Starting phenix.real_space_refine on Thu Sep 26 07:54:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/09_2024/7zj6_14742.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/09_2024/7zj6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/09_2024/7zj6_14742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/09_2024/7zj6_14742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/09_2024/7zj6_14742.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/09_2024/7zj6_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-5461/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: 8.37, 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=6, 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 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: 3.72 Conformation dependent library (CDL) restraints added in 1.4 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: 1.97 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: 5.27 Time building geometry restraints manager: 4.11 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: 7470 23.07 - 46.15: 456 46.15 - 69.22: 75 69.22 - 92.29: 60 92.29 - 115.36: 36 Dihedral angle restraints: 8097 sinusoidal: 3840 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 8094 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: 2.04 - 2.61: 45 2.61 - 3.18: 9354 3.18 - 3.75: 17355 3.75 - 4.33: 25803 4.33 - 4.90: 40868 Nonbonded interactions: 93425 Sorted by model distance: nonbonded pdb=" SG CYS B 14 " pdb=" SG CYS B 466 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS C 14 " pdb=" SG CYS C 466 " model vdw 2.037 3.760 nonbonded pdb=" SG CYS B 97 " pdb=" SG CYS B 139 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS C 473 " pdb=" SG CYS C 477 " model vdw 2.049 3.760 ... (remaining 93420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.370 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.250 ------------------------------------------------------------------------------- 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 12525 Z= 0.866 Angle : 1.771 8.223 16986 Z= 1.261 Chirality : 0.091 0.464 2010 Planarity : 0.011 0.183 2154 Dihedral : 18.227 115.364 5349 Min Nonbonded Distance : 2.035 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 1.360 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: 1.1746 time to fit residues: 274.5163 Evaluate side-chains 143 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 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: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12525 Z= 0.186 Angle : 0.622 9.232 16986 Z= 0.324 Chirality : 0.045 0.193 2010 Planarity : 0.004 0.033 2154 Dihedral : 13.375 88.635 2574 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.17 % Allowed : 12.61 % 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: -0.48 (0.19), residues: 1476 helix: 2.14 (0.26), residues: 333 sheet: -0.06 (0.29), residues: 303 loop : -1.53 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.007 0.002 HIS A 75 PHE 0.016 0.002 PHE C 258 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG C 329 *********************** 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 181 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7578 (p) cc_final: 0.7242 (t) REVERT: A 188 ASN cc_start: 0.7644 (t0) cc_final: 0.7183 (m-40) REVERT: A 189 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7114 (tp40) REVERT: A 275 ASP cc_start: 0.7303 (t0) cc_final: 0.6674 (p0) REVERT: A 341 ASN cc_start: 0.6750 (p0) cc_final: 0.6511 (p0) REVERT: A 401 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7026 (mp0) REVERT: A 452 ARG cc_start: 0.6155 (ttp80) cc_final: 0.5825 (tmt170) REVERT: A 468 LYS cc_start: 0.6709 (tttt) cc_final: 0.6247 (ttmm) REVERT: A 482 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6299 (mtp180) REVERT: A 487 ASP cc_start: 0.7399 (t0) cc_final: 0.7142 (t0) REVERT: A 497 ASN cc_start: 0.7516 (m-40) cc_final: 0.7232 (m-40) REVERT: B 70 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8404 (tt) REVERT: B 188 ASN cc_start: 0.7667 (t0) cc_final: 0.7347 (m-40) REVERT: B 189 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6925 (tp40) REVERT: B 208 ARG cc_start: 0.6793 (ptt180) cc_final: 0.6468 (ptm160) REVERT: B 275 ASP cc_start: 0.6770 (t0) cc_final: 0.6447 (p0) REVERT: B 341 ASN cc_start: 0.6779 (p0) cc_final: 0.6528 (p0) REVERT: B 355 HIS cc_start: 0.6302 (p90) cc_final: 0.6054 (p90) REVERT: B 401 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7157 (mp0) REVERT: B 452 ARG cc_start: 0.6182 (ttp80) cc_final: 0.5643 (tmt170) REVERT: B 468 LYS cc_start: 0.6786 (tttt) cc_final: 0.6403 (tttp) REVERT: B 479 GLU cc_start: 0.7238 (tp30) cc_final: 0.6756 (tp30) REVERT: B 482 ARG cc_start: 0.6611 (mtm-85) cc_final: 0.6058 (mtp180) REVERT: B 487 ASP cc_start: 0.7327 (t0) cc_final: 0.7028 (t0) REVERT: C 78 VAL cc_start: 0.8159 (t) cc_final: 0.7834 (p) REVERT: C 159 SER cc_start: 0.7140 (m) cc_final: 0.6935 (p) REVERT: C 187 THR cc_start: 0.7749 (p) cc_final: 0.7302 (t) REVERT: C 188 ASN cc_start: 0.7465 (t0) cc_final: 0.7037 (m-40) REVERT: C 189 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7051 (tp40) REVERT: C 264 LYS cc_start: 0.8452 (pttp) cc_final: 0.8221 (pttt) REVERT: C 371 GLN cc_start: 0.6833 (tp40) cc_final: 0.6158 (tp-100) REVERT: C 382 ASN cc_start: 0.7231 (m-40) cc_final: 0.6990 (m110) REVERT: C 401 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7075 (mm-30) REVERT: C 444 MET cc_start: 0.8052 (tpt) cc_final: 0.7480 (tpt) REVERT: C 452 ARG cc_start: 0.6128 (ttp80) cc_final: 0.5773 (tmt170) REVERT: C 468 LYS cc_start: 0.6780 (tttt) cc_final: 0.6261 (tttp) REVERT: C 470 TYR cc_start: 0.7286 (m-80) cc_final: 0.7078 (m-80) outliers start: 28 outliers final: 10 residues processed: 171 average time/residue: 1.0244 time to fit residues: 193.3133 Evaluate side-chains 138 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 B residue 439 LEU Chi-restraints excluded: chain C residue 155 THR 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 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 376 GLN C 295 GLN C 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 12525 Z= 0.156 Angle : 0.561 7.685 16986 Z= 0.286 Chirality : 0.044 0.218 2010 Planarity : 0.004 0.053 2154 Dihedral : 11.019 80.557 2570 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.71 % Allowed : 13.15 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.20), residues: 1476 helix: 2.91 (0.26), residues: 333 sheet: 0.32 (0.29), residues: 321 loop : -1.18 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 421 HIS 0.012 0.001 HIS A 355 PHE 0.009 0.001 PHE C 258 TYR 0.009 0.001 TYR C 486 ARG 0.002 0.000 ARG A 201 *********************** 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 167 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7590 (p) cc_final: 0.7291 (t) REVERT: A 188 ASN cc_start: 0.7654 (t0) cc_final: 0.7152 (m-40) REVERT: A 189 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7086 (tp40) REVERT: A 341 ASN cc_start: 0.6829 (p0) cc_final: 0.6620 (p0) REVERT: A 361 THR cc_start: 0.6988 (m) cc_final: 0.6588 (p) REVERT: A 371 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6510 (tp40) REVERT: A 401 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6902 (mp0) REVERT: A 468 LYS cc_start: 0.6792 (tttt) cc_final: 0.6302 (ttmm) REVERT: A 482 ARG cc_start: 0.6786 (mtm-85) cc_final: 0.6404 (mtm-85) REVERT: A 497 ASN cc_start: 0.7640 (m-40) cc_final: 0.7426 (m-40) REVERT: A 498 ASN cc_start: 0.6666 (m-40) cc_final: 0.6421 (m110) REVERT: B 188 ASN cc_start: 0.7611 (t0) cc_final: 0.7279 (m-40) REVERT: B 189 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6831 (tp40) REVERT: B 208 ARG cc_start: 0.6797 (ptt180) cc_final: 0.6509 (ptm160) REVERT: B 275 ASP cc_start: 0.6910 (t0) cc_final: 0.6525 (p0) REVERT: B 341 ASN cc_start: 0.6777 (p0) cc_final: 0.6518 (p0) REVERT: B 355 HIS cc_start: 0.6454 (p90) cc_final: 0.5952 (p90) REVERT: B 401 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7040 (mp0) REVERT: B 452 ARG cc_start: 0.5949 (ttp80) cc_final: 0.5682 (tmt170) REVERT: B 468 LYS cc_start: 0.6738 (tttt) cc_final: 0.6296 (ttmm) REVERT: B 479 GLU cc_start: 0.6897 (tp30) cc_final: 0.6359 (tt0) REVERT: C 78 VAL cc_start: 0.8132 (t) cc_final: 0.7817 (p) REVERT: C 187 THR cc_start: 0.7776 (p) cc_final: 0.7352 (t) REVERT: C 188 ASN cc_start: 0.7525 (t0) cc_final: 0.7089 (m-40) REVERT: C 189 GLN cc_start: 0.7321 (tm-30) cc_final: 0.6873 (tp40) REVERT: C 321 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7292 (ptp-170) REVERT: C 371 GLN cc_start: 0.6782 (tp40) cc_final: 0.6153 (tp-100) REVERT: C 401 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7101 (mm-30) REVERT: C 444 MET cc_start: 0.8111 (tpt) cc_final: 0.7595 (tpt) REVERT: C 468 LYS cc_start: 0.6743 (tttt) cc_final: 0.6254 (tttp) REVERT: C 487 ASP cc_start: 0.6913 (t0) cc_final: 0.6662 (t0) outliers start: 35 outliers final: 13 residues processed: 158 average time/residue: 0.9816 time to fit residues: 172.2123 Evaluate side-chains 136 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 439 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 439 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR 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 132 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 0.0020 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS B 363 GLN C 216 ASN C 248 ASN C 295 GLN C 363 GLN C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 12525 Z= 0.159 Angle : 0.538 7.204 16986 Z= 0.277 Chirality : 0.044 0.215 2010 Planarity : 0.004 0.055 2154 Dihedral : 9.011 72.154 2568 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 13.69 % Favored : 83.76 % 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: 0.44 (0.21), residues: 1476 helix: 3.28 (0.26), residues: 333 sheet: 0.21 (0.28), residues: 354 loop : -1.04 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 222 HIS 0.012 0.001 HIS A 355 PHE 0.010 0.001 PHE C 258 TYR 0.009 0.001 TYR A 257 ARG 0.003 0.000 ARG B 482 *********************** 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 162 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7704 (p) cc_final: 0.7356 (t) REVERT: A 188 ASN cc_start: 0.7581 (t0) cc_final: 0.7156 (m-40) REVERT: A 275 ASP cc_start: 0.6892 (t0) cc_final: 0.6576 (p0) REVERT: A 341 ASN cc_start: 0.6897 (p0) cc_final: 0.6678 (p0) REVERT: A 361 THR cc_start: 0.6996 (m) cc_final: 0.6680 (p) REVERT: A 371 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6594 (tp40) REVERT: A 401 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6923 (mp0) REVERT: A 468 LYS cc_start: 0.6796 (tttt) cc_final: 0.6299 (ttmm) REVERT: A 482 ARG cc_start: 0.6704 (mtm-85) cc_final: 0.6439 (mtm-85) REVERT: A 497 ASN cc_start: 0.7381 (m-40) cc_final: 0.7160 (m-40) REVERT: B 188 ASN cc_start: 0.7551 (t0) cc_final: 0.7193 (m-40) REVERT: B 208 ARG cc_start: 0.6995 (ptt180) cc_final: 0.6596 (ptm160) REVERT: B 275 ASP cc_start: 0.6982 (t0) cc_final: 0.6618 (p0) REVERT: B 341 ASN cc_start: 0.6848 (p0) cc_final: 0.6591 (p0) REVERT: B 355 HIS cc_start: 0.6318 (p90) cc_final: 0.5850 (p90) REVERT: B 371 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6264 (tp40) REVERT: B 401 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7065 (mp0) REVERT: B 468 LYS cc_start: 0.6691 (tttt) cc_final: 0.6289 (ttmm) REVERT: C 78 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7766 (p) REVERT: C 187 THR cc_start: 0.7852 (p) cc_final: 0.7452 (t) REVERT: C 188 ASN cc_start: 0.7547 (t0) cc_final: 0.7092 (m-40) REVERT: C 189 GLN cc_start: 0.7296 (tm-30) cc_final: 0.6817 (tp40) REVERT: C 371 GLN cc_start: 0.6970 (tp40) cc_final: 0.6309 (tp-100) REVERT: C 401 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7138 (mm-30) REVERT: C 444 MET cc_start: 0.8117 (tpt) cc_final: 0.7571 (tpt) REVERT: C 446 LYS cc_start: 0.7253 (mtmt) cc_final: 0.7052 (mtmm) REVERT: C 468 LYS cc_start: 0.6726 (tttt) cc_final: 0.6249 (tttp) outliers start: 33 outliers final: 18 residues processed: 153 average time/residue: 0.9968 time to fit residues: 169.4335 Evaluate side-chains 138 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain 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 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 363 GLN C 295 GLN C 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12525 Z= 0.444 Angle : 0.785 14.131 16986 Z= 0.405 Chirality : 0.053 0.286 2010 Planarity : 0.006 0.057 2154 Dihedral : 10.078 72.685 2568 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 15.78 % Favored : 81.52 % 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: -0.22 (0.20), residues: 1476 helix: 2.50 (0.25), residues: 333 sheet: -0.09 (0.28), residues: 339 loop : -1.38 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 421 HIS 0.010 0.002 HIS A 355 PHE 0.021 0.003 PHE C 125 TYR 0.020 0.003 TYR B 308 ARG 0.010 0.001 ARG B 109 *********************** 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 fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7769 (p) cc_final: 0.7336 (t) REVERT: A 208 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7067 (ptm160) REVERT: A 401 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7223 (mp0) REVERT: A 452 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6023 (tmt170) REVERT: A 468 LYS cc_start: 0.7023 (tttt) cc_final: 0.6520 (ttmm) REVERT: A 482 ARG cc_start: 0.6593 (mtm-85) cc_final: 0.6092 (mtm-85) REVERT: B 70 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 208 ARG cc_start: 0.7169 (ptt180) cc_final: 0.6533 (ptm160) REVERT: B 275 ASP cc_start: 0.6947 (t0) cc_final: 0.6489 (p0) REVERT: B 355 HIS cc_start: 0.6414 (p90) cc_final: 0.5987 (p90) REVERT: B 371 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6231 (tp40) REVERT: B 401 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7448 (mp0) REVERT: B 452 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6521 (tmt170) REVERT: B 468 LYS cc_start: 0.6964 (tttt) cc_final: 0.6582 (tttp) REVERT: C 78 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7941 (p) REVERT: C 187 THR cc_start: 0.7932 (p) cc_final: 0.7504 (t) REVERT: C 188 ASN cc_start: 0.7767 (t0) cc_final: 0.7269 (m-40) REVERT: C 371 GLN cc_start: 0.6751 (tp40) cc_final: 0.6054 (tp40) REVERT: C 401 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7321 (mm-30) REVERT: C 444 MET cc_start: 0.7932 (tpt) cc_final: 0.7554 (tpt) REVERT: C 449 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6573 (mm-30) REVERT: C 468 LYS cc_start: 0.6878 (tttt) cc_final: 0.6407 (tttp) outliers start: 35 outliers final: 19 residues processed: 134 average time/residue: 1.0385 time to fit residues: 153.8189 Evaluate side-chains 131 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 A 497 ASN C 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12525 Z= 0.149 Angle : 0.539 10.475 16986 Z= 0.278 Chirality : 0.043 0.235 2010 Planarity : 0.004 0.056 2154 Dihedral : 8.986 65.936 2568 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.09 % Allowed : 16.32 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.34 (0.21), residues: 1476 helix: 3.14 (0.26), residues: 333 sheet: 0.23 (0.28), residues: 339 loop : -1.10 (0.19), residues: 804 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 0.008 0.001 PHE B 353 TYR 0.008 0.001 TYR A 98 ARG 0.002 0.000 ARG B 482 *********************** 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 136 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7584 (p) cc_final: 0.7307 (t) REVERT: A 361 THR cc_start: 0.6736 (m) cc_final: 0.6407 (p) REVERT: A 468 LYS cc_start: 0.6954 (tttt) cc_final: 0.6447 (ttmm) REVERT: B 70 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8518 (tp) REVERT: B 208 ARG cc_start: 0.7074 (ptt180) cc_final: 0.6663 (ptm160) REVERT: B 355 HIS cc_start: 0.6493 (p90) cc_final: 0.5980 (p90) REVERT: B 371 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6152 (tp40) REVERT: B 401 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7211 (mp0) REVERT: B 445 ASN cc_start: 0.6994 (t0) cc_final: 0.6384 (m-40) REVERT: B 466 CYS cc_start: 0.7517 (m) cc_final: 0.7284 (m) REVERT: B 468 LYS cc_start: 0.6686 (tttt) cc_final: 0.6279 (tttp) REVERT: C 70 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8632 (tp) REVERT: C 78 VAL cc_start: 0.8155 (t) cc_final: 0.7913 (p) REVERT: C 187 THR cc_start: 0.7856 (p) cc_final: 0.7497 (t) REVERT: C 188 ASN cc_start: 0.7714 (t0) cc_final: 0.7154 (m-40) REVERT: C 371 GLN cc_start: 0.6842 (tp40) cc_final: 0.6120 (tp40) REVERT: C 401 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7199 (mm-30) REVERT: C 444 MET cc_start: 0.7972 (tpt) cc_final: 0.7499 (tpt) REVERT: C 468 LYS cc_start: 0.6820 (tttt) cc_final: 0.6377 (tttp) outliers start: 27 outliers final: 18 residues processed: 128 average time/residue: 0.9908 time to fit residues: 141.5536 Evaluate side-chains 124 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 88 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS C 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12525 Z= 0.227 Angle : 0.596 11.253 16986 Z= 0.306 Chirality : 0.045 0.245 2010 Planarity : 0.005 0.057 2154 Dihedral : 8.897 65.714 2568 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.32 % Allowed : 16.71 % Favored : 80.97 % 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: 0.24 (0.20), residues: 1476 helix: 3.10 (0.26), residues: 333 sheet: 0.17 (0.28), residues: 339 loop : -1.19 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.008 0.001 HIS A 355 PHE 0.013 0.002 PHE C 125 TYR 0.013 0.002 TYR B 308 ARG 0.005 0.000 ARG A 482 *********************** 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 135 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 187 THR cc_start: 0.7576 (p) cc_final: 0.7231 (t) REVERT: A 361 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6312 (p) REVERT: A 452 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5893 (tmt170) REVERT: A 468 LYS cc_start: 0.7146 (tttt) cc_final: 0.6638 (ttmm) REVERT: B 70 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8424 (tp) REVERT: B 208 ARG cc_start: 0.7136 (ptt180) cc_final: 0.6703 (ptm160) REVERT: B 355 HIS cc_start: 0.6444 (p90) cc_final: 0.5951 (p90) REVERT: B 371 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6192 (tp40) REVERT: B 401 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7282 (mp0) REVERT: B 445 ASN cc_start: 0.6981 (t0) cc_final: 0.6373 (m-40) REVERT: B 466 CYS cc_start: 0.7605 (m) cc_final: 0.7398 (m) REVERT: C 78 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7815 (p) REVERT: C 187 THR cc_start: 0.7925 (p) cc_final: 0.7577 (t) REVERT: C 188 ASN cc_start: 0.7738 (t0) cc_final: 0.7068 (m-40) REVERT: C 371 GLN cc_start: 0.6849 (tp40) cc_final: 0.6134 (tp40) REVERT: C 401 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7257 (mm-30) REVERT: C 444 MET cc_start: 0.7932 (tpt) cc_final: 0.7475 (tpt) outliers start: 30 outliers final: 18 residues processed: 126 average time/residue: 0.9958 time to fit residues: 139.5418 Evaluate side-chains 124 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12525 Z= 0.172 Angle : 0.547 10.251 16986 Z= 0.281 Chirality : 0.044 0.240 2010 Planarity : 0.004 0.057 2154 Dihedral : 8.477 63.340 2568 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.17 % Allowed : 16.94 % Favored : 80.90 % 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: 0.37 (0.21), residues: 1476 helix: 3.27 (0.26), residues: 333 sheet: 0.22 (0.28), residues: 339 loop : -1.12 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.009 0.001 HIS A 75 PHE 0.009 0.001 PHE A 258 TYR 0.009 0.001 TYR A 257 ARG 0.003 0.000 ARG A 482 *********************** 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 132 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 187 THR cc_start: 0.7608 (p) cc_final: 0.7303 (t) REVERT: A 361 THR cc_start: 0.6775 (m) cc_final: 0.6405 (p) REVERT: A 452 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5752 (tmt170) REVERT: B 70 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 208 ARG cc_start: 0.7024 (ptt180) cc_final: 0.6630 (ptm160) REVERT: B 355 HIS cc_start: 0.6456 (p90) cc_final: 0.5965 (p90) REVERT: B 371 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6161 (tp40) REVERT: B 401 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 445 ASN cc_start: 0.6928 (t0) cc_final: 0.6348 (m-40) REVERT: C 78 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7822 (p) REVERT: C 187 THR cc_start: 0.7933 (p) cc_final: 0.7647 (t) REVERT: C 371 GLN cc_start: 0.6843 (tp40) cc_final: 0.6076 (tp40) REVERT: C 401 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7219 (mm-30) REVERT: C 444 MET cc_start: 0.8019 (tpt) cc_final: 0.7548 (tpt) outliers start: 28 outliers final: 19 residues processed: 125 average time/residue: 0.9649 time to fit residues: 135.0691 Evaluate side-chains 119 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 419 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS C 295 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12525 Z= 0.183 Angle : 0.565 10.181 16986 Z= 0.291 Chirality : 0.044 0.240 2010 Planarity : 0.004 0.057 2154 Dihedral : 8.382 61.953 2568 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.17 % Allowed : 17.17 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.36 (0.21), residues: 1476 helix: 3.28 (0.26), residues: 333 sheet: 0.21 (0.28), residues: 339 loop : -1.14 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.011 0.001 HIS A 75 PHE 0.010 0.001 PHE A 258 TYR 0.010 0.001 TYR B 308 ARG 0.003 0.000 ARG A 482 *********************** 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 127 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 361 THR cc_start: 0.6767 (m) cc_final: 0.6413 (p) REVERT: A 452 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5508 (tmt170) REVERT: A 464 ASN cc_start: 0.7111 (t0) cc_final: 0.6337 (t0) REVERT: A 468 LYS cc_start: 0.7156 (tttt) cc_final: 0.6585 (ttmm) REVERT: B 70 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 208 ARG cc_start: 0.6989 (ptt180) cc_final: 0.6618 (ptm160) REVERT: B 355 HIS cc_start: 0.6474 (p90) cc_final: 0.5990 (p90) REVERT: B 371 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6161 (tp40) REVERT: B 401 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7243 (mp0) REVERT: B 445 ASN cc_start: 0.6939 (t0) cc_final: 0.6368 (m-40) REVERT: B 452 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6147 (tmt170) REVERT: C 78 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7825 (p) REVERT: C 187 THR cc_start: 0.7899 (p) cc_final: 0.7630 (t) REVERT: C 371 GLN cc_start: 0.6847 (tp40) cc_final: 0.6082 (tp40) REVERT: C 401 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7222 (mm-30) REVERT: C 444 MET cc_start: 0.7994 (tpt) cc_final: 0.7548 (tpt) REVERT: C 452 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5651 (tpp80) outliers start: 28 outliers final: 19 residues processed: 119 average time/residue: 1.0036 time to fit residues: 132.5612 Evaluate side-chains 121 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 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 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 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 452 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN C 295 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12525 Z= 0.167 Angle : 0.547 9.858 16986 Z= 0.281 Chirality : 0.044 0.239 2010 Planarity : 0.004 0.057 2154 Dihedral : 8.098 60.493 2568 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 : 0.14 % 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: 0.43 (0.21), residues: 1476 helix: 3.35 (0.26), residues: 333 sheet: 0.24 (0.28), residues: 339 loop : -1.09 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.005 0.001 HIS A 75 PHE 0.009 0.001 PHE A 258 TYR 0.009 0.001 TYR A 257 ARG 0.002 0.000 ARG A 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 THR cc_start: 0.6860 (m) cc_final: 0.6520 (p) REVERT: A 452 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5500 (tmt170) REVERT: A 464 ASN cc_start: 0.7145 (t0) cc_final: 0.6425 (t0) REVERT: B 70 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8497 (tp) REVERT: B 208 ARG cc_start: 0.6969 (ptt180) cc_final: 0.6592 (ptm160) REVERT: B 355 HIS cc_start: 0.6624 (p90) cc_final: 0.6075 (p90) REVERT: B 371 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6184 (tp40) REVERT: B 401 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7227 (mp0) REVERT: B 445 ASN cc_start: 0.6931 (t0) cc_final: 0.6293 (m110) REVERT: B 452 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6111 (tmt170) REVERT: C 70 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8623 (tp) REVERT: C 78 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7755 (p) REVERT: C 187 THR cc_start: 0.7876 (p) cc_final: 0.7616 (t) REVERT: C 371 GLN cc_start: 0.6847 (tp40) cc_final: 0.6085 (tp40) REVERT: C 401 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7207 (mm-30) REVERT: C 444 MET cc_start: 0.8030 (tpt) cc_final: 0.7559 (tpt) REVERT: C 452 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5607 (tpp80) REVERT: C 456 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7025 (ttm-80) outliers start: 28 outliers final: 19 residues processed: 118 average time/residue: 1.0501 time to fit residues: 137.2095 Evaluate side-chains 123 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 452 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.2980 chunk 116 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119414 restraints weight = 14875.251| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.79 r_work: 0.3156 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12525 Z= 0.148 Angle : 0.522 9.435 16986 Z= 0.268 Chirality : 0.043 0.230 2010 Planarity : 0.004 0.057 2154 Dihedral : 7.705 58.419 2568 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.86 % Allowed : 17.79 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.55 (0.21), residues: 1476 helix: 3.50 (0.26), residues: 333 sheet: 0.29 (0.28), residues: 339 loop : -1.02 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 258 TYR 0.008 0.001 TYR A 257 ARG 0.002 0.000 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3740.86 seconds wall clock time: 66 minutes 38.19 seconds (3998.19 seconds total)