7529 (t0) cc_final: 0.7313 (t0) REVERT: A 497 ASN cc_start: 0.7533 (m-40) cc_final: 0.7178 (m-40) REVERT: B 70 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8610 (tt) REVERT: B 188 ASN cc_start: 0.7732 (t0) cc_final: 0.7482 (m-40) REVERT: B 189 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7140 (tp40) REVERT: B 341 ASN cc_start: 0.7174 (p0) cc_final: 0.6951 (p0) REVERT: B 355 HIS cc_start: 0.6668 (p90) cc_final: 0.6440 (p90) REVERT: B 401 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7498 (mp0) REVERT: B 452 ARG cc_start: 0.6473 (ttp80) cc_final: 0.5854 (tmt170) REVERT: B 468 LYS cc_start: 0.7007 (tttt) cc_final: 0.6657 (tttp) REVERT: B 479 GLU cc_start: 0.6762 (tp30) cc_final: 0.5932 (tp30) REVERT: B 482 ARG cc_start: 0.6986 (mtm-85) cc_final: 0.6656 (mtm-85) REVERT: B 487 ASP cc_start: 0.7489 (t0) cc_final: 0.7190 (t0) REVERT: C 78 VAL cc_start: 0.8643 (t) cc_final: 0.8312 (p) REVERT: C 187 THR cc_start: 0.7780 (p) cc_final: 0.7446 (t) REVERT: C 188 ASN cc_start: 0.7539 (t0) cc_final: 0.7271 (m-40) REVERT: C 189 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7283 (tp40) REVERT: C 371 GLN cc_start: 0.7132 (tp40) cc_final: 0.6505 (tp-100) REVERT: C 401 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7456 (mm-30) REVERT: C 444 MET cc_start: 0.8401 (tpt) cc_final: 0.7899 (tpt) REVERT: C 452 ARG cc_start: 0.6449 (ttp80) cc_final: 0.6027 (tmt170) REVERT: C 468 LYS cc_start: 0.6967 (tttt) cc_final: 0.6480 (tttp) REVERT: C 470 TYR cc_start: 0.7361 (m-80) cc_final: 0.7156 (m-80) outliers start: 32 outliers final: 11 residues processed: 179 average time/residue: 1.1883 time to fit residues: 233.8617 Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 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 = 0.3753 r_free = 0.3753 target = 0.148474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109400 restraints weight = 14928.459| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.07 r_work: 0.3098 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 12591 Z= 0.239 Angle : 0.816 11.645 17166 Z= 0.409 Chirality : 0.052 0.217 2010 Planarity : 0.005 0.036 2154 Dihedral : 12.253 87.665 2570 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.78 % Allowed : 14.31 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1476 helix: 2.21 (0.26), residues: 333 sheet: 0.12 (0.29), residues: 321 loop : -1.55 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.011 0.002 HIS A 355 PHE 0.019 0.002 PHE C 125 TYR 0.020 0.003 TYR B 308 ARG 0.007 0.001 ARG B 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 18) link_NAG-ASN : angle 2.78761 ( 54) link_ALPHA1-6 : bond 0.00275 ( 3) link_ALPHA1-6 : angle 1.65643 ( 9) link_BETA1-4 : bond 0.00317 ( 21) link_BETA1-4 : angle 2.65128 ( 63) link_ALPHA1-3 : bond 0.01041 ( 3) link_ALPHA1-3 : angle 1.29851 ( 9) hydrogen bonds : bond 0.08282 ( 447) hydrogen bonds : angle 4.94674 ( 1323) link_BETA1-6 : bond 0.00481 ( 3) link_BETA1-6 : angle 1.22820 ( 9) SS BOND : bond 0.00281 ( 18) SS BOND : angle 3.92147 ( 36) covalent geometry : bond 0.00576 (12525) covalent geometry : angle 0.76526 (16986) *********************** 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 : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7718 (p) cc_final: 0.7453 (t) REVERT: A 188 ASN cc_start: 0.7852 (t0) cc_final: 0.7432 (m-40) REVERT: A 468 LYS cc_start: 0.7187 (tttt) cc_final: 0.6701 (ttmm) REVERT: A 482 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6765 (mtp180) REVERT: A 497 ASN cc_start: 0.7540 (m-40) cc_final: 0.7265 (m-40) REVERT: B 70 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 208 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6848 (ptm160) REVERT: B 275 ASP cc_start: 0.7333 (p0) cc_final: 0.6846 (p0) REVERT: B 341 ASN cc_start: 0.7366 (p0) cc_final: 0.7080 (p0) REVERT: B 355 HIS cc_start: 0.6933 (p90) cc_final: 0.6367 (p90) REVERT: B 401 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7656 (mp0) REVERT: B 468 LYS cc_start: 0.7204 (tttt) cc_final: 0.6847 (tttp) REVERT: B 487 ASP cc_start: 0.7510 (t0) cc_final: 0.7295 (t0) REVERT: C 78 VAL cc_start: 0.8729 (t) cc_final: 0.8412 (p) REVERT: C 187 THR cc_start: 0.7806 (p) cc_final: 0.7468 (t) REVERT: C 188 ASN cc_start: 0.7697 (t0) cc_final: 0.7344 (m-40) REVERT: C 189 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7146 (tp40) REVERT: C 321 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7378 (ptp-170) REVERT: C 371 GLN cc_start: 0.7212 (tp40) cc_final: 0.6599 (tp-100) REVERT: C 401 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7647 (mm-30) REVERT: C 444 MET cc_start: 0.8361 (tpt) cc_final: 0.7943 (tpt) REVERT: C 452 ARG cc_start: 0.6354 (ttp80) cc_final: 0.5955 (tmt170) REVERT: C 468 LYS cc_start: 0.7001 (tttt) cc_final: 0.6523 (tttp) REVERT: C 487 ASP cc_start: 0.7286 (t0) cc_final: 0.6991 (t0) outliers start: 36 outliers final: 18 residues processed: 146 average time/residue: 1.5155 time to fit residues: 242.7810 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 339 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 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 18 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS C 216 ASN C 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112410 restraints weight = 14780.813| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.06 r_work: 0.3152 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 12591 Z= 0.139 Angle : 0.633 10.462 17166 Z= 0.317 Chirality : 0.045 0.196 2010 Planarity : 0.004 0.034 2154 Dihedral : 10.314 78.401 2570 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.25 % Allowed : 14.54 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1476 helix: 2.79 (0.26), residues: 333 sheet: -0.03 (0.27), residues: 354 loop : -1.23 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 421 HIS 0.011 0.001 HIS A 355 PHE 0.009 0.001 PHE A 258 TYR 0.008 0.001 TYR A 257 ARG 0.003 0.000 ARG B 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 18) link_NAG-ASN : angle 1.85948 ( 54) link_ALPHA1-6 : bond 0.00484 ( 3) link_ALPHA1-6 : angle 1.82275 ( 9) link_BETA1-4 : bond 0.00387 ( 21) link_BETA1-4 : angle 2.27432 ( 63) link_ALPHA1-3 : bond 0.01113 ( 3) link_ALPHA1-3 : angle 1.58351 ( 9) hydrogen bonds : bond 0.06591 ( 447) hydrogen bonds : angle 4.63081 ( 1323) link_BETA1-6 : bond 0.00421 ( 3) link_BETA1-6 : angle 1.19585 ( 9) SS BOND : bond 0.00343 ( 18) SS BOND : angle 3.60598 ( 36) covalent geometry : bond 0.00311 (12525) covalent geometry : angle 0.58626 (16986) *********************** 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 158 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7382 (t) REVERT: A 187 THR cc_start: 0.7767 (p) cc_final: 0.7508 (t) REVERT: A 188 ASN cc_start: 0.7701 (t0) cc_final: 0.7355 (m-40) REVERT: A 401 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7406 (mp0) REVERT: A 468 LYS cc_start: 0.7157 (tttt) cc_final: 0.6708 (ttmm) REVERT: A 482 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6725 (mtm-85) REVERT: A 497 ASN cc_start: 0.7764 (m-40) cc_final: 0.7489 (m-40) REVERT: B 52 CYS cc_start: 0.7494 (m) cc_final: 0.7037 (m) REVERT: B 70 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8763 (tp) REVERT: B 341 ASN cc_start: 0.7288 (p0) cc_final: 0.7019 (p0) REVERT: B 355 HIS cc_start: 0.6857 (p90) cc_final: 0.6258 (p90) REVERT: B 371 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6703 (tp40) REVERT: B 401 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7521 (mp0) REVERT: B 468 LYS cc_start: 0.7072 (tttt) cc_final: 0.6704 (tttp) REVERT: C 78 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8449 (p) REVERT: C 187 THR cc_start: 0.7803 (p) cc_final: 0.7528 (t) REVERT: C 188 ASN cc_start: 0.7668 (t0) cc_final: 0.7308 (m-40) REVERT: C 189 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7163 (tp40) REVERT: C 371 GLN cc_start: 0.7097 (tp40) cc_final: 0.6415 (tp40) REVERT: C 401 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7502 (mm-30) REVERT: C 444 MET cc_start: 0.8351 (tpt) cc_final: 0.7855 (tpt) REVERT: C 468 LYS cc_start: 0.7074 (tttt) cc_final: 0.6600 (tttp) outliers start: 42 outliers final: 18 residues processed: 149 average time/residue: 1.1107 time to fit residues: 183.7571 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 222 TRP 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 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 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 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 355 HIS C 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113003 restraints weight = 14834.849| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.07 r_work: 0.3168 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12591 Z= 0.125 Angle : 0.601 9.194 17166 Z= 0.301 Chirality : 0.044 0.218 2010 Planarity : 0.004 0.035 2154 Dihedral : 9.358 72.776 2570 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.55 % Allowed : 15.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1476 helix: 3.07 (0.27), residues: 333 sheet: 0.08 (0.28), residues: 354 loop : -1.13 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 222 HIS 0.009 0.001 HIS A 355 PHE 0.009 0.001 PHE B 467 TYR 0.009 0.001 TYR A 257 ARG 0.003 0.000 ARG B 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 18) link_NAG-ASN : angle 1.89260 ( 54) link_ALPHA1-6 : bond 0.00610 ( 3) link_ALPHA1-6 : angle 1.79555 ( 9) link_BETA1-4 : bond 0.00370 ( 21) link_BETA1-4 : angle 2.06103 ( 63) link_ALPHA1-3 : bond 0.01143 ( 3) link_ALPHA1-3 : angle 1.79447 ( 9) hydrogen bonds : bond 0.06331 ( 447) hydrogen bonds : angle 4.57210 ( 1323) link_BETA1-6 : bond 0.00388 ( 3) link_BETA1-6 : angle 1.15091 ( 9) SS BOND : bond 0.00400 ( 18) SS BOND : angle 3.00978 ( 36) covalent geometry : bond 0.00279 (12525) covalent geometry : angle 0.56049 (16986) *********************** 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 146 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7367 (t) REVERT: A 187 THR cc_start: 0.7797 (p) cc_final: 0.7514 (t) REVERT: A 188 ASN cc_start: 0.7720 (t0) cc_final: 0.7350 (m-40) REVERT: A 361 THR cc_start: 0.7309 (m) cc_final: 0.6760 (p) REVERT: A 452 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6131 (tmt170) REVERT: A 468 LYS cc_start: 0.7118 (tttt) cc_final: 0.6619 (ttmm) REVERT: A 497 ASN cc_start: 0.7644 (m-40) cc_final: 0.7413 (m-40) REVERT: B 341 ASN cc_start: 0.7335 (p0) cc_final: 0.7086 (p0) REVERT: B 355 HIS cc_start: 0.6883 (p90) cc_final: 0.6246 (p90) REVERT: B 371 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6660 (tp40) REVERT: B 401 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7506 (mp0) REVERT: B 445 ASN cc_start: 0.7301 (t0) cc_final: 0.6742 (m-40) REVERT: B 468 LYS cc_start: 0.6995 (tttt) cc_final: 0.6617 (tttp) REVERT: C 78 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8455 (p) REVERT: C 187 THR cc_start: 0.7802 (p) cc_final: 0.7537 (t) REVERT: C 188 ASN cc_start: 0.7801 (t0) cc_final: 0.7350 (m-40) REVERT: C 371 GLN cc_start: 0.7066 (tp40) cc_final: 0.6403 (tp40) REVERT: C 401 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7495 (mm-30) REVERT: C 444 MET cc_start: 0.8371 (tpt) cc_final: 0.7918 (tpt) REVERT: C 468 LYS cc_start: 0.7019 (tttt) cc_final: 0.6537 (tttp) outliers start: 33 outliers final: 21 residues processed: 136 average time/residue: 1.2197 time to fit residues: 184.4943 Evaluate side-chains 129 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 355 HIS C 248 ASN C 295 GLN C 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113865 restraints weight = 15078.997| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.11 r_work: 0.3165 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12591 Z= 0.113 Angle : 0.559 8.429 17166 Z= 0.279 Chirality : 0.043 0.231 2010 Planarity : 0.004 0.035 2154 Dihedral : 8.568 66.062 2568 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.32 % Allowed : 16.09 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1476 helix: 3.27 (0.27), residues: 333 sheet: 0.30 (0.28), residues: 339 loop : -1.03 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 222 HIS 0.008 0.001 HIS A 355 PHE 0.008 0.001 PHE A 258 TYR 0.007 0.001 TYR C 257 ARG 0.004 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 18) link_NAG-ASN : angle 1.74074 ( 54) link_ALPHA1-6 : bond 0.00766 ( 3) link_ALPHA1-6 : angle 1.93126 ( 9) link_BETA1-4 : bond 0.00382 ( 21) link_BETA1-4 : angle 1.85480 ( 63) link_ALPHA1-3 : bond 0.01280 ( 3) link_ALPHA1-3 : angle 1.99823 ( 9) hydrogen bonds : bond 0.05869 ( 447) hydrogen bonds : angle 4.41119 ( 1323) link_BETA1-6 : bond 0.00417 ( 3) link_BETA1-6 : angle 1.14154 ( 9) SS BOND : bond 0.00360 ( 18) SS BOND : angle 2.68785 ( 36) covalent geometry : bond 0.00247 (12525) covalent geometry : angle 0.52266 (16986) *********************** 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 147 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7617 (OUTLIER) cc_final: 0.7324 (t) REVERT: A 187 THR cc_start: 0.7855 (p) cc_final: 0.7565 (t) REVERT: A 361 THR cc_start: 0.7369 (m) cc_final: 0.6823 (p) REVERT: A 468 LYS cc_start: 0.7089 (tttt) cc_final: 0.6714 (tttp) REVERT: A 497 ASN cc_start: 0.7654 (m-40) cc_final: 0.7429 (m-40) REVERT: B 52 CYS cc_start: 0.7474 (m) cc_final: 0.7063 (m) REVERT: B 341 ASN cc_start: 0.7361 (p0) cc_final: 0.7101 (p0) REVERT: B 355 HIS cc_start: 0.6889 (p90) cc_final: 0.6242 (p90) REVERT: B 371 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6711 (tp40) REVERT: B 401 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7471 (mp0) REVERT: B 445 ASN cc_start: 0.7271 (t0) cc_final: 0.6661 (m110) REVERT: C 78 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 187 THR cc_start: 0.7863 (p) cc_final: 0.7614 (t) REVERT: C 188 ASN cc_start: 0.7792 (t0) cc_final: 0.7299 (m-40) REVERT: C 371 GLN cc_start: 0.7116 (tp40) cc_final: 0.6396 (tp40) REVERT: C 401 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7446 (mm-30) REVERT: C 444 MET cc_start: 0.8378 (tpt) cc_final: 0.7919 (tpt) REVERT: C 468 LYS cc_start: 0.6964 (tttt) cc_final: 0.6522 (tttp) outliers start: 30 outliers final: 20 residues processed: 137 average time/residue: 0.9814 time to fit residues: 149.6832 Evaluate side-chains 129 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 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 439 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 135 optimal weight: 0.0030 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.149741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112274 restraints weight = 14943.880| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.46 r_work: 0.3120 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12591 Z= 0.180 Angle : 0.690 12.838 17166 Z= 0.347 Chirality : 0.047 0.249 2010 Planarity : 0.005 0.034 2154 Dihedral : 8.907 66.678 2568 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.63 % Allowed : 16.01 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1476 helix: 2.86 (0.26), residues: 333 sheet: -0.05 (0.28), residues: 339 loop : -1.25 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 222 HIS 0.008 0.001 HIS A 75 PHE 0.016 0.002 PHE C 125 TYR 0.015 0.002 TYR B 308 ARG 0.005 0.001 ARG B 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 18) link_NAG-ASN : angle 1.71830 ( 54) link_ALPHA1-6 : bond 0.00577 ( 3) link_ALPHA1-6 : angle 1.84260 ( 9) link_BETA1-4 : bond 0.00343 ( 21) link_BETA1-4 : angle 1.98062 ( 63) link_ALPHA1-3 : bond 0.01196 ( 3) link_ALPHA1-3 : angle 1.93967 ( 9) hydrogen bonds : bond 0.07172 ( 447) hydrogen bonds : angle 4.69826 ( 1323) link_BETA1-6 : bond 0.00396 ( 3) link_BETA1-6 : angle 1.09078 ( 9) SS BOND : bond 0.00527 ( 18) SS BOND : angle 3.21180 ( 36) covalent geometry : bond 0.00423 (12525) covalent geometry : angle 0.65633 (16986) *********************** 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 141 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7392 (t) REVERT: A 187 THR cc_start: 0.7784 (p) cc_final: 0.7468 (t) REVERT: A 361 THR cc_start: 0.7234 (m) cc_final: 0.6666 (p) REVERT: A 452 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6036 (tmt170) REVERT: A 468 LYS cc_start: 0.7362 (tttt) cc_final: 0.6879 (ttmm) REVERT: A 497 ASN cc_start: 0.7675 (m-40) cc_final: 0.7465 (m-40) REVERT: B 52 CYS cc_start: 0.7602 (m) cc_final: 0.7212 (m) REVERT: B 70 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8710 (tp) REVERT: B 355 HIS cc_start: 0.6849 (p90) cc_final: 0.6323 (p90) REVERT: B 371 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6638 (tp40) REVERT: B 401 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7596 (mp0) REVERT: B 445 ASN cc_start: 0.7310 (t0) cc_final: 0.6739 (m-40) REVERT: B 452 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6380 (tmt170) REVERT: C 78 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8434 (p) REVERT: C 187 THR cc_start: 0.7940 (p) cc_final: 0.7632 (t) REVERT: C 188 ASN cc_start: 0.7897 (t0) cc_final: 0.7379 (m-40) REVERT: C 371 GLN cc_start: 0.6999 (tp40) cc_final: 0.6304 (tp40) REVERT: C 401 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7584 (mm-30) outliers start: 34 outliers final: 20 residues processed: 129 average time/residue: 0.9931 time to fit residues: 142.1785 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 : 1.262 ------------------------------------------------------------------------------- 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 419 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 457 GLU 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 371 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG 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 320 MET 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 132 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.151055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112416 restraints weight = 14984.659| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.08 r_work: 0.3161 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12591 Z= 0.137 Angle : 0.613 11.105 17166 Z= 0.308 Chirality : 0.045 0.241 2010 Planarity : 0.004 0.033 2154 Dihedral : 8.569 64.594 2568 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.24 % Allowed : 16.86 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1476 helix: 3.01 (0.26), residues: 333 sheet: 0.14 (0.28), residues: 339 loop : -1.21 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 222 HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE A 258 TYR 0.009 0.001 TYR A 257 ARG 0.003 0.000 ARG C 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 18) link_NAG-ASN : angle 1.46888 ( 54) link_ALPHA1-6 : bond 0.00712 ( 3) link_ALPHA1-6 : angle 1.87155 ( 9) link_BETA1-4 : bond 0.00354 ( 21) link_BETA1-4 : angle 1.83889 ( 63) link_ALPHA1-3 : bond 0.01190 ( 3) link_ALPHA1-3 : angle 1.93761 ( 9) hydrogen bonds : bond 0.06461 ( 447) hydrogen bonds : angle 4.59636 ( 1323) link_BETA1-6 : bond 0.00355 ( 3) link_BETA1-6 : angle 1.14803 ( 9) SS BOND : bond 0.00587 ( 18) SS BOND : angle 2.80287 ( 36) covalent geometry : bond 0.00314 (12525) covalent geometry : angle 0.58221 (16986) *********************** 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 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7724 (p) cc_final: 0.7447 (t) REVERT: A 361 THR cc_start: 0.7229 (m) cc_final: 0.6676 (p) REVERT: A 452 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.5827 (tmt170) REVERT: A 468 LYS cc_start: 0.7362 (tttt) cc_final: 0.6876 (ttmm) REVERT: B 52 CYS cc_start: 0.7502 (m) cc_final: 0.7134 (m) REVERT: B 355 HIS cc_start: 0.6838 (p90) cc_final: 0.6328 (p90) REVERT: B 371 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6632 (tp40) REVERT: B 445 ASN cc_start: 0.7318 (t0) cc_final: 0.6784 (m-40) REVERT: B 464 ASN cc_start: 0.7406 (m-40) cc_final: 0.7041 (t0) REVERT: C 52 CYS cc_start: 0.7334 (m) cc_final: 0.6942 (m) REVERT: C 78 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (p) REVERT: C 187 THR cc_start: 0.7924 (p) cc_final: 0.7644 (t) REVERT: C 371 GLN cc_start: 0.6958 (tp40) cc_final: 0.6289 (tp40) REVERT: C 401 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7531 (mm-30) REVERT: C 468 LYS cc_start: 0.6942 (tttt) cc_final: 0.6477 (tttp) outliers start: 29 outliers final: 17 residues processed: 126 average time/residue: 1.0978 time to fit residues: 152.3290 Evaluate side-chains 121 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR 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 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111612 restraints weight = 14884.908| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.09 r_work: 0.3142 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12591 Z= 0.162 Angle : 0.655 11.935 17166 Z= 0.330 Chirality : 0.046 0.243 2010 Planarity : 0.005 0.032 2154 Dihedral : 8.698 64.623 2568 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.17 % Allowed : 17.32 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1476 helix: 2.88 (0.26), residues: 333 sheet: 0.01 (0.29), residues: 324 loop : -1.33 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.012 0.001 HIS A 75 PHE 0.014 0.002 PHE C 125 TYR 0.013 0.002 TYR B 308 ARG 0.004 0.000 ARG B 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 18) link_NAG-ASN : angle 1.50515 ( 54) link_ALPHA1-6 : bond 0.00600 ( 3) link_ALPHA1-6 : angle 1.89095 ( 9) link_BETA1-4 : bond 0.00354 ( 21) link_BETA1-4 : angle 1.89726 ( 63) link_ALPHA1-3 : bond 0.01203 ( 3) link_ALPHA1-3 : angle 1.96628 ( 9) hydrogen bonds : bond 0.06845 ( 447) hydrogen bonds : angle 4.63536 ( 1323) link_BETA1-6 : bond 0.00319 ( 3) link_BETA1-6 : angle 1.15863 ( 9) SS BOND : bond 0.00538 ( 18) SS BOND : angle 2.93730 ( 36) covalent geometry : bond 0.00380 (12525) covalent geometry : angle 0.62411 (16986) *********************** 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 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 THR cc_start: 0.7306 (m) cc_final: 0.6729 (p) REVERT: A 452 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.5910 (tmt170) REVERT: A 464 ASN cc_start: 0.7221 (m-40) cc_final: 0.6642 (t0) REVERT: A 468 LYS cc_start: 0.7442 (tttt) cc_final: 0.6916 (ttmm) REVERT: B 70 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8745 (tp) REVERT: B 355 HIS cc_start: 0.6801 (p90) cc_final: 0.6507 (p90) REVERT: B 371 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6672 (tp40) REVERT: B 445 ASN cc_start: 0.7372 (t0) cc_final: 0.6791 (m-40) REVERT: B 452 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6303 (tmt170) REVERT: B 464 ASN cc_start: 0.7443 (m-40) cc_final: 0.7010 (t0) REVERT: C 52 CYS cc_start: 0.7339 (m) cc_final: 0.6962 (m) REVERT: C 78 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8301 (p) REVERT: C 187 THR cc_start: 0.7916 (p) cc_final: 0.7640 (t) REVERT: C 371 GLN cc_start: 0.6978 (tp40) cc_final: 0.6299 (tp40) REVERT: C 401 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7585 (mm-30) REVERT: C 464 ASN cc_start: 0.7478 (m-40) cc_final: 0.7068 (t160) REVERT: C 468 LYS cc_start: 0.7022 (tttt) cc_final: 0.6551 (tttp) outliers start: 28 outliers final: 18 residues processed: 124 average time/residue: 1.0585 time to fit residues: 145.4386 Evaluate side-chains 123 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 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 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG 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 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 60 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 136 optimal weight: 0.0470 chunk 99 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.150108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111260 restraints weight = 14825.873| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.07 r_work: 0.3136 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12591 Z= 0.183 Angle : 0.681 11.930 17166 Z= 0.345 Chirality : 0.048 0.247 2010 Planarity : 0.005 0.037 2154 Dihedral : 8.950 65.129 2568 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.09 % Allowed : 17.63 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1476 helix: 2.75 (0.26), residues: 333 sheet: -0.04 (0.29), residues: 324 loop : -1.41 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 222 HIS 0.014 0.002 HIS C 75 PHE 0.015 0.002 PHE C 125 TYR 0.013 0.002 TYR B 308 ARG 0.005 0.001 ARG B 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 18) link_NAG-ASN : angle 1.54003 ( 54) link_ALPHA1-6 : bond 0.00543 ( 3) link_ALPHA1-6 : angle 1.86917 ( 9) link_BETA1-4 : bond 0.00352 ( 21) link_BETA1-4 : angle 1.94664 ( 63) link_ALPHA1-3 : bond 0.01170 ( 3) link_ALPHA1-3 : angle 1.91026 ( 9) hydrogen bonds : bond 0.07171 ( 447) hydrogen bonds : angle 4.68491 ( 1323) link_BETA1-6 : bond 0.00295 ( 3) link_BETA1-6 : angle 1.18663 ( 9) SS BOND : bond 0.00498 ( 18) SS BOND : angle 2.82062 ( 36) covalent geometry : bond 0.00434 (12525) covalent geometry : angle 0.65250 (16986) ********************** 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 125 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5954 (tmt170) REVERT: A 464 ASN cc_start: 0.7207 (m-40) cc_final: 0.6638 (t0) REVERT: A 468 LYS cc_start: 0.7473 (tttt) cc_final: 0.6960 (ttmm) REVERT: B 70 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 355 HIS cc_start: 0.6768 (p90) cc_final: 0.6495 (p90) REVERT: B 371 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6661 (tp40) REVERT: B 383 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7451 (mtm-85) REVERT: B 445 ASN cc_start: 0.7381 (t0) cc_final: 0.6805 (m-40) REVERT: B 452 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6409 (tmt170) REVERT: B 464 ASN cc_start: 0.7436 (m-40) cc_final: 0.7061 (t0) REVERT: C 52 CYS cc_start: 0.7303 (m) cc_final: 0.6937 (m) REVERT: C 187 THR cc_start: 0.7955 (p) cc_final: 0.7697 (t) REVERT: C 371 GLN cc_start: 0.7001 (tp40) cc_final: 0.6334 (tp40) REVERT: C 401 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7610 (mm-30) REVERT: C 464 ASN cc_start: 0.7570 (m-40) cc_final: 0.7165 (t0) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 1.1114 time to fit residues: 144.8660 Evaluate side-chains 118 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 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 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG 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 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111769 restraints weight = 14832.885| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.09 r_work: 0.3150 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12591 Z= 0.154 Angle : 0.641 11.623 17166 Z= 0.324 Chirality : 0.046 0.242 2010 Planarity : 0.004 0.032 2154 Dihedral : 8.778 63.675 2568 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.93 % Allowed : 17.79 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1476 helix: 2.92 (0.26), residues: 333 sheet: -0.04 (0.29), residues: 324 loop : -1.35 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 222 HIS 0.006 0.001 HIS C 75 PHE 0.011 0.001 PHE C 125 TYR 0.010 0.002 TYR A 257 ARG 0.004 0.000 ARG C 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 18) link_NAG-ASN : angle 1.44770 ( 54) link_ALPHA1-6 : bond 0.00598 ( 3) link_ALPHA1-6 : angle 1.85984 ( 9) link_BETA1-4 : bond 0.00363 ( 21) link_BETA1-4 : angle 1.87430 ( 63) link_ALPHA1-3 : bond 0.01141 ( 3) link_ALPHA1-3 : angle 1.94597 ( 9) hydrogen bonds : bond 0.06741 ( 447) hydrogen bonds : angle 4.63766 ( 1323) link_BETA1-6 : bond 0.00313 ( 3) link_BETA1-6 : angle 1.17652 ( 9) SS BOND : bond 0.00553 ( 18) SS BOND : angle 2.93501 ( 36) covalent geometry : bond 0.00358 (12525) covalent geometry : angle 0.61048 (16986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10462.89 seconds wall clock time: 184 minutes 39.87 seconds (11079.87 seconds total)