Starting phenix.real_space_refine on Tue Mar 3 14:56:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7q_15224/03_2026/8a7q_15224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7q_15224/03_2026/8a7q_15224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2026/8a7q_15224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2026/8a7q_15224.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2026/8a7q_15224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2026/8a7q_15224.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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 36 5.16 5 C 4164 2.51 5 N 1020 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "G" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "H" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "J" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "L" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Time building chain proxies: 1.34, per 1000 atoms: 0.21 Number of scatterers: 6492 At special positions: 0 Unit cell: (147.58, 149.46, 33.84, 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 36 16.00 O 1272 8.00 N 1020 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 80 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 80 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 80 " distance=2.03 Simple disulfide: pdb=" SG CYS J 25 " - pdb=" SG CYS J 80 " distance=2.03 Simple disulfide: pdb=" SG CYS K 25 " - pdb=" SG CYS K 80 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 321.8 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.872A pdb=" N ASP E 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP I 34 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.579A pdb=" N VAL A 49 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 49 " --> pdb=" O GLU I 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.989A pdb=" N TYR E 63 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 64 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU E 65 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 66 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR I 63 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 64 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU I 65 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR E 66 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA6, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.003A pdb=" N SER B 33 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU F 36 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 35 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP F 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 37 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER F 33 " --> pdb=" O ASP J 34 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU J 36 " --> pdb=" O SER F 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 35 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP J 38 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL F 37 " --> pdb=" O ASP J 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 53 removed outlier: 9.434A pdb=" N LYS B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N HIS F 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 50 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP F 53 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LYS F 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N HIS J 51 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU F 50 " --> pdb=" O HIS J 51 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ASP J 53 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER F 52 " --> pdb=" O ASP J 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 66 removed outlier: 6.984A pdb=" N TYR F 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR B 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR J 63 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU F 64 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU J 65 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR F 66 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 78 removed outlier: 6.576A pdb=" N GLU B 74 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU F 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 76 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU F 74 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU J 77 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP F 76 " --> pdb=" O GLU J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.184A pdb=" N VAL B 82 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL F 82 " --> pdb=" O ASN J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 22 through 24 removed outlier: 6.739A pdb=" N LEU C 23 " --> pdb=" O ASN G 24 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 39 removed outlier: 6.943A pdb=" N ASP G 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP K 34 " --> pdb=" O SER G 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.533A pdb=" N VAL C 49 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL G 49 " --> pdb=" O GLU K 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.023A pdb=" N TYR G 63 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU C 64 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU G 65 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C 66 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR K 63 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU G 64 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU K 65 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR G 66 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AC2, first strand: chain 'C' and resid 73 through 78 removed outlier: 3.505A pdb=" N GLU G 74 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AC4, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AC5, first strand: chain 'D' and resid 33 through 39 removed outlier: 5.937A pdb=" N SER D 33 " --> pdb=" O ASP H 34 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU H 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 35 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP H 38 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 37 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 33 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLU L 36 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE H 35 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASP L 38 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL H 37 " --> pdb=" O ASP L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.601A pdb=" N VAL D 49 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER H 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS H 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N HIS L 51 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU H 50 " --> pdb=" O HIS L 51 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP L 53 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER H 52 " --> pdb=" O ASP L 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 59 through 66 removed outlier: 6.966A pdb=" N TYR H 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 64 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU H 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR D 66 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR L 63 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU H 64 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU L 65 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR H 66 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 69 through 70 Processing sheet with id=AC9, first strand: chain 'D' and resid 74 through 78 removed outlier: 6.565A pdb=" N GLU D 74 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU H 77 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 76 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU H 74 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU L 77 " --> pdb=" O GLU H 74 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP H 76 " --> pdb=" O GLU L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.088A pdb=" N VAL D 82 " --> pdb=" O ASN H 83 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL H 82 " --> pdb=" O ASN L 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 93 hydrogen bonds defined for protein. 279 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: 0.80 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1974 1.34 - 1.46: 1269 1.46 - 1.57: 3393 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6684 Sorted by residual: bond pdb=" N GLU G 77 " pdb=" CA GLU G 77 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.23e+00 bond pdb=" N GLU K 77 " pdb=" CA GLU K 77 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N ASP G 76 " pdb=" CA ASP G 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.78e+00 bond pdb=" N GLU I 77 " pdb=" CA GLU I 77 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.68e+00 ... (remaining 6679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 7909 0.89 - 1.77: 824 1.77 - 2.66: 217 2.66 - 3.54: 72 3.54 - 4.43: 14 Bond angle restraints: 9036 Sorted by residual: angle pdb=" CA ASP E 76 " pdb=" CB ASP E 76 " pdb=" CG ASP E 76 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" CA ASP I 76 " pdb=" CB ASP I 76 " pdb=" CG ASP I 76 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASP K 76 " pdb=" CB ASP K 76 " pdb=" CG ASP K 76 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " pdb=" CG ASP A 76 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASP C 76 " pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " ideal model delta sigma weight residual 112.60 116.92 -4.32 1.00e+00 1.00e+00 1.87e+01 ... (remaining 9031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3690 17.02 - 34.05: 189 34.05 - 51.07: 24 51.07 - 68.09: 12 68.09 - 85.12: 9 Dihedral angle restraints: 3924 sinusoidal: 1620 harmonic: 2304 Sorted by residual: dihedral pdb=" CB GLU B 47 " pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " pdb=" OE1 GLU B 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.12 85.12 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CB GLU J 47 " pdb=" CG GLU J 47 " pdb=" CD GLU J 47 " pdb=" OE1 GLU J 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU L 47 " pdb=" CG GLU L 47 " pdb=" CD GLU L 47 " pdb=" OE1 GLU L 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 3921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 635 0.043 - 0.087: 156 0.087 - 0.130: 88 0.130 - 0.174: 23 0.174 - 0.217: 10 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA LYS B 75 " pdb=" N LYS B 75 " pdb=" C LYS B 75 " pdb=" CB LYS B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LYS D 75 " pdb=" N LYS D 75 " pdb=" C LYS D 75 " pdb=" CB LYS D 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LYS J 75 " pdb=" N LYS J 75 " pdb=" C LYS J 75 " pdb=" CB LYS J 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 909 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 70 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C PHE L 70 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE L 70 " -0.007 2.00e-02 2.50e+03 pdb=" N THR L 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 70 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C PHE J 70 " -0.018 2.00e-02 2.50e+03 pdb=" O PHE J 70 " 0.007 2.00e-02 2.50e+03 pdb=" N THR J 71 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 70 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C PHE D 70 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE D 70 " -0.007 2.00e-02 2.50e+03 pdb=" N THR D 71 " -0.006 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 275 2.74 - 3.28: 5580 3.28 - 3.82: 10221 3.82 - 4.36: 12070 4.36 - 4.90: 21788 Nonbonded interactions: 49934 Sorted by model distance: nonbonded pdb=" O LYS D 58 " pdb=" N LYS H 58 " model vdw 2.197 3.120 nonbonded pdb=" O LYS A 58 " pdb=" N LYS E 58 " model vdw 2.229 3.120 nonbonded pdb=" OE2 GLU F 44 " pdb=" NH2 ARG K 45 " model vdw 2.246 3.120 nonbonded pdb=" O LYS F 58 " pdb=" N LYS J 58 " model vdw 2.251 3.120 nonbonded pdb=" O LYS B 58 " pdb=" N LYS F 58 " model vdw 2.252 3.120 ... (remaining 49929 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.660 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.004 0.033 6696 Z= 0.289 Angle : 0.673 4.426 9060 Z= 0.451 Chirality : 0.055 0.217 912 Planarity : 0.003 0.022 1164 Dihedral : 11.640 85.115 2400 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.17), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.13), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 81 TYR 0.007 0.001 TYR H 63 PHE 0.009 0.001 PHE J 70 TRP 0.002 0.001 TRP L 60 HIS 0.004 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6684) covalent geometry : angle 0.67348 ( 9036) SS BOND : bond 0.00155 ( 12) SS BOND : angle 0.58244 ( 24) hydrogen bonds : bond 0.26326 ( 93) hydrogen bonds : angle 10.67194 ( 279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7174 (tmm160) REVERT: B 38 ASP cc_start: 0.7219 (p0) cc_final: 0.6481 (p0) REVERT: C 45 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7093 (tmm160) REVERT: D 38 ASP cc_start: 0.7311 (p0) cc_final: 0.6643 (p0) REVERT: H 38 ASP cc_start: 0.7238 (p0) cc_final: 0.6763 (p0) REVERT: J 27 MET cc_start: 0.7761 (ttt) cc_final: 0.7484 (ttt) REVERT: J 38 ASP cc_start: 0.7302 (p0) cc_final: 0.7083 (p0) REVERT: J 53 ASP cc_start: 0.8012 (t0) cc_final: 0.7677 (t0) REVERT: L 27 MET cc_start: 0.7790 (ttt) cc_final: 0.7503 (ttt) REVERT: L 38 ASP cc_start: 0.7561 (p0) cc_final: 0.7214 (p0) REVERT: L 53 ASP cc_start: 0.8006 (t0) cc_final: 0.7726 (t0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.5041 time to fit residues: 198.6529 Evaluate side-chains 293 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN B 24 ASN C 83 ASN D 24 ASN E 24 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS H 24 ASN I 24 ASN ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.104671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.098602 restraints weight = 21361.967| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.85 r_work: 0.4027 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6696 Z= 0.230 Angle : 0.806 7.443 9060 Z= 0.417 Chirality : 0.047 0.153 912 Planarity : 0.004 0.033 1164 Dihedral : 4.986 13.187 840 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.74 % Allowed : 26.37 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.18), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.14), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 81 TYR 0.020 0.002 TYR A 66 PHE 0.015 0.002 PHE H 22 TRP 0.001 0.000 TRP L 60 HIS 0.004 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 6684) covalent geometry : angle 0.80663 ( 9036) SS BOND : bond 0.00200 ( 12) SS BOND : angle 0.44001 ( 24) hydrogen bonds : bond 0.04615 ( 93) hydrogen bonds : angle 7.57950 ( 279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.5683 (pm20) cc_final: 0.5375 (pm20) REVERT: A 45 ARG cc_start: 0.9074 (mtt180) cc_final: 0.7061 (tmm160) REVERT: A 50 GLU cc_start: 0.5076 (pm20) cc_final: 0.4873 (pm20) REVERT: B 41 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4230 (pmmt) REVERT: B 48 LYS cc_start: 0.8857 (mttt) cc_final: 0.7280 (pmtt) REVERT: B 50 GLU cc_start: 0.8417 (mp0) cc_final: 0.8063 (mp0) REVERT: B 74 GLU cc_start: 0.3782 (mm-30) cc_final: 0.3519 (tp30) REVERT: C 36 GLU cc_start: 0.5488 (pm20) cc_final: 0.5021 (pm20) REVERT: C 44 GLU cc_start: 0.8854 (tt0) cc_final: 0.8417 (tt0) REVERT: C 45 ARG cc_start: 0.9100 (mtt180) cc_final: 0.7060 (tmm160) REVERT: C 76 ASP cc_start: 0.8206 (m-30) cc_final: 0.7789 (m-30) REVERT: D 35 ILE cc_start: 0.9410 (mt) cc_final: 0.9169 (mp) REVERT: D 36 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7419 (tm-30) REVERT: D 38 ASP cc_start: 0.8515 (p0) cc_final: 0.7977 (p0) REVERT: D 41 LYS cc_start: 0.5687 (OUTLIER) cc_final: 0.4620 (pmmt) REVERT: D 48 LYS cc_start: 0.8830 (mttt) cc_final: 0.7245 (pmtt) REVERT: D 50 GLU cc_start: 0.8399 (mp0) cc_final: 0.8087 (mp0) REVERT: D 74 GLU cc_start: 0.3883 (mm-30) cc_final: 0.3638 (tp30) REVERT: F 34 ASP cc_start: 0.9027 (t0) cc_final: 0.8795 (t0) REVERT: F 36 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7860 (tm-30) REVERT: F 38 ASP cc_start: 0.8492 (p0) cc_final: 0.8265 (p0) REVERT: F 53 ASP cc_start: 0.8797 (t0) cc_final: 0.8509 (t0) REVERT: F 73 THR cc_start: 0.9440 (m) cc_final: 0.9119 (t) REVERT: H 36 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7278 (tm-30) REVERT: H 38 ASP cc_start: 0.8500 (p0) cc_final: 0.7422 (p0) REVERT: H 53 ASP cc_start: 0.8741 (t0) cc_final: 0.8420 (t0) REVERT: I 33 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8686 (t) REVERT: I 48 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4061 (mmpt) REVERT: J 27 MET cc_start: 0.7395 (ttt) cc_final: 0.6703 (ttt) REVERT: J 34 ASP cc_start: 0.9217 (t0) cc_final: 0.8957 (t0) REVERT: J 36 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7918 (tm-30) REVERT: J 38 ASP cc_start: 0.8451 (p0) cc_final: 0.7838 (p0) REVERT: J 48 LYS cc_start: 0.8662 (mttt) cc_final: 0.7926 (mmpt) REVERT: J 53 ASP cc_start: 0.8876 (t0) cc_final: 0.8263 (t0) REVERT: J 75 LYS cc_start: 0.4771 (mmpt) cc_final: 0.4525 (mmmt) REVERT: K 33 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8721 (t) REVERT: K 38 ASP cc_start: 0.8765 (p0) cc_final: 0.7689 (p0) REVERT: K 48 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.3914 (mmpt) REVERT: L 27 MET cc_start: 0.7432 (ttt) cc_final: 0.6723 (ttt) REVERT: L 34 ASP cc_start: 0.9116 (t0) cc_final: 0.8899 (t0) REVERT: L 36 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7553 (tm-30) REVERT: L 38 ASP cc_start: 0.8336 (p0) cc_final: 0.7441 (p0) REVERT: L 48 LYS cc_start: 0.8676 (mttt) cc_final: 0.7939 (mmpt) REVERT: L 53 ASP cc_start: 0.8894 (t0) cc_final: 0.8351 (t0) outliers start: 42 outliers final: 12 residues processed: 338 average time/residue: 0.5011 time to fit residues: 177.3295 Evaluate side-chains 313 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 295 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 48 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.103780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.098017 restraints weight = 21278.536| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.70 r_work: 0.4034 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6696 Z= 0.186 Angle : 0.777 10.404 9060 Z= 0.392 Chirality : 0.046 0.177 912 Planarity : 0.004 0.032 1164 Dihedral : 5.014 17.480 840 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.74 % Allowed : 25.96 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.19), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 81 TYR 0.007 0.001 TYR D 63 PHE 0.008 0.001 PHE F 70 TRP 0.001 0.000 TRP I 60 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6684) covalent geometry : angle 0.77795 ( 9036) SS BOND : bond 0.00149 ( 12) SS BOND : angle 0.25379 ( 24) hydrogen bonds : bond 0.03926 ( 93) hydrogen bonds : angle 6.85409 ( 279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.5133 (pm20) cc_final: 0.4749 (pm20) REVERT: A 45 ARG cc_start: 0.9108 (mtt180) cc_final: 0.7209 (tmm160) REVERT: A 69 GLU cc_start: 0.4244 (pm20) cc_final: 0.3931 (pm20) REVERT: A 74 GLU cc_start: 0.3601 (tp30) cc_final: 0.3290 (tp30) REVERT: B 35 ILE cc_start: 0.9369 (mt) cc_final: 0.9124 (mp) REVERT: B 36 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 38 ASP cc_start: 0.8489 (p0) cc_final: 0.8163 (p0) REVERT: B 41 LYS cc_start: 0.5199 (OUTLIER) cc_final: 0.3644 (mppt) REVERT: B 47 GLU cc_start: 0.5482 (pm20) cc_final: 0.5167 (pm20) REVERT: B 48 LYS cc_start: 0.8705 (mttt) cc_final: 0.7355 (pmtt) REVERT: B 50 GLU cc_start: 0.8357 (mp0) cc_final: 0.8026 (mp0) REVERT: B 77 GLU cc_start: 0.3765 (pm20) cc_final: 0.3540 (pm20) REVERT: C 36 GLU cc_start: 0.5028 (pm20) cc_final: 0.4499 (pm20) REVERT: C 44 GLU cc_start: 0.8804 (tt0) cc_final: 0.8374 (tt0) REVERT: C 45 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7104 (tmm160) REVERT: C 69 GLU cc_start: 0.4351 (pm20) cc_final: 0.4121 (pm20) REVERT: D 36 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7440 (tm-30) REVERT: D 38 ASP cc_start: 0.8540 (p0) cc_final: 0.7943 (p0) REVERT: D 41 LYS cc_start: 0.5240 (OUTLIER) cc_final: 0.3724 (mppt) REVERT: D 47 GLU cc_start: 0.5511 (pm20) cc_final: 0.4854 (pm20) REVERT: D 48 LYS cc_start: 0.8607 (mttt) cc_final: 0.7132 (pmtt) REVERT: D 50 GLU cc_start: 0.8317 (mp0) cc_final: 0.7927 (mp0) REVERT: E 38 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8343 (t0) REVERT: E 44 GLU cc_start: 0.8823 (tt0) cc_final: 0.8555 (tt0) REVERT: E 48 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8419 (mtpm) REVERT: E 50 GLU cc_start: 0.8508 (mp0) cc_final: 0.8303 (mp0) REVERT: F 34 ASP cc_start: 0.9108 (t0) cc_final: 0.8834 (t0) REVERT: F 36 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 38 ASP cc_start: 0.8366 (p0) cc_final: 0.7425 (p0) REVERT: F 41 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8743 (ttmm) REVERT: F 47 GLU cc_start: 0.8663 (tp30) cc_final: 0.8357 (tp30) REVERT: F 50 GLU cc_start: 0.8476 (mp0) cc_final: 0.8040 (mp0) REVERT: F 53 ASP cc_start: 0.8850 (t0) cc_final: 0.8480 (t0) REVERT: F 73 THR cc_start: 0.9443 (m) cc_final: 0.9090 (t) REVERT: G 48 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8616 (mtpp) REVERT: G 74 GLU cc_start: 0.8699 (pm20) cc_final: 0.8455 (pm20) REVERT: G 75 LYS cc_start: 0.8515 (mppt) cc_final: 0.8219 (tptp) REVERT: H 34 ASP cc_start: 0.9091 (t0) cc_final: 0.8789 (t0) REVERT: H 36 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7404 (tm-30) REVERT: H 38 ASP cc_start: 0.8511 (p0) cc_final: 0.7403 (p0) REVERT: H 47 GLU cc_start: 0.8608 (tp30) cc_final: 0.8378 (tp30) REVERT: H 50 GLU cc_start: 0.8667 (mp0) cc_final: 0.7963 (mp0) REVERT: H 53 ASP cc_start: 0.8845 (t0) cc_final: 0.8457 (t0) REVERT: I 38 ASP cc_start: 0.8831 (p0) cc_final: 0.7790 (p0) REVERT: I 44 GLU cc_start: 0.8708 (tt0) cc_final: 0.7970 (tm-30) REVERT: I 47 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: I 48 LYS cc_start: 0.5233 (OUTLIER) cc_final: 0.3963 (mmpt) REVERT: I 50 GLU cc_start: 0.8335 (mp0) cc_final: 0.8107 (mp0) REVERT: J 27 MET cc_start: 0.7401 (ttt) cc_final: 0.6724 (ttt) REVERT: J 34 ASP cc_start: 0.9205 (t0) cc_final: 0.8960 (t0) REVERT: J 36 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7946 (tm-30) REVERT: J 38 ASP cc_start: 0.8570 (p0) cc_final: 0.7818 (p0) REVERT: J 48 LYS cc_start: 0.8738 (mttt) cc_final: 0.7988 (mmpt) REVERT: J 53 ASP cc_start: 0.8850 (t0) cc_final: 0.8228 (t0) REVERT: J 76 ASP cc_start: 0.7695 (m-30) cc_final: 0.6375 (m-30) REVERT: K 44 GLU cc_start: 0.8715 (tt0) cc_final: 0.7996 (tm-30) REVERT: K 48 LYS cc_start: 0.4761 (OUTLIER) cc_final: 0.3625 (mmpt) REVERT: L 27 MET cc_start: 0.7409 (ttt) cc_final: 0.6727 (ttt) REVERT: L 34 ASP cc_start: 0.9180 (t0) cc_final: 0.8955 (t0) REVERT: L 36 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7852 (tm-30) REVERT: L 38 ASP cc_start: 0.8423 (p0) cc_final: 0.7718 (p0) REVERT: L 48 LYS cc_start: 0.8747 (mttt) cc_final: 0.7985 (mmpt) REVERT: L 53 ASP cc_start: 0.8892 (t0) cc_final: 0.8324 (t0) outliers start: 42 outliers final: 16 residues processed: 337 average time/residue: 0.5133 time to fit residues: 180.9245 Evaluate side-chains 318 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** 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 = 0.4244 r_free = 0.4244 target = 0.102669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.096864 restraints weight = 21386.776| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 3.71 r_work: 0.4017 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6696 Z= 0.184 Angle : 0.788 13.407 9060 Z= 0.392 Chirality : 0.046 0.159 912 Planarity : 0.004 0.035 1164 Dihedral : 5.054 18.300 840 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.60 % Allowed : 28.55 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 81 TYR 0.022 0.001 TYR D 66 PHE 0.015 0.001 PHE J 22 TRP 0.002 0.001 TRP G 60 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 6684) covalent geometry : angle 0.78907 ( 9036) SS BOND : bond 0.00172 ( 12) SS BOND : angle 0.22349 ( 24) hydrogen bonds : bond 0.03648 ( 93) hydrogen bonds : angle 6.54987 ( 279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 314 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.5146 (pm20) cc_final: 0.4549 (pm20) REVERT: A 39 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9160 (tt) REVERT: A 44 GLU cc_start: 0.8855 (tt0) cc_final: 0.8191 (tt0) REVERT: A 45 ARG cc_start: 0.9057 (mtt180) cc_final: 0.7079 (tmm160) REVERT: A 69 GLU cc_start: 0.4376 (pm20) cc_final: 0.4067 (pm20) REVERT: B 41 LYS cc_start: 0.5156 (pmtt) cc_final: 0.3656 (mppt) REVERT: B 48 LYS cc_start: 0.8614 (mttt) cc_final: 0.7403 (pmtt) REVERT: B 50 GLU cc_start: 0.8375 (mp0) cc_final: 0.8069 (mp0) REVERT: C 36 GLU cc_start: 0.4971 (pm20) cc_final: 0.4319 (pm20) REVERT: C 44 GLU cc_start: 0.8872 (tt0) cc_final: 0.8620 (tt0) REVERT: C 45 ARG cc_start: 0.9050 (mtt180) cc_final: 0.7114 (tmm160) REVERT: D 36 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 38 ASP cc_start: 0.8491 (p0) cc_final: 0.7845 (p0) REVERT: D 41 LYS cc_start: 0.5422 (pmtt) cc_final: 0.3882 (mppt) REVERT: D 48 LYS cc_start: 0.8536 (mttt) cc_final: 0.7241 (pmtt) REVERT: D 50 GLU cc_start: 0.8394 (mp0) cc_final: 0.7992 (mp0) REVERT: E 45 ARG cc_start: 0.9569 (mtt-85) cc_final: 0.9330 (mtt-85) REVERT: E 48 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8755 (mtpm) REVERT: E 50 GLU cc_start: 0.8554 (mp0) cc_final: 0.8173 (mp0) REVERT: F 34 ASP cc_start: 0.9094 (t0) cc_final: 0.8814 (t0) REVERT: F 36 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7534 (tm-30) REVERT: F 38 ASP cc_start: 0.8296 (p0) cc_final: 0.7472 (p0) REVERT: F 41 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8753 (ttmm) REVERT: F 47 GLU cc_start: 0.8599 (tp30) cc_final: 0.8278 (tp30) REVERT: F 48 LYS cc_start: 0.8707 (mttt) cc_final: 0.8450 (ttmt) REVERT: F 53 ASP cc_start: 0.8904 (t0) cc_final: 0.8547 (t0) REVERT: F 73 THR cc_start: 0.9404 (m) cc_final: 0.9073 (t) REVERT: G 47 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8477 (tm-30) REVERT: G 48 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8797 (ptpp) REVERT: G 50 GLU cc_start: 0.9007 (mp0) cc_final: 0.8724 (mp0) REVERT: H 34 ASP cc_start: 0.9132 (t0) cc_final: 0.8847 (t0) REVERT: H 36 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7502 (tm-30) REVERT: H 38 ASP cc_start: 0.8482 (p0) cc_final: 0.7458 (p0) REVERT: H 47 GLU cc_start: 0.8531 (tp30) cc_final: 0.8315 (tp30) REVERT: H 50 GLU cc_start: 0.8618 (mp0) cc_final: 0.7894 (mp0) REVERT: H 53 ASP cc_start: 0.8864 (t0) cc_final: 0.8436 (t0) REVERT: I 38 ASP cc_start: 0.8773 (p0) cc_final: 0.8008 (p0) REVERT: I 44 GLU cc_start: 0.8713 (tt0) cc_final: 0.8051 (tm-30) REVERT: I 48 LYS cc_start: 0.5058 (OUTLIER) cc_final: 0.3690 (mmpt) REVERT: J 27 MET cc_start: 0.7326 (ttt) cc_final: 0.6652 (ttt) REVERT: J 34 ASP cc_start: 0.9168 (t0) cc_final: 0.8925 (t0) REVERT: J 36 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7939 (tm-30) REVERT: J 38 ASP cc_start: 0.8598 (p0) cc_final: 0.7806 (p0) REVERT: J 44 GLU cc_start: 0.9008 (tt0) cc_final: 0.8707 (tt0) REVERT: J 48 LYS cc_start: 0.8799 (mttt) cc_final: 0.8007 (mmpt) REVERT: J 50 GLU cc_start: 0.8220 (mp0) cc_final: 0.7957 (mp0) REVERT: J 53 ASP cc_start: 0.8877 (t0) cc_final: 0.8278 (t0) REVERT: J 75 LYS cc_start: 0.5412 (OUTLIER) cc_final: 0.5096 (mmpt) REVERT: K 44 GLU cc_start: 0.8726 (tt0) cc_final: 0.8111 (tm-30) REVERT: K 48 LYS cc_start: 0.4824 (OUTLIER) cc_final: 0.3611 (mmpt) REVERT: K 50 GLU cc_start: 0.8382 (mp0) cc_final: 0.8144 (mp0) REVERT: L 27 MET cc_start: 0.7308 (ttt) cc_final: 0.6643 (ttt) REVERT: L 34 ASP cc_start: 0.9195 (t0) cc_final: 0.8958 (t0) REVERT: L 36 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8003 (tm-30) REVERT: L 38 ASP cc_start: 0.8532 (p0) cc_final: 0.7952 (p0) REVERT: L 44 GLU cc_start: 0.8830 (tt0) cc_final: 0.8479 (tt0) REVERT: L 48 LYS cc_start: 0.8796 (mttt) cc_final: 0.8015 (mmpt) REVERT: L 50 GLU cc_start: 0.8266 (mp0) cc_final: 0.8015 (mp0) REVERT: L 53 ASP cc_start: 0.8901 (t0) cc_final: 0.8374 (t0) REVERT: L 75 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5454 (mmmt) outliers start: 41 outliers final: 23 residues processed: 327 average time/residue: 0.5164 time to fit residues: 176.4811 Evaluate side-chains 313 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 75 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.102202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.096332 restraints weight = 21996.695| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.76 r_work: 0.4013 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6696 Z= 0.197 Angle : 0.822 12.939 9060 Z= 0.409 Chirality : 0.046 0.164 912 Planarity : 0.003 0.038 1164 Dihedral : 5.183 18.896 840 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.74 % Allowed : 28.55 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 81 TYR 0.011 0.001 TYR E 66 PHE 0.009 0.002 PHE G 22 TRP 0.002 0.000 TRP C 60 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6684) covalent geometry : angle 0.82334 ( 9036) SS BOND : bond 0.00201 ( 12) SS BOND : angle 0.26689 ( 24) hydrogen bonds : bond 0.03527 ( 93) hydrogen bonds : angle 6.49421 ( 279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8837 (tt0) cc_final: 0.8403 (tt0) REVERT: A 45 ARG cc_start: 0.9102 (mtt180) cc_final: 0.7187 (tmm160) REVERT: A 69 GLU cc_start: 0.4476 (pm20) cc_final: 0.4207 (pm20) REVERT: B 36 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7607 (tm-30) REVERT: B 38 ASP cc_start: 0.8501 (p0) cc_final: 0.8236 (p0) REVERT: B 41 LYS cc_start: 0.5471 (OUTLIER) cc_final: 0.3733 (pttm) REVERT: B 48 LYS cc_start: 0.8526 (mttt) cc_final: 0.7310 (pmtt) REVERT: B 50 GLU cc_start: 0.8463 (mp0) cc_final: 0.8124 (mp0) REVERT: C 44 GLU cc_start: 0.8820 (tt0) cc_final: 0.8584 (tt0) REVERT: C 45 ARG cc_start: 0.9036 (mtt180) cc_final: 0.7171 (tmm160) REVERT: D 36 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7458 (tm-30) REVERT: D 38 ASP cc_start: 0.8533 (p0) cc_final: 0.7985 (p0) REVERT: D 41 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.3663 (pttm) REVERT: D 48 LYS cc_start: 0.8391 (mttt) cc_final: 0.7077 (pmtt) REVERT: D 50 GLU cc_start: 0.8426 (mp0) cc_final: 0.8012 (mp0) REVERT: E 48 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8654 (mtpm) REVERT: E 50 GLU cc_start: 0.8561 (mp0) cc_final: 0.8216 (mp0) REVERT: E 58 LYS cc_start: 0.9286 (mmtp) cc_final: 0.9044 (mmtt) REVERT: E 74 GLU cc_start: 0.8469 (mp0) cc_final: 0.8186 (mp0) REVERT: F 34 ASP cc_start: 0.9124 (t0) cc_final: 0.8842 (t0) REVERT: F 36 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7655 (tm-30) REVERT: F 38 ASP cc_start: 0.8344 (p0) cc_final: 0.7750 (p0) REVERT: F 48 LYS cc_start: 0.8724 (mttt) cc_final: 0.8467 (ttmt) REVERT: F 53 ASP cc_start: 0.8894 (t0) cc_final: 0.8537 (t0) REVERT: F 73 THR cc_start: 0.9346 (m) cc_final: 0.9057 (t) REVERT: G 48 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8757 (mtpm) REVERT: G 50 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: G 58 LYS cc_start: 0.9247 (mmtp) cc_final: 0.9011 (mmtt) REVERT: G 74 GLU cc_start: 0.8658 (pm20) cc_final: 0.8433 (pm20) REVERT: H 34 ASP cc_start: 0.9122 (t0) cc_final: 0.8827 (t0) REVERT: H 36 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7476 (tm-30) REVERT: H 38 ASP cc_start: 0.8353 (p0) cc_final: 0.7284 (p0) REVERT: H 47 GLU cc_start: 0.8468 (tp30) cc_final: 0.8222 (tp30) REVERT: H 50 GLU cc_start: 0.8636 (mp0) cc_final: 0.7835 (mp0) REVERT: H 53 ASP cc_start: 0.8898 (t0) cc_final: 0.8500 (t0) REVERT: I 44 GLU cc_start: 0.8655 (tt0) cc_final: 0.8110 (tm-30) REVERT: I 50 GLU cc_start: 0.8354 (mp0) cc_final: 0.8025 (mp0) REVERT: I 74 GLU cc_start: 0.8544 (pm20) cc_final: 0.8308 (mp0) REVERT: J 27 MET cc_start: 0.7313 (ttt) cc_final: 0.6638 (ttt) REVERT: J 34 ASP cc_start: 0.9202 (t0) cc_final: 0.8962 (t0) REVERT: J 36 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7980 (tm-30) REVERT: J 38 ASP cc_start: 0.8538 (p0) cc_final: 0.7896 (p0) REVERT: J 44 GLU cc_start: 0.8971 (tt0) cc_final: 0.8707 (tt0) REVERT: J 48 LYS cc_start: 0.8869 (mttt) cc_final: 0.8014 (mmpt) REVERT: J 50 GLU cc_start: 0.8205 (mp0) cc_final: 0.7970 (mp0) REVERT: J 53 ASP cc_start: 0.8904 (t0) cc_final: 0.8313 (t0) REVERT: K 44 GLU cc_start: 0.8729 (tt0) cc_final: 0.8197 (tm-30) REVERT: K 48 LYS cc_start: 0.4604 (OUTLIER) cc_final: 0.4385 (mmpt) REVERT: L 27 MET cc_start: 0.7271 (ttt) cc_final: 0.6602 (ttt) REVERT: L 34 ASP cc_start: 0.9194 (t0) cc_final: 0.8968 (t0) REVERT: L 36 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7974 (tm-30) REVERT: L 38 ASP cc_start: 0.8408 (p0) cc_final: 0.7802 (p0) REVERT: L 48 LYS cc_start: 0.8820 (mttt) cc_final: 0.8057 (mmpt) REVERT: L 50 GLU cc_start: 0.8171 (mp0) cc_final: 0.7936 (mp0) REVERT: L 53 ASP cc_start: 0.8866 (t0) cc_final: 0.8325 (t0) outliers start: 42 outliers final: 23 residues processed: 318 average time/residue: 0.5645 time to fit residues: 187.5314 Evaluate side-chains 310 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 48 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.100093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.094058 restraints weight = 22602.897| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.83 r_work: 0.3971 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6696 Z= 0.304 Angle : 0.910 12.794 9060 Z= 0.460 Chirality : 0.049 0.280 912 Planarity : 0.004 0.043 1164 Dihedral : 5.636 18.744 840 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.87 % Allowed : 30.46 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 81 TYR 0.020 0.002 TYR C 66 PHE 0.023 0.002 PHE A 22 TRP 0.004 0.001 TRP E 60 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 6684) covalent geometry : angle 0.91099 ( 9036) SS BOND : bond 0.00319 ( 12) SS BOND : angle 0.31472 ( 24) hydrogen bonds : bond 0.04572 ( 93) hydrogen bonds : angle 6.91883 ( 279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7760 (ttt) cc_final: 0.7545 (ttt) REVERT: A 44 GLU cc_start: 0.8889 (tt0) cc_final: 0.8420 (tt0) REVERT: A 45 ARG cc_start: 0.9120 (mtt180) cc_final: 0.6907 (tmm160) REVERT: B 36 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 38 ASP cc_start: 0.8577 (p0) cc_final: 0.8165 (p0) REVERT: B 41 LYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4263 (pttm) REVERT: B 48 LYS cc_start: 0.8514 (mttt) cc_final: 0.7185 (pmtt) REVERT: B 50 GLU cc_start: 0.8483 (mp0) cc_final: 0.8174 (mp0) REVERT: C 44 GLU cc_start: 0.8935 (tt0) cc_final: 0.8559 (tt0) REVERT: C 45 ARG cc_start: 0.9061 (mtt180) cc_final: 0.6981 (tmm160) REVERT: D 36 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7639 (tm-30) REVERT: D 38 ASP cc_start: 0.8501 (p0) cc_final: 0.7966 (p0) REVERT: D 48 LYS cc_start: 0.8495 (mttt) cc_final: 0.7116 (pmtt) REVERT: D 50 GLU cc_start: 0.8455 (mp0) cc_final: 0.8169 (mp0) REVERT: E 44 GLU cc_start: 0.8805 (tt0) cc_final: 0.8592 (tt0) REVERT: E 58 LYS cc_start: 0.9340 (mmtp) cc_final: 0.9119 (mmtt) REVERT: F 34 ASP cc_start: 0.9115 (t0) cc_final: 0.8742 (t0) REVERT: F 36 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 38 ASP cc_start: 0.8367 (p0) cc_final: 0.7948 (p0) REVERT: F 41 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8830 (ttmm) REVERT: F 47 GLU cc_start: 0.8592 (tp30) cc_final: 0.8103 (tp30) REVERT: F 48 LYS cc_start: 0.8773 (mttt) cc_final: 0.8444 (mtpt) REVERT: F 53 ASP cc_start: 0.8868 (t0) cc_final: 0.8513 (t0) REVERT: F 73 THR cc_start: 0.9356 (m) cc_final: 0.9011 (t) REVERT: G 58 LYS cc_start: 0.9319 (mmtp) cc_final: 0.9076 (mmtt) REVERT: H 34 ASP cc_start: 0.9098 (t0) cc_final: 0.8769 (t0) REVERT: H 36 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7681 (tm-30) REVERT: H 38 ASP cc_start: 0.8483 (p0) cc_final: 0.7386 (p0) REVERT: H 47 GLU cc_start: 0.8517 (tp30) cc_final: 0.8257 (tp30) REVERT: H 50 GLU cc_start: 0.8667 (mp0) cc_final: 0.8325 (mp0) REVERT: H 53 ASP cc_start: 0.8829 (t0) cc_final: 0.8510 (t0) REVERT: I 44 GLU cc_start: 0.8659 (tt0) cc_final: 0.8184 (tm-30) REVERT: I 48 LYS cc_start: 0.4231 (OUTLIER) cc_final: 0.2989 (mmpt) REVERT: J 27 MET cc_start: 0.7208 (ttt) cc_final: 0.6587 (ttt) REVERT: J 34 ASP cc_start: 0.9198 (t0) cc_final: 0.8952 (t0) REVERT: J 36 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8015 (tm-30) REVERT: J 38 ASP cc_start: 0.8597 (p0) cc_final: 0.7953 (p0) REVERT: J 48 LYS cc_start: 0.8805 (mttt) cc_final: 0.7909 (mmpt) REVERT: J 53 ASP cc_start: 0.8809 (t0) cc_final: 0.8208 (t0) REVERT: K 44 GLU cc_start: 0.8718 (tt0) cc_final: 0.8212 (tm-30) REVERT: K 48 LYS cc_start: 0.4261 (OUTLIER) cc_final: 0.2923 (mmpt) REVERT: K 50 GLU cc_start: 0.8698 (mp0) cc_final: 0.8027 (mp0) REVERT: L 27 MET cc_start: 0.7175 (ttt) cc_final: 0.6544 (ttt) REVERT: L 34 ASP cc_start: 0.9168 (t0) cc_final: 0.8944 (t0) REVERT: L 36 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7959 (tm-30) REVERT: L 38 ASP cc_start: 0.8614 (p0) cc_final: 0.7988 (p0) REVERT: L 53 ASP cc_start: 0.8807 (t0) cc_final: 0.8231 (t0) outliers start: 43 outliers final: 26 residues processed: 296 average time/residue: 0.5918 time to fit residues: 182.7306 Evaluate side-chains 294 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 HIS ** K 31 HIS ** 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 = 0.4242 r_free = 0.4242 target = 0.102039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.096171 restraints weight = 21932.785| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.74 r_work: 0.4015 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6696 Z= 0.196 Angle : 0.931 15.703 9060 Z= 0.449 Chirality : 0.047 0.186 912 Planarity : 0.004 0.071 1164 Dihedral : 5.568 21.777 840 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.92 % Allowed : 31.56 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 81 TYR 0.012 0.001 TYR G 66 PHE 0.026 0.001 PHE C 22 TRP 0.004 0.000 TRP J 60 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 6684) covalent geometry : angle 0.93214 ( 9036) SS BOND : bond 0.00227 ( 12) SS BOND : angle 0.38193 ( 24) hydrogen bonds : bond 0.03375 ( 93) hydrogen bonds : angle 6.42283 ( 279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8848 (tt0) cc_final: 0.8447 (tt0) REVERT: A 45 ARG cc_start: 0.9066 (mtt180) cc_final: 0.7041 (tmm160) REVERT: A 69 GLU cc_start: 0.4239 (pm20) cc_final: 0.3775 (pm20) REVERT: B 36 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 38 ASP cc_start: 0.8506 (p0) cc_final: 0.8098 (OUTLIER) REVERT: B 41 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4514 (pttm) REVERT: B 48 LYS cc_start: 0.8374 (mttt) cc_final: 0.7027 (pmtt) REVERT: B 50 GLU cc_start: 0.8455 (mp0) cc_final: 0.8086 (mp0) REVERT: C 44 GLU cc_start: 0.8835 (tt0) cc_final: 0.8569 (tt0) REVERT: C 45 ARG cc_start: 0.9015 (mtt180) cc_final: 0.7316 (ppt170) REVERT: D 36 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 38 ASP cc_start: 0.8514 (p0) cc_final: 0.7975 (p0) REVERT: D 41 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4493 (pttm) REVERT: D 58 LYS cc_start: 0.4677 (OUTLIER) cc_final: 0.3799 (pmtt) REVERT: E 44 GLU cc_start: 0.8847 (tt0) cc_final: 0.8479 (tt0) REVERT: E 47 GLU cc_start: 0.8786 (tp30) cc_final: 0.8130 (tt0) REVERT: E 48 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8612 (mtpm) REVERT: E 50 GLU cc_start: 0.8614 (mp0) cc_final: 0.8396 (mp0) REVERT: F 34 ASP cc_start: 0.9111 (t0) cc_final: 0.8766 (t0) REVERT: F 36 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7707 (tm-30) REVERT: F 38 ASP cc_start: 0.8282 (p0) cc_final: 0.7694 (p0) REVERT: F 48 LYS cc_start: 0.8700 (mttt) cc_final: 0.8460 (mtpt) REVERT: F 50 GLU cc_start: 0.8568 (mp0) cc_final: 0.7916 (mp0) REVERT: F 53 ASP cc_start: 0.8902 (t0) cc_final: 0.8505 (t0) REVERT: F 73 THR cc_start: 0.9305 (m) cc_final: 0.8986 (t) REVERT: F 77 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8725 (tm-30) REVERT: G 48 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8654 (mtpm) REVERT: G 50 GLU cc_start: 0.9043 (mp0) cc_final: 0.8289 (mp0) REVERT: G 58 LYS cc_start: 0.9186 (mmtp) cc_final: 0.8945 (mmtt) REVERT: H 34 ASP cc_start: 0.9138 (t0) cc_final: 0.8849 (t0) REVERT: H 36 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7453 (tm-30) REVERT: H 38 ASP cc_start: 0.8325 (p0) cc_final: 0.7126 (p0) REVERT: H 41 LYS cc_start: 0.9031 (ttmp) cc_final: 0.8517 (ttmm) REVERT: H 44 GLU cc_start: 0.8741 (tt0) cc_final: 0.8255 (pm20) REVERT: H 47 GLU cc_start: 0.8484 (tp30) cc_final: 0.8204 (tp30) REVERT: H 50 GLU cc_start: 0.8605 (mp0) cc_final: 0.7718 (mp0) REVERT: H 53 ASP cc_start: 0.8865 (t0) cc_final: 0.8473 (t0) REVERT: I 44 GLU cc_start: 0.8728 (tt0) cc_final: 0.8225 (tm-30) REVERT: I 74 GLU cc_start: 0.8522 (pm20) cc_final: 0.8271 (mp0) REVERT: J 27 MET cc_start: 0.7215 (ttt) cc_final: 0.6591 (ttt) REVERT: J 34 ASP cc_start: 0.9174 (t0) cc_final: 0.8921 (t0) REVERT: J 36 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7846 (tm-30) REVERT: J 38 ASP cc_start: 0.8595 (p0) cc_final: 0.7725 (p0) REVERT: J 48 LYS cc_start: 0.8870 (mttt) cc_final: 0.8058 (mmpt) REVERT: J 50 GLU cc_start: 0.8291 (mp0) cc_final: 0.7978 (mp0) REVERT: J 53 ASP cc_start: 0.8901 (t0) cc_final: 0.8329 (t0) REVERT: K 36 GLU cc_start: 0.8652 (tt0) cc_final: 0.8419 (tm-30) REVERT: K 44 GLU cc_start: 0.8631 (tt0) cc_final: 0.8173 (tm-30) REVERT: K 48 LYS cc_start: 0.4292 (OUTLIER) cc_final: 0.3060 (mmpt) REVERT: K 50 GLU cc_start: 0.8705 (mp0) cc_final: 0.8094 (mp0) REVERT: L 27 MET cc_start: 0.7190 (ttt) cc_final: 0.6553 (ttt) REVERT: L 34 ASP cc_start: 0.9174 (t0) cc_final: 0.8945 (t0) REVERT: L 36 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8027 (tm-30) REVERT: L 38 ASP cc_start: 0.8620 (p0) cc_final: 0.7963 (p0) REVERT: L 48 LYS cc_start: 0.8939 (mtmt) cc_final: 0.7812 (mmpt) REVERT: L 53 ASP cc_start: 0.8836 (t0) cc_final: 0.8287 (t0) outliers start: 36 outliers final: 24 residues processed: 303 average time/residue: 0.5782 time to fit residues: 182.9624 Evaluate side-chains 305 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 40.0000 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.102581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.096437 restraints weight = 21824.910| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.84 r_work: 0.4019 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6696 Z= 0.198 Angle : 0.958 15.237 9060 Z= 0.460 Chirality : 0.048 0.186 912 Planarity : 0.004 0.048 1164 Dihedral : 5.557 22.422 840 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.10 % Allowed : 34.15 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 81 TYR 0.024 0.001 TYR C 66 PHE 0.025 0.002 PHE A 22 TRP 0.003 0.000 TRP L 60 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 6684) covalent geometry : angle 0.95953 ( 9036) SS BOND : bond 0.00209 ( 12) SS BOND : angle 0.36791 ( 24) hydrogen bonds : bond 0.03500 ( 93) hydrogen bonds : angle 6.36531 ( 279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8838 (tt0) cc_final: 0.8481 (tt0) REVERT: A 45 ARG cc_start: 0.9118 (mtt180) cc_final: 0.7138 (tmm160) REVERT: A 69 GLU cc_start: 0.4190 (pm20) cc_final: 0.3780 (pm20) REVERT: B 36 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 38 ASP cc_start: 0.8485 (p0) cc_final: 0.8101 (p0) REVERT: B 41 LYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4384 (pttm) REVERT: B 48 LYS cc_start: 0.8310 (mttt) cc_final: 0.6986 (pmtt) REVERT: B 50 GLU cc_start: 0.8449 (mp0) cc_final: 0.8017 (mp0) REVERT: C 44 GLU cc_start: 0.8818 (tt0) cc_final: 0.8607 (tt0) REVERT: C 45 ARG cc_start: 0.9015 (mtt180) cc_final: 0.7118 (tmm160) REVERT: C 69 GLU cc_start: 0.3912 (pm20) cc_final: 0.3500 (pm20) REVERT: D 36 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7550 (tm-30) REVERT: D 38 ASP cc_start: 0.8426 (p0) cc_final: 0.7926 (p0) REVERT: D 41 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4482 (pttm) REVERT: E 44 GLU cc_start: 0.8755 (tt0) cc_final: 0.8438 (tt0) REVERT: E 47 GLU cc_start: 0.8804 (tp30) cc_final: 0.8170 (tt0) REVERT: E 48 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8400 (mtpt) REVERT: E 59 ASP cc_start: 0.9028 (m-30) cc_final: 0.8809 (m-30) REVERT: F 34 ASP cc_start: 0.9116 (t0) cc_final: 0.8795 (t0) REVERT: F 36 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7646 (tm-30) REVERT: F 38 ASP cc_start: 0.8314 (p0) cc_final: 0.7439 (p0) REVERT: F 44 GLU cc_start: 0.8899 (tt0) cc_final: 0.8679 (tm-30) REVERT: F 48 LYS cc_start: 0.8723 (mttt) cc_final: 0.8430 (mtpt) REVERT: F 50 GLU cc_start: 0.8617 (mp0) cc_final: 0.7859 (mp0) REVERT: F 53 ASP cc_start: 0.8895 (t0) cc_final: 0.8520 (t0) REVERT: F 73 THR cc_start: 0.9326 (m) cc_final: 0.8998 (t) REVERT: G 44 GLU cc_start: 0.8911 (tt0) cc_final: 0.8680 (tt0) REVERT: G 48 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8683 (mtpm) REVERT: G 50 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: G 74 GLU cc_start: 0.8420 (mp0) cc_final: 0.7907 (mm-30) REVERT: H 34 ASP cc_start: 0.9122 (t0) cc_final: 0.8825 (t0) REVERT: H 36 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7435 (tm-30) REVERT: H 38 ASP cc_start: 0.8105 (p0) cc_final: 0.7034 (p0) REVERT: H 44 GLU cc_start: 0.8775 (tt0) cc_final: 0.8256 (pm20) REVERT: H 47 GLU cc_start: 0.8544 (tp30) cc_final: 0.8244 (tp30) REVERT: H 50 GLU cc_start: 0.8594 (mp0) cc_final: 0.7927 (mp0) REVERT: H 53 ASP cc_start: 0.8847 (t0) cc_final: 0.8496 (t0) REVERT: I 44 GLU cc_start: 0.8742 (tt0) cc_final: 0.8258 (tm-30) REVERT: I 47 GLU cc_start: 0.8269 (tp30) cc_final: 0.7961 (tp30) REVERT: I 50 GLU cc_start: 0.8675 (mp0) cc_final: 0.8415 (mp0) REVERT: J 27 MET cc_start: 0.7165 (ttt) cc_final: 0.6552 (ttt) REVERT: J 34 ASP cc_start: 0.9193 (t0) cc_final: 0.8945 (t0) REVERT: J 36 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7911 (tm-30) REVERT: J 38 ASP cc_start: 0.8632 (p0) cc_final: 0.7848 (p0) REVERT: J 48 LYS cc_start: 0.8871 (mttt) cc_final: 0.8598 (mtpp) REVERT: J 50 GLU cc_start: 0.8323 (mp0) cc_final: 0.7654 (mp0) REVERT: J 53 ASP cc_start: 0.8870 (t0) cc_final: 0.8304 (t0) REVERT: K 44 GLU cc_start: 0.8639 (tt0) cc_final: 0.8152 (tm-30) REVERT: K 48 LYS cc_start: 0.4525 (OUTLIER) cc_final: 0.3232 (mmpt) REVERT: K 50 GLU cc_start: 0.8649 (mp0) cc_final: 0.8020 (mp0) REVERT: L 27 MET cc_start: 0.7165 (ttt) cc_final: 0.6554 (ttt) REVERT: L 34 ASP cc_start: 0.9185 (t0) cc_final: 0.8958 (t0) REVERT: L 36 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7884 (tm-30) REVERT: L 38 ASP cc_start: 0.8491 (p0) cc_final: 0.7832 (p0) REVERT: L 48 LYS cc_start: 0.8949 (mtmt) cc_final: 0.7912 (mmpt) REVERT: L 50 GLU cc_start: 0.8316 (mp0) cc_final: 0.8081 (mp0) REVERT: L 53 ASP cc_start: 0.8841 (t0) cc_final: 0.8310 (t0) outliers start: 30 outliers final: 22 residues processed: 302 average time/residue: 0.5772 time to fit residues: 181.9991 Evaluate side-chains 304 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 34 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 48 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 0.0000 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 0.0370 chunk 17 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.104218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.098280 restraints weight = 21782.754| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.77 r_work: 0.4060 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6696 Z= 0.168 Angle : 1.008 17.275 9060 Z= 0.477 Chirality : 0.047 0.172 912 Planarity : 0.003 0.049 1164 Dihedral : 5.416 20.368 840 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.01 % Allowed : 35.38 % Favored : 61.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 81 TYR 0.011 0.001 TYR G 66 PHE 0.022 0.001 PHE C 22 TRP 0.004 0.000 TRP K 60 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6684) covalent geometry : angle 1.00912 ( 9036) SS BOND : bond 0.00142 ( 12) SS BOND : angle 0.42876 ( 24) hydrogen bonds : bond 0.02727 ( 93) hydrogen bonds : angle 6.06445 ( 279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 44 GLU cc_start: 0.8785 (tt0) cc_final: 0.8488 (tt0) REVERT: A 45 ARG cc_start: 0.9018 (mtt180) cc_final: 0.7153 (tmm160) REVERT: A 69 GLU cc_start: 0.4323 (pm20) cc_final: 0.4036 (pm20) REVERT: B 50 GLU cc_start: 0.8422 (mp0) cc_final: 0.8203 (mp0) REVERT: B 58 LYS cc_start: 0.5066 (OUTLIER) cc_final: 0.3779 (pmtt) REVERT: C 44 GLU cc_start: 0.8772 (tt0) cc_final: 0.8468 (tt0) REVERT: C 45 ARG cc_start: 0.8989 (mtt180) cc_final: 0.7318 (ppt170) REVERT: C 69 GLU cc_start: 0.4380 (pm20) cc_final: 0.4052 (pm20) REVERT: D 36 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 38 ASP cc_start: 0.8448 (p0) cc_final: 0.7931 (p0) REVERT: E 47 GLU cc_start: 0.8722 (tp30) cc_final: 0.8105 (tt0) REVERT: E 48 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8418 (mtpp) REVERT: E 74 GLU cc_start: 0.8521 (mp0) cc_final: 0.8315 (mp0) REVERT: F 34 ASP cc_start: 0.9117 (t0) cc_final: 0.8829 (t0) REVERT: F 36 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7545 (tm-30) REVERT: F 38 ASP cc_start: 0.8158 (p0) cc_final: 0.7343 (p0) REVERT: F 44 GLU cc_start: 0.8725 (tt0) cc_final: 0.8115 (tm-30) REVERT: F 48 LYS cc_start: 0.8690 (mttt) cc_final: 0.8370 (mtpt) REVERT: F 50 GLU cc_start: 0.8652 (mp0) cc_final: 0.8116 (mp0) REVERT: F 53 ASP cc_start: 0.8924 (t0) cc_final: 0.8541 (t0) REVERT: F 73 THR cc_start: 0.9310 (m) cc_final: 0.8961 (t) REVERT: G 44 GLU cc_start: 0.8914 (tt0) cc_final: 0.8659 (tt0) REVERT: G 48 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8534 (mtpp) REVERT: G 50 GLU cc_start: 0.9090 (mp0) cc_final: 0.8804 (mp0) REVERT: G 74 GLU cc_start: 0.8451 (mp0) cc_final: 0.7912 (mm-30) REVERT: H 34 ASP cc_start: 0.9108 (t0) cc_final: 0.8816 (t0) REVERT: H 36 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7485 (tm-30) REVERT: H 38 ASP cc_start: 0.8054 (p0) cc_final: 0.7048 (p0) REVERT: H 50 GLU cc_start: 0.8577 (mp0) cc_final: 0.7772 (mp0) REVERT: H 53 ASP cc_start: 0.8897 (t0) cc_final: 0.8502 (t0) REVERT: I 44 GLU cc_start: 0.8698 (tt0) cc_final: 0.8226 (tm-30) REVERT: I 48 LYS cc_start: 0.4268 (tptp) cc_final: 0.3823 (tptp) REVERT: J 27 MET cc_start: 0.7159 (ttt) cc_final: 0.6540 (ttt) REVERT: J 34 ASP cc_start: 0.9170 (t0) cc_final: 0.8939 (t0) REVERT: J 36 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7917 (tm-30) REVERT: J 38 ASP cc_start: 0.8589 (p0) cc_final: 0.7867 (p0) REVERT: J 44 GLU cc_start: 0.9117 (tt0) cc_final: 0.8772 (tt0) REVERT: J 48 LYS cc_start: 0.8862 (mttt) cc_final: 0.8651 (mtpt) REVERT: J 53 ASP cc_start: 0.8879 (t0) cc_final: 0.8291 (t0) REVERT: K 33 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8753 (t) REVERT: K 44 GLU cc_start: 0.8636 (tt0) cc_final: 0.8119 (tm-30) REVERT: K 48 LYS cc_start: 0.4715 (OUTLIER) cc_final: 0.4261 (tptp) REVERT: K 50 GLU cc_start: 0.8665 (mp0) cc_final: 0.7892 (mp0) REVERT: L 27 MET cc_start: 0.7108 (ttt) cc_final: 0.6504 (ttt) REVERT: L 34 ASP cc_start: 0.9183 (t0) cc_final: 0.8973 (t0) REVERT: L 36 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7989 (tm-30) REVERT: L 38 ASP cc_start: 0.8250 (p0) cc_final: 0.7632 (p0) REVERT: L 48 LYS cc_start: 0.8958 (mtmt) cc_final: 0.7808 (mmpt) REVERT: L 50 GLU cc_start: 0.8247 (mp0) cc_final: 0.7994 (mp0) REVERT: L 53 ASP cc_start: 0.8878 (t0) cc_final: 0.8366 (t0) outliers start: 22 outliers final: 15 residues processed: 309 average time/residue: 0.5524 time to fit residues: 178.4260 Evaluate side-chains 306 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 40.0000 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.103489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.097729 restraints weight = 21688.191| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 3.69 r_work: 0.4049 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6696 Z= 0.194 Angle : 1.070 15.466 9060 Z= 0.504 Chirality : 0.049 0.293 912 Planarity : 0.004 0.051 1164 Dihedral : 5.585 23.047 840 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.01 % Allowed : 36.75 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 81 TYR 0.023 0.001 TYR C 66 PHE 0.023 0.002 PHE A 22 TRP 0.003 0.000 TRP H 60 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6684) covalent geometry : angle 1.07170 ( 9036) SS BOND : bond 0.00172 ( 12) SS BOND : angle 0.35392 ( 24) hydrogen bonds : bond 0.03075 ( 93) hydrogen bonds : angle 6.26588 ( 279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8829 (tt0) cc_final: 0.8439 (tt0) REVERT: A 45 ARG cc_start: 0.9048 (mtt180) cc_final: 0.7121 (tmm160) REVERT: A 69 GLU cc_start: 0.4126 (pm20) cc_final: 0.3834 (pm20) REVERT: A 74 GLU cc_start: 0.3528 (tp30) cc_final: 0.3323 (mm-30) REVERT: A 76 ASP cc_start: 0.8849 (t0) cc_final: 0.7616 (t0) REVERT: B 36 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 38 ASP cc_start: 0.8249 (p0) cc_final: 0.8016 (p0) REVERT: B 48 LYS cc_start: 0.8121 (mttt) cc_final: 0.6958 (pmtt) REVERT: B 50 GLU cc_start: 0.8445 (mp0) cc_final: 0.7984 (mp0) REVERT: B 58 LYS cc_start: 0.4738 (OUTLIER) cc_final: 0.3889 (pmtt) REVERT: C 44 GLU cc_start: 0.8764 (tt0) cc_final: 0.8561 (tt0) REVERT: C 45 ARG cc_start: 0.9002 (mtt180) cc_final: 0.7134 (tmm160) REVERT: C 69 GLU cc_start: 0.4015 (pm20) cc_final: 0.3710 (pm20) REVERT: C 76 ASP cc_start: 0.7515 (m-30) cc_final: 0.7269 (m-30) REVERT: D 36 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7504 (tm-30) REVERT: D 38 ASP cc_start: 0.8269 (p0) cc_final: 0.7787 (p0) REVERT: D 48 LYS cc_start: 0.8245 (mttt) cc_final: 0.7015 (pmtt) REVERT: D 50 GLU cc_start: 0.8350 (mp0) cc_final: 0.8061 (mp0) REVERT: D 76 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8100 (t0) REVERT: E 44 GLU cc_start: 0.8671 (tt0) cc_final: 0.8388 (tt0) REVERT: E 47 GLU cc_start: 0.8768 (tp30) cc_final: 0.8185 (tt0) REVERT: E 48 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8526 (mmpt) REVERT: E 59 ASP cc_start: 0.9000 (m-30) cc_final: 0.8768 (m-30) REVERT: F 34 ASP cc_start: 0.9123 (t0) cc_final: 0.8847 (t0) REVERT: F 36 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7481 (tm-30) REVERT: F 38 ASP cc_start: 0.8067 (p0) cc_final: 0.7243 (p0) REVERT: F 44 GLU cc_start: 0.8843 (tt0) cc_final: 0.8251 (tm-30) REVERT: F 48 LYS cc_start: 0.8638 (mttt) cc_final: 0.8347 (mtpt) REVERT: F 50 GLU cc_start: 0.8656 (mp0) cc_final: 0.8111 (mp0) REVERT: F 53 ASP cc_start: 0.8873 (t0) cc_final: 0.8497 (t0) REVERT: F 73 THR cc_start: 0.9318 (m) cc_final: 0.8957 (t) REVERT: G 44 GLU cc_start: 0.8948 (tt0) cc_final: 0.8623 (tt0) REVERT: G 48 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8413 (mtpt) REVERT: G 50 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: G 74 GLU cc_start: 0.8459 (mp0) cc_final: 0.8024 (mm-30) REVERT: H 34 ASP cc_start: 0.9120 (t0) cc_final: 0.8839 (t0) REVERT: H 36 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7402 (tm-30) REVERT: H 38 ASP cc_start: 0.8114 (p0) cc_final: 0.7064 (p0) REVERT: H 50 GLU cc_start: 0.8607 (mp0) cc_final: 0.7840 (mp0) REVERT: H 53 ASP cc_start: 0.8898 (t0) cc_final: 0.8561 (t0) REVERT: I 44 GLU cc_start: 0.8685 (tt0) cc_final: 0.8189 (tm-30) REVERT: I 48 LYS cc_start: 0.4307 (tptp) cc_final: 0.3935 (tptp) REVERT: I 50 GLU cc_start: 0.8626 (mp0) cc_final: 0.8326 (mp0) REVERT: J 27 MET cc_start: 0.7119 (ttt) cc_final: 0.6529 (ttt) REVERT: J 34 ASP cc_start: 0.9159 (t0) cc_final: 0.8915 (t0) REVERT: J 36 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8009 (tm-30) REVERT: J 38 ASP cc_start: 0.8363 (p0) cc_final: 0.7714 (p0) REVERT: J 48 LYS cc_start: 0.8830 (mttt) cc_final: 0.7958 (mmpt) REVERT: J 50 GLU cc_start: 0.8281 (mp0) cc_final: 0.7979 (mp0) REVERT: J 53 ASP cc_start: 0.8877 (t0) cc_final: 0.8330 (t0) REVERT: K 33 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8821 (t) REVERT: K 39 LEU cc_start: 0.8771 (tm) cc_final: 0.8384 (tm) REVERT: K 44 GLU cc_start: 0.8644 (tt0) cc_final: 0.8070 (tm-30) REVERT: K 47 GLU cc_start: 0.8270 (tp30) cc_final: 0.8027 (tp30) REVERT: K 48 LYS cc_start: 0.4818 (OUTLIER) cc_final: 0.4433 (tptp) REVERT: K 50 GLU cc_start: 0.8678 (mp0) cc_final: 0.7961 (mp0) REVERT: L 27 MET cc_start: 0.7089 (ttt) cc_final: 0.6479 (ttt) REVERT: L 34 ASP cc_start: 0.9148 (t0) cc_final: 0.8942 (t0) REVERT: L 36 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7906 (tm-30) REVERT: L 38 ASP cc_start: 0.8279 (p0) cc_final: 0.7742 (p0) REVERT: L 48 LYS cc_start: 0.8954 (mtmt) cc_final: 0.7684 (mmpt) REVERT: L 50 GLU cc_start: 0.8274 (mp0) cc_final: 0.8036 (mp0) REVERT: L 53 ASP cc_start: 0.8882 (t0) cc_final: 0.8371 (t0) outliers start: 22 outliers final: 18 residues processed: 298 average time/residue: 0.5687 time to fit residues: 177.2414 Evaluate side-chains 307 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 9.9990 chunk 55 optimal weight: 0.2980 chunk 45 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.103408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.097636 restraints weight = 21992.978| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 3.73 r_work: 0.4047 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6696 Z= 0.203 Angle : 1.069 16.843 9060 Z= 0.504 Chirality : 0.049 0.276 912 Planarity : 0.003 0.051 1164 Dihedral : 5.619 22.473 840 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.42 % Allowed : 37.02 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 81 TYR 0.013 0.001 TYR K 66 PHE 0.023 0.001 PHE C 22 TRP 0.003 0.000 TRP H 60 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 6684) covalent geometry : angle 1.07008 ( 9036) SS BOND : bond 0.00200 ( 12) SS BOND : angle 0.41666 ( 24) hydrogen bonds : bond 0.03094 ( 93) hydrogen bonds : angle 6.35726 ( 279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.83 seconds wall clock time: 58 minutes 46.27 seconds (3526.27 seconds total)