Starting phenix.real_space_refine on Tue Mar 11 17:01:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7q_15224/03_2025/8a7q_15224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7q_15224/03_2025/8a7q_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_2025/8a7q_15224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2025/8a7q_15224.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2025/8a7q_15224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7q_15224/03_2025/8a7q_15224.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.87, per 1000 atoms: 0.75 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: 1.41 Conformation dependent library (CDL) restraints added in 849.2 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: 0.99 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: 1.58 Time building geometry restraints manager: 1.73 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: 0.01 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: 1.970 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- 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 6684 Z= 0.258 Angle : 0.673 4.426 9036 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.002 0.001 TRP L 60 HIS 0.004 0.001 HIS L 31 PHE 0.009 0.001 PHE J 70 TYR 0.007 0.001 TYR H 63 ARG 0.001 0.000 ARG E 81 *********************** 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 : 0.739 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: 1.2114 time to fit residues: 477.8113 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 : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 56 optimal weight: 0.0770 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 overall best weight: 11.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 K 24 ASN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.102105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.096050 restraints weight = 21680.494| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.81 r_work: 0.3977 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 6684 Z= 0.511 Angle : 0.860 7.382 9036 Z= 0.455 Chirality : 0.049 0.169 912 Planarity : 0.004 0.041 1164 Dihedral : 5.360 15.117 840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.42 % Allowed : 25.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.18), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.14), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 60 HIS 0.006 0.002 HIS A 31 PHE 0.017 0.002 PHE H 22 TYR 0.016 0.002 TYR B 66 ARG 0.009 0.001 ARG G 81 *********************** 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 361 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.5440 (pm20) cc_final: 0.4905 (pm20) REVERT: A 45 ARG cc_start: 0.9150 (mtt180) cc_final: 0.7074 (tmm160) REVERT: B 36 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 38 ASP cc_start: 0.8560 (p0) cc_final: 0.8053 (p0) REVERT: B 41 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.4026 (mppt) REVERT: B 48 LYS cc_start: 0.8877 (mttt) cc_final: 0.7412 (pmtt) REVERT: B 50 GLU cc_start: 0.8488 (mp0) cc_final: 0.8187 (mp0) REVERT: B 74 GLU cc_start: 0.4227 (mm-30) cc_final: 0.3950 (tp30) REVERT: B 77 GLU cc_start: 0.3955 (pm20) cc_final: 0.3744 (pm20) REVERT: C 44 GLU cc_start: 0.8865 (tt0) cc_final: 0.8527 (tt0) REVERT: C 45 ARG cc_start: 0.9179 (mtt180) cc_final: 0.7127 (tmm160) REVERT: C 76 ASP cc_start: 0.8259 (m-30) cc_final: 0.7829 (m-30) REVERT: D 36 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 38 ASP cc_start: 0.8457 (p0) cc_final: 0.7890 (p0) REVERT: D 41 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.4102 (mppt) REVERT: D 48 LYS cc_start: 0.8857 (mttt) cc_final: 0.7395 (pmtt) REVERT: D 50 GLU cc_start: 0.8458 (mp0) cc_final: 0.8181 (mp0) REVERT: D 74 GLU cc_start: 0.4352 (mm-30) cc_final: 0.4078 (tp30) REVERT: D 77 GLU cc_start: 0.3994 (pm20) cc_final: 0.3721 (pm20) REVERT: E 50 GLU cc_start: 0.8412 (mp0) cc_final: 0.8172 (mp0) REVERT: E 58 LYS cc_start: 0.9328 (mmmt) cc_final: 0.9118 (mmtt) REVERT: F 34 ASP cc_start: 0.9064 (t0) cc_final: 0.8763 (t0) REVERT: F 36 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7873 (tm-30) REVERT: F 38 ASP cc_start: 0.8541 (p0) cc_final: 0.8307 (p0) REVERT: F 50 GLU cc_start: 0.8560 (mp0) cc_final: 0.8308 (mp0) REVERT: F 53 ASP cc_start: 0.8833 (t0) cc_final: 0.8557 (t0) REVERT: F 73 THR cc_start: 0.9450 (m) cc_final: 0.9144 (t) REVERT: F 76 ASP cc_start: 0.8443 (m-30) cc_final: 0.8160 (m-30) REVERT: G 58 LYS cc_start: 0.9307 (mmmt) cc_final: 0.9103 (mmtt) REVERT: H 34 ASP cc_start: 0.8986 (t0) cc_final: 0.8643 (t0) REVERT: H 36 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7448 (tm-30) REVERT: H 38 ASP cc_start: 0.8537 (p0) cc_final: 0.7394 (p0) REVERT: H 53 ASP cc_start: 0.8786 (t0) cc_final: 0.8486 (t0) REVERT: I 33 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8683 (t) REVERT: I 48 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.3215 (mmpt) REVERT: J 27 MET cc_start: 0.7384 (ttt) cc_final: 0.6691 (ttt) REVERT: J 34 ASP cc_start: 0.9197 (t0) cc_final: 0.8950 (t0) REVERT: J 36 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7963 (tm-30) REVERT: J 38 ASP cc_start: 0.8554 (p0) cc_final: 0.7956 (p0) REVERT: J 48 LYS cc_start: 0.8774 (mttt) cc_final: 0.7982 (mmpt) REVERT: J 53 ASP cc_start: 0.8819 (t0) cc_final: 0.8187 (t0) REVERT: K 33 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8665 (t) REVERT: K 38 ASP cc_start: 0.8861 (p0) cc_final: 0.8270 (p0) REVERT: K 48 LYS cc_start: 0.4535 (OUTLIER) cc_final: 0.3343 (mmpt) REVERT: L 27 MET cc_start: 0.7379 (ttt) cc_final: 0.6678 (ttt) REVERT: L 36 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7870 (tm-30) REVERT: L 38 ASP cc_start: 0.8419 (p0) cc_final: 0.7828 (p0) REVERT: L 48 LYS cc_start: 0.8759 (mttt) cc_final: 0.7965 (mmpt) REVERT: L 53 ASP cc_start: 0.8851 (t0) cc_final: 0.8218 (t0) outliers start: 47 outliers final: 15 residues processed: 325 average time/residue: 1.1746 time to fit residues: 399.7410 Evaluate side-chains 298 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 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 58 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 68 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 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 14 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN I 51 HIS K 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.102289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.096337 restraints weight = 21679.763| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.81 r_work: 0.3997 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6684 Z= 0.376 Angle : 0.801 10.381 9036 Z= 0.412 Chirality : 0.047 0.160 912 Planarity : 0.004 0.033 1164 Dihedral : 5.287 16.043 840 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.28 % Allowed : 27.60 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.19), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 60 HIS 0.004 0.001 HIS C 31 PHE 0.011 0.002 PHE I 22 TYR 0.007 0.001 TYR B 63 ARG 0.008 0.001 ARG G 81 *********************** 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 355 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9158 (mtt180) cc_final: 0.7041 (tmm160) REVERT: B 36 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7731 (tm-30) REVERT: B 38 ASP cc_start: 0.8621 (p0) cc_final: 0.8218 (p0) REVERT: B 41 LYS cc_start: 0.5144 (OUTLIER) cc_final: 0.3426 (pttm) REVERT: B 48 LYS cc_start: 0.8903 (mttt) cc_final: 0.7471 (pmtt) REVERT: B 50 GLU cc_start: 0.8433 (mp0) cc_final: 0.8082 (mp0) REVERT: B 58 LYS cc_start: 0.4272 (OUTLIER) cc_final: 0.3351 (pmtt) REVERT: C 44 GLU cc_start: 0.8871 (tt0) cc_final: 0.8455 (tt0) REVERT: C 45 ARG cc_start: 0.9170 (mtt180) cc_final: 0.7118 (tmm160) REVERT: D 36 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 38 ASP cc_start: 0.8533 (p0) cc_final: 0.7972 (p0) REVERT: D 41 LYS cc_start: 0.5330 (OUTLIER) cc_final: 0.4040 (pttm) REVERT: D 48 LYS cc_start: 0.8955 (mttt) cc_final: 0.7581 (pmtt) REVERT: D 50 GLU cc_start: 0.8454 (mp0) cc_final: 0.8077 (mp0) REVERT: D 58 LYS cc_start: 0.4519 (OUTLIER) cc_final: 0.3400 (pmtt) REVERT: E 48 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8766 (mtpm) REVERT: E 50 GLU cc_start: 0.8534 (mp0) cc_final: 0.8100 (mp0) REVERT: E 58 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9114 (mmtt) REVERT: E 74 GLU cc_start: 0.9021 (pm20) cc_final: 0.8793 (mp0) REVERT: F 34 ASP cc_start: 0.9080 (t0) cc_final: 0.8766 (t0) REVERT: F 36 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7957 (tm-30) REVERT: F 38 ASP cc_start: 0.8492 (p0) cc_final: 0.8284 (p0) REVERT: F 47 GLU cc_start: 0.8605 (tp30) cc_final: 0.8186 (tp30) REVERT: F 48 LYS cc_start: 0.8662 (mttt) cc_final: 0.8397 (mtmt) REVERT: F 50 GLU cc_start: 0.8509 (mp0) cc_final: 0.8253 (mp0) REVERT: F 53 ASP cc_start: 0.8837 (t0) cc_final: 0.8491 (t0) REVERT: F 73 THR cc_start: 0.9432 (m) cc_final: 0.9084 (t) REVERT: G 41 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (tttt) REVERT: G 45 ARG cc_start: 0.9501 (mtp85) cc_final: 0.9300 (mtt-85) REVERT: G 48 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8812 (ptpp) REVERT: G 50 GLU cc_start: 0.8968 (mp0) cc_final: 0.8607 (mp0) REVERT: G 58 LYS cc_start: 0.9341 (mmmt) cc_final: 0.9082 (mmtt) REVERT: H 34 ASP cc_start: 0.8981 (t0) cc_final: 0.8693 (t0) REVERT: H 36 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7515 (tm-30) REVERT: H 38 ASP cc_start: 0.8533 (p0) cc_final: 0.7423 (p0) REVERT: H 47 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7738 (tm-30) REVERT: H 53 ASP cc_start: 0.8855 (t0) cc_final: 0.8475 (t0) REVERT: I 44 GLU cc_start: 0.8795 (tt0) cc_final: 0.8069 (tm-30) REVERT: I 48 LYS cc_start: 0.4589 (OUTLIER) cc_final: 0.3484 (mmpt) REVERT: J 27 MET cc_start: 0.7278 (ttt) cc_final: 0.6603 (ttt) REVERT: J 34 ASP cc_start: 0.9185 (t0) cc_final: 0.8938 (t0) REVERT: J 36 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7962 (tm-30) REVERT: J 38 ASP cc_start: 0.8600 (p0) cc_final: 0.7908 (p0) REVERT: J 44 GLU cc_start: 0.8907 (tt0) cc_final: 0.8366 (tt0) REVERT: J 48 LYS cc_start: 0.8726 (mttt) cc_final: 0.7966 (mmpt) REVERT: J 53 ASP cc_start: 0.8851 (t0) cc_final: 0.8246 (t0) REVERT: J 76 ASP cc_start: 0.7745 (m-30) cc_final: 0.6336 (m-30) REVERT: K 44 GLU cc_start: 0.8750 (tt0) cc_final: 0.8007 (tm-30) REVERT: K 48 LYS cc_start: 0.4701 (OUTLIER) cc_final: 0.3663 (mmpt) REVERT: L 27 MET cc_start: 0.7293 (ttt) cc_final: 0.6625 (ttt) REVERT: L 36 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7917 (tm-30) REVERT: L 38 ASP cc_start: 0.8521 (p0) cc_final: 0.7873 (p0) REVERT: L 48 LYS cc_start: 0.8708 (mttt) cc_final: 0.7956 (mmpt) REVERT: L 50 GLU cc_start: 0.8227 (mp0) cc_final: 0.7884 (mp0) REVERT: L 53 ASP cc_start: 0.8895 (t0) cc_final: 0.8349 (t0) outliers start: 46 outliers final: 21 residues processed: 322 average time/residue: 1.1907 time to fit residues: 400.8766 Evaluate side-chains 308 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 41 LYS 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 33 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 49 VAL 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 41 LYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** F 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 = 0.4250 r_free = 0.4250 target = 0.103313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.097323 restraints weight = 21636.101| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.85 r_work: 0.4023 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6684 Z= 0.289 Angle : 0.800 12.450 9036 Z= 0.398 Chirality : 0.046 0.147 912 Planarity : 0.004 0.039 1164 Dihedral : 5.266 16.046 840 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.01 % Allowed : 27.73 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.002 0.000 TRP K 60 HIS 0.005 0.001 HIS A 31 PHE 0.023 0.002 PHE A 22 TYR 0.025 0.001 TYR D 66 ARG 0.009 0.001 ARG G 81 *********************** 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 358 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 314 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9296 (tt) cc_final: 0.9062 (tt) REVERT: A 45 ARG cc_start: 0.9129 (mtt180) cc_final: 0.7036 (tmm160) REVERT: B 36 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 38 ASP cc_start: 0.8631 (p0) cc_final: 0.8219 (p0) REVERT: B 41 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.4159 (pttm) REVERT: B 48 LYS cc_start: 0.8884 (mttt) cc_final: 0.7422 (pmtt) REVERT: B 50 GLU cc_start: 0.8454 (mp0) cc_final: 0.8154 (mp0) REVERT: B 58 LYS cc_start: 0.4395 (OUTLIER) cc_final: 0.3453 (pmtt) REVERT: C 44 GLU cc_start: 0.8858 (tt0) cc_final: 0.8594 (tt0) REVERT: C 45 ARG cc_start: 0.9045 (mtt180) cc_final: 0.7131 (tmm160) REVERT: D 36 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7503 (tm-30) REVERT: D 38 ASP cc_start: 0.8509 (p0) cc_final: 0.7937 (p0) REVERT: D 41 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.4141 (pttm) REVERT: D 48 LYS cc_start: 0.8904 (mttt) cc_final: 0.7506 (pmtt) REVERT: D 50 GLU cc_start: 0.8416 (mp0) cc_final: 0.8159 (mp0) REVERT: D 58 LYS cc_start: 0.4711 (OUTLIER) cc_final: 0.3629 (pmtt) REVERT: E 48 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8657 (mtpm) REVERT: E 50 GLU cc_start: 0.8592 (mp0) cc_final: 0.8099 (mp0) REVERT: E 58 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9058 (mmtt) REVERT: F 34 ASP cc_start: 0.9122 (t0) cc_final: 0.8800 (t0) REVERT: F 36 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7976 (tm-30) REVERT: F 48 LYS cc_start: 0.8593 (mttt) cc_final: 0.8298 (ttmt) REVERT: F 53 ASP cc_start: 0.8888 (t0) cc_final: 0.8539 (t0) REVERT: F 73 THR cc_start: 0.9379 (m) cc_final: 0.9064 (t) REVERT: G 44 GLU cc_start: 0.8783 (tt0) cc_final: 0.8538 (tt0) REVERT: G 48 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8836 (ptpp) REVERT: G 74 GLU cc_start: 0.8754 (pm20) cc_final: 0.8526 (pm20) REVERT: G 75 LYS cc_start: 0.8520 (mppt) cc_final: 0.8303 (tptp) REVERT: H 34 ASP cc_start: 0.9010 (t0) cc_final: 0.8704 (t0) REVERT: H 36 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7455 (tm-30) REVERT: H 38 ASP cc_start: 0.8411 (p0) cc_final: 0.7289 (p0) REVERT: H 47 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7562 (tm-30) REVERT: H 48 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8536 (ttpt) REVERT: H 53 ASP cc_start: 0.8904 (t0) cc_final: 0.8515 (t0) REVERT: I 33 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8788 (t) REVERT: I 44 GLU cc_start: 0.8792 (tt0) cc_final: 0.8120 (tm-30) REVERT: I 47 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: I 48 LYS cc_start: 0.4681 (OUTLIER) cc_final: 0.3425 (mmpt) REVERT: J 27 MET cc_start: 0.7263 (ttt) cc_final: 0.6563 (ttt) REVERT: J 34 ASP cc_start: 0.9201 (t0) cc_final: 0.8954 (t0) REVERT: J 36 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7910 (tm-30) REVERT: J 38 ASP cc_start: 0.8561 (p0) cc_final: 0.7892 (p0) REVERT: J 48 LYS cc_start: 0.8845 (mttt) cc_final: 0.7970 (mmpt) REVERT: J 50 GLU cc_start: 0.8207 (mp0) cc_final: 0.7908 (mp0) REVERT: J 53 ASP cc_start: 0.8884 (t0) cc_final: 0.8304 (t0) REVERT: K 33 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8762 (t) REVERT: K 44 GLU cc_start: 0.8760 (tt0) cc_final: 0.8151 (tm-30) REVERT: K 48 LYS cc_start: 0.4700 (OUTLIER) cc_final: 0.3553 (mmpt) REVERT: K 50 GLU cc_start: 0.8469 (mp0) cc_final: 0.8226 (mp0) REVERT: L 27 MET cc_start: 0.7259 (ttt) cc_final: 0.6583 (ttt) REVERT: L 36 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7917 (tm-30) REVERT: L 38 ASP cc_start: 0.8563 (p0) cc_final: 0.7910 (p0) REVERT: L 48 LYS cc_start: 0.8792 (mttt) cc_final: 0.7951 (mmpt) REVERT: L 50 GLU cc_start: 0.8230 (mp0) cc_final: 0.7851 (mp0) REVERT: L 53 ASP cc_start: 0.8917 (t0) cc_final: 0.8411 (t0) outliers start: 44 outliers final: 18 residues processed: 329 average time/residue: 1.2156 time to fit residues: 417.8447 Evaluate side-chains 316 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG 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 48 LYS Chi-restraints excluded: chain C residue 49 VAL 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 G residue 33 SER Chi-restraints excluded: chain G residue 49 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.102653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.096748 restraints weight = 21810.392| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.74 r_work: 0.4017 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6684 Z= 0.308 Angle : 0.838 13.430 9036 Z= 0.412 Chirality : 0.047 0.195 912 Planarity : 0.004 0.038 1164 Dihedral : 5.383 19.033 840 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 6.01 % Allowed : 28.55 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (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 TRP 0.002 0.000 TRP L 60 HIS 0.005 0.001 HIS A 31 PHE 0.024 0.002 PHE C 22 TYR 0.013 0.001 TYR G 66 ARG 0.010 0.001 ARG G 81 *********************** 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 343 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9028 (mtt180) cc_final: 0.6980 (tmm160) REVERT: A 69 GLU cc_start: 0.4086 (pm20) cc_final: 0.3663 (pm20) REVERT: A 74 GLU cc_start: 0.3666 (tp30) cc_final: 0.3375 (mm-30) REVERT: B 41 LYS cc_start: 0.5310 (OUTLIER) cc_final: 0.4026 (pttm) REVERT: B 48 LYS cc_start: 0.8911 (mttt) cc_final: 0.7299 (pmtt) REVERT: B 50 GLU cc_start: 0.8459 (mp0) cc_final: 0.8174 (mp0) REVERT: C 44 GLU cc_start: 0.8791 (tt0) cc_final: 0.8555 (tt0) REVERT: C 45 ARG cc_start: 0.9070 (mtt180) cc_final: 0.7131 (tmm160) REVERT: D 36 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 38 ASP cc_start: 0.8481 (p0) cc_final: 0.7932 (OUTLIER) REVERT: D 41 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.4090 (pttm) REVERT: D 48 LYS cc_start: 0.8914 (mttt) cc_final: 0.7500 (pmtt) REVERT: D 50 GLU cc_start: 0.8400 (mp0) cc_final: 0.8090 (mp0) REVERT: D 58 LYS cc_start: 0.4370 (OUTLIER) cc_final: 0.3482 (pmtt) REVERT: E 48 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8749 (mtpm) REVERT: E 50 GLU cc_start: 0.8588 (mp0) cc_final: 0.8074 (mp0) REVERT: F 34 ASP cc_start: 0.9138 (t0) cc_final: 0.8828 (t0) REVERT: F 36 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7914 (tm-30) REVERT: F 38 ASP cc_start: 0.8419 (p0) cc_final: 0.8022 (p0) REVERT: F 48 LYS cc_start: 0.8633 (mttt) cc_final: 0.8350 (ttmt) REVERT: F 53 ASP cc_start: 0.8916 (t0) cc_final: 0.8580 (t0) REVERT: F 73 THR cc_start: 0.9317 (m) cc_final: 0.9042 (t) REVERT: G 41 LYS cc_start: 0.8920 (tttm) cc_final: 0.8595 (mttt) REVERT: G 48 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8833 (ptpp) REVERT: G 50 GLU cc_start: 0.9044 (mp0) cc_final: 0.8151 (mp0) REVERT: G 59 ASP cc_start: 0.9116 (m-30) cc_final: 0.8911 (m-30) REVERT: G 75 LYS cc_start: 0.8619 (mppt) cc_final: 0.8319 (tptp) REVERT: H 34 ASP cc_start: 0.9014 (t0) cc_final: 0.8700 (t0) REVERT: H 36 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7478 (tm-30) REVERT: H 38 ASP cc_start: 0.8365 (p0) cc_final: 0.7285 (p0) REVERT: H 47 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7859 (tp30) REVERT: H 48 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8485 (ttpt) REVERT: H 53 ASP cc_start: 0.8879 (t0) cc_final: 0.8472 (t0) REVERT: I 44 GLU cc_start: 0.8677 (tt0) cc_final: 0.8090 (tm-30) REVERT: I 47 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: I 48 LYS cc_start: 0.4660 (OUTLIER) cc_final: 0.3489 (mmpt) REVERT: J 27 MET cc_start: 0.7221 (ttt) cc_final: 0.6577 (ttt) REVERT: J 34 ASP cc_start: 0.9224 (t0) cc_final: 0.8996 (t0) REVERT: J 36 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7812 (tm-30) REVERT: J 38 ASP cc_start: 0.8581 (p0) cc_final: 0.7895 (p0) REVERT: J 48 LYS cc_start: 0.8853 (mttt) cc_final: 0.8005 (mmpt) REVERT: J 53 ASP cc_start: 0.8883 (t0) cc_final: 0.8306 (t0) REVERT: K 44 GLU cc_start: 0.8665 (tt0) cc_final: 0.8148 (tm-30) REVERT: K 48 LYS cc_start: 0.4442 (OUTLIER) cc_final: 0.4074 (mmpt) REVERT: K 50 GLU cc_start: 0.8405 (mp0) cc_final: 0.7776 (mp0) REVERT: L 27 MET cc_start: 0.7236 (ttt) cc_final: 0.6579 (ttt) REVERT: L 36 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7825 (tm-30) REVERT: L 38 ASP cc_start: 0.8596 (p0) cc_final: 0.7880 (p0) REVERT: L 48 LYS cc_start: 0.8816 (mttt) cc_final: 0.7948 (mmpt) REVERT: L 50 GLU cc_start: 0.8216 (mp0) cc_final: 0.7830 (mp0) REVERT: L 53 ASP cc_start: 0.8876 (t0) cc_final: 0.8353 (t0) outliers start: 44 outliers final: 24 residues processed: 309 average time/residue: 1.1738 time to fit residues: 379.2725 Evaluate side-chains 312 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG 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 48 LYS 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 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 34 ASP 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 34 ASP Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4257 r_free = 0.4257 target = 0.103838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.097904 restraints weight = 21534.024| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 3.73 r_work: 0.4033 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6684 Z= 0.280 Angle : 0.869 14.394 9036 Z= 0.421 Chirality : 0.046 0.154 912 Planarity : 0.004 0.042 1164 Dihedral : 5.328 15.977 840 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.51 % Allowed : 30.19 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 60 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.002 PHE A 22 TYR 0.023 0.001 TYR B 66 ARG 0.010 0.001 ARG E 81 *********************** 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 334 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9036 (mtt180) cc_final: 0.7048 (tmm160) REVERT: A 69 GLU cc_start: 0.4087 (pm20) cc_final: 0.3725 (pm20) REVERT: B 48 LYS cc_start: 0.8849 (mttt) cc_final: 0.7039 (pmtt) REVERT: B 50 GLU cc_start: 0.8465 (mp0) cc_final: 0.8112 (mp0) REVERT: B 58 LYS cc_start: 0.4753 (OUTLIER) cc_final: 0.3716 (pmtt) REVERT: C 44 GLU cc_start: 0.8776 (tt0) cc_final: 0.8546 (tt0) REVERT: C 45 ARG cc_start: 0.8986 (mtt180) cc_final: 0.7128 (tmm160) REVERT: C 69 GLU cc_start: 0.4175 (pm20) cc_final: 0.3865 (pm20) REVERT: D 36 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 38 ASP cc_start: 0.8423 (p0) cc_final: 0.7912 (p0) REVERT: D 48 LYS cc_start: 0.8913 (mttt) cc_final: 0.7479 (pmtt) REVERT: D 50 GLU cc_start: 0.8354 (mp0) cc_final: 0.7955 (mp0) REVERT: E 48 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8812 (mtpm) REVERT: E 50 GLU cc_start: 0.8543 (mp0) cc_final: 0.8044 (mp0) REVERT: F 34 ASP cc_start: 0.9133 (t0) cc_final: 0.8837 (t0) REVERT: F 36 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7439 (tm-30) REVERT: F 38 ASP cc_start: 0.8365 (p0) cc_final: 0.7423 (p0) REVERT: F 44 GLU cc_start: 0.8672 (tt0) cc_final: 0.8322 (tm-30) REVERT: F 48 LYS cc_start: 0.8639 (mttt) cc_final: 0.8347 (ttmt) REVERT: F 53 ASP cc_start: 0.8928 (t0) cc_final: 0.8552 (t0) REVERT: F 73 THR cc_start: 0.9293 (m) cc_final: 0.8996 (t) REVERT: G 48 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8738 (mtpm) REVERT: G 50 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: G 58 LYS cc_start: 0.9259 (mmtp) cc_final: 0.9027 (mmtt) REVERT: G 59 ASP cc_start: 0.9092 (m-30) cc_final: 0.8864 (m-30) REVERT: H 34 ASP cc_start: 0.9009 (t0) cc_final: 0.8672 (t0) REVERT: H 36 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7453 (tm-30) REVERT: H 38 ASP cc_start: 0.8335 (p0) cc_final: 0.7281 (p0) REVERT: H 44 GLU cc_start: 0.8721 (tt0) cc_final: 0.8235 (pm20) REVERT: H 50 GLU cc_start: 0.8511 (mp0) cc_final: 0.7966 (mp0) REVERT: H 53 ASP cc_start: 0.8910 (t0) cc_final: 0.8515 (t0) REVERT: I 44 GLU cc_start: 0.8786 (tt0) cc_final: 0.8212 (tm-30) REVERT: I 48 LYS cc_start: 0.4635 (OUTLIER) cc_final: 0.3399 (mmpt) REVERT: I 50 GLU cc_start: 0.8389 (mp0) cc_final: 0.8185 (mp0) REVERT: J 27 MET cc_start: 0.7234 (ttt) cc_final: 0.6596 (ttt) REVERT: J 34 ASP cc_start: 0.9227 (t0) cc_final: 0.8993 (t0) REVERT: J 36 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7819 (tm-30) REVERT: J 38 ASP cc_start: 0.8595 (p0) cc_final: 0.7857 (p0) REVERT: J 48 LYS cc_start: 0.8905 (mttt) cc_final: 0.8003 (mmpt) REVERT: J 50 GLU cc_start: 0.8240 (mp0) cc_final: 0.7860 (mp0) REVERT: J 53 ASP cc_start: 0.8921 (t0) cc_final: 0.8360 (t0) REVERT: K 44 GLU cc_start: 0.8590 (tt0) cc_final: 0.8182 (tm-30) REVERT: K 48 LYS cc_start: 0.4372 (OUTLIER) cc_final: 0.3222 (mmpt) REVERT: L 27 MET cc_start: 0.7218 (ttt) cc_final: 0.6585 (ttt) REVERT: L 36 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7841 (tm-30) REVERT: L 38 ASP cc_start: 0.8422 (p0) cc_final: 0.7706 (p0) REVERT: L 48 LYS cc_start: 0.8825 (mttt) cc_final: 0.7953 (mmpt) REVERT: L 53 ASP cc_start: 0.8901 (t0) cc_final: 0.8345 (t0) outliers start: 33 outliers final: 22 residues processed: 311 average time/residue: 1.2228 time to fit residues: 397.5250 Evaluate side-chains 310 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 SER 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 E residue 69 GLU 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 48 LYS Chi-restraints excluded: chain I residue 52 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 10 optimal weight: 0.0670 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 0.2980 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.0724 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.103921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.097895 restraints weight = 21443.137| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 3.80 r_work: 0.4043 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6684 Z= 0.268 Angle : 0.916 15.031 9036 Z= 0.438 Chirality : 0.047 0.161 912 Planarity : 0.004 0.046 1164 Dihedral : 5.338 19.139 840 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.37 % Allowed : 32.92 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.21), 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 TRP 0.003 0.000 TRP K 60 HIS 0.004 0.001 HIS A 31 PHE 0.022 0.001 PHE C 22 TYR 0.011 0.001 TYR E 66 ARG 0.010 0.001 ARG E 81 *********************** 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 333 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5637 (pmtt) cc_final: 0.5018 (pmtt) REVERT: A 45 ARG cc_start: 0.9079 (mtt180) cc_final: 0.7090 (tmm160) REVERT: A 69 GLU cc_start: 0.4338 (pm20) cc_final: 0.3980 (pm20) REVERT: A 74 GLU cc_start: 0.3359 (mm-30) cc_final: 0.3039 (tp30) REVERT: B 41 LYS cc_start: 0.5253 (OUTLIER) cc_final: 0.4021 (pttm) REVERT: B 48 LYS cc_start: 0.8661 (mttt) cc_final: 0.7120 (OUTLIER) REVERT: B 50 GLU cc_start: 0.8458 (mp0) cc_final: 0.8103 (mp0) REVERT: C 44 GLU cc_start: 0.8836 (tt0) cc_final: 0.8547 (tt0) REVERT: C 45 ARG cc_start: 0.9031 (mtt180) cc_final: 0.7153 (tmm160) REVERT: C 69 GLU cc_start: 0.4345 (pm20) cc_final: 0.4000 (pm20) REVERT: D 36 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7463 (tm-30) REVERT: D 38 ASP cc_start: 0.8458 (p0) cc_final: 0.7953 (OUTLIER) REVERT: D 48 LYS cc_start: 0.8900 (mttt) cc_final: 0.7454 (pmtt) REVERT: D 50 GLU cc_start: 0.8329 (mp0) cc_final: 0.8074 (mp0) REVERT: D 76 ASP cc_start: 0.7663 (m-30) cc_final: 0.7204 (m-30) REVERT: E 48 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8806 (mtpm) REVERT: E 50 GLU cc_start: 0.8601 (mp0) cc_final: 0.8107 (mp0) REVERT: E 76 ASP cc_start: 0.8509 (m-30) cc_final: 0.8099 (m-30) REVERT: F 34 ASP cc_start: 0.9121 (t0) cc_final: 0.8823 (t0) REVERT: F 36 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7446 (tm-30) REVERT: F 38 ASP cc_start: 0.8274 (p0) cc_final: 0.7412 (p0) REVERT: F 44 GLU cc_start: 0.8659 (tt0) cc_final: 0.8337 (tm-30) REVERT: F 48 LYS cc_start: 0.8763 (mttt) cc_final: 0.8479 (mtpt) REVERT: F 50 GLU cc_start: 0.8592 (mp0) cc_final: 0.8065 (mp0) REVERT: F 53 ASP cc_start: 0.8927 (t0) cc_final: 0.8539 (t0) REVERT: F 73 THR cc_start: 0.9308 (m) cc_final: 0.9001 (t) REVERT: G 48 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8633 (mtpm) REVERT: G 50 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8669 (mp0) REVERT: G 58 LYS cc_start: 0.9240 (mmtp) cc_final: 0.9040 (mmtt) REVERT: H 34 ASP cc_start: 0.9016 (t0) cc_final: 0.8702 (t0) REVERT: H 36 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7364 (tm-30) REVERT: H 38 ASP cc_start: 0.8240 (p0) cc_final: 0.7112 (p0) REVERT: H 44 GLU cc_start: 0.8764 (tt0) cc_final: 0.8244 (pm20) REVERT: H 48 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8398 (ttmm) REVERT: H 53 ASP cc_start: 0.8912 (t0) cc_final: 0.8477 (t0) REVERT: H 76 ASP cc_start: 0.8834 (m-30) cc_final: 0.8402 (m-30) REVERT: I 44 GLU cc_start: 0.8702 (tt0) cc_final: 0.8187 (tm-30) REVERT: I 48 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.4225 (mmpt) REVERT: J 27 MET cc_start: 0.7176 (ttt) cc_final: 0.6557 (ttt) REVERT: J 34 ASP cc_start: 0.9219 (t0) cc_final: 0.9002 (t0) REVERT: J 36 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7879 (tm-30) REVERT: J 38 ASP cc_start: 0.8341 (p0) cc_final: 0.7655 (p0) REVERT: J 48 LYS cc_start: 0.8938 (mttt) cc_final: 0.8055 (mmpt) REVERT: J 53 ASP cc_start: 0.8885 (t0) cc_final: 0.8332 (t0) REVERT: K 44 GLU cc_start: 0.8619 (tt0) cc_final: 0.8157 (tm-30) REVERT: K 48 LYS cc_start: 0.4591 (OUTLIER) cc_final: 0.4375 (mmpt) REVERT: L 27 MET cc_start: 0.7138 (ttt) cc_final: 0.6525 (ttt) REVERT: L 36 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7969 (tm-30) REVERT: L 38 ASP cc_start: 0.8477 (p0) cc_final: 0.7803 (p0) REVERT: L 48 LYS cc_start: 0.8867 (mttt) cc_final: 0.7937 (mmpt) REVERT: L 50 GLU cc_start: 0.8360 (mp0) cc_final: 0.8069 (mp0) REVERT: L 53 ASP cc_start: 0.8857 (t0) cc_final: 0.8302 (t0) outliers start: 32 outliers final: 21 residues processed: 311 average time/residue: 1.1942 time to fit residues: 388.4769 Evaluate side-chains 312 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 289 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER 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 61 SER 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 E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 50 GLU 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 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 Chi-restraints excluded: chain K residue 69 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** ** 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 = 0.4270 r_free = 0.4270 target = 0.103776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.097608 restraints weight = 21276.456| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.81 r_work: 0.4037 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6684 Z= 0.274 Angle : 0.927 14.007 9036 Z= 0.447 Chirality : 0.047 0.156 912 Planarity : 0.004 0.049 1164 Dihedral : 5.371 18.324 840 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.83 % Allowed : 34.15 % Favored : 62.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 60 HIS 0.004 0.001 HIS A 31 PHE 0.022 0.001 PHE A 22 TYR 0.023 0.001 TYR D 66 ARG 0.011 0.001 ARG E 81 *********************** 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 324 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9151 (mtt180) cc_final: 0.6985 (tmm160) REVERT: A 69 GLU cc_start: 0.4261 (pm20) cc_final: 0.3933 (pm20) REVERT: A 76 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7785 (t0) REVERT: B 48 LYS cc_start: 0.8596 (mttt) cc_final: 0.7018 (OUTLIER) REVERT: B 50 GLU cc_start: 0.8459 (mp0) cc_final: 0.8248 (mp0) REVERT: C 44 GLU cc_start: 0.8825 (tt0) cc_final: 0.8522 (tt0) REVERT: C 45 ARG cc_start: 0.9063 (mtt180) cc_final: 0.7127 (tmm160) REVERT: C 69 GLU cc_start: 0.4199 (pm20) cc_final: 0.3876 (pm20) REVERT: D 36 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7495 (tm-30) REVERT: D 38 ASP cc_start: 0.8407 (p0) cc_final: 0.7910 (OUTLIER) REVERT: D 48 LYS cc_start: 0.8876 (mttt) cc_final: 0.7480 (pmtt) REVERT: D 50 GLU cc_start: 0.8436 (mp0) cc_final: 0.8111 (mp0) REVERT: E 48 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8962 (mtpt) REVERT: E 50 GLU cc_start: 0.8633 (mp0) cc_final: 0.8246 (mp0) REVERT: F 34 ASP cc_start: 0.9135 (t0) cc_final: 0.8864 (t0) REVERT: F 36 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7506 (tm-30) REVERT: F 38 ASP cc_start: 0.8342 (p0) cc_final: 0.7346 (p0) REVERT: F 44 GLU cc_start: 0.8674 (tt0) cc_final: 0.8319 (tm-30) REVERT: F 48 LYS cc_start: 0.8824 (mttt) cc_final: 0.8501 (ttmt) REVERT: F 53 ASP cc_start: 0.8894 (t0) cc_final: 0.8541 (t0) REVERT: F 73 THR cc_start: 0.9289 (m) cc_final: 0.8964 (t) REVERT: F 77 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8749 (tm-30) REVERT: G 48 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8692 (mtpm) REVERT: G 50 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: H 36 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7407 (tm-30) REVERT: H 38 ASP cc_start: 0.8148 (p0) cc_final: 0.7229 (p0) REVERT: H 44 GLU cc_start: 0.8783 (tt0) cc_final: 0.8270 (pm20) REVERT: H 48 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8359 (ttmm) REVERT: H 53 ASP cc_start: 0.8913 (t0) cc_final: 0.8514 (t0) REVERT: I 44 GLU cc_start: 0.8764 (tt0) cc_final: 0.8254 (tm-30) REVERT: J 27 MET cc_start: 0.7178 (ttt) cc_final: 0.6587 (ttt) REVERT: J 34 ASP cc_start: 0.9200 (t0) cc_final: 0.8972 (t0) REVERT: J 36 GLU cc_start: 0.8569 (tm-30) cc_final: 0.7937 (tm-30) REVERT: J 38 ASP cc_start: 0.8373 (p0) cc_final: 0.7773 (p0) REVERT: J 48 LYS cc_start: 0.8932 (mttt) cc_final: 0.8081 (mmpt) REVERT: J 50 GLU cc_start: 0.8255 (mp0) cc_final: 0.7908 (mp0) REVERT: J 53 ASP cc_start: 0.8876 (t0) cc_final: 0.8323 (t0) REVERT: K 44 GLU cc_start: 0.8620 (tt0) cc_final: 0.8108 (tm-30) REVERT: K 48 LYS cc_start: 0.4809 (OUTLIER) cc_final: 0.3535 (mmpt) REVERT: L 27 MET cc_start: 0.7175 (ttt) cc_final: 0.6561 (ttt) REVERT: L 36 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7661 (tm-30) REVERT: L 38 ASP cc_start: 0.8284 (p0) cc_final: 0.7302 (p0) REVERT: L 48 LYS cc_start: 0.8861 (mttt) cc_final: 0.7992 (mmpt) REVERT: L 50 GLU cc_start: 0.8290 (mp0) cc_final: 0.8003 (mp0) REVERT: L 53 ASP cc_start: 0.8889 (t0) cc_final: 0.8318 (t0) outliers start: 28 outliers final: 24 residues processed: 303 average time/residue: 1.1921 time to fit residues: 377.5662 Evaluate side-chains 310 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 52 SER 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 48 LYS Chi-restraints excluded: chain C residue 61 SER 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 E residue 69 GLU 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 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 K residue 33 SER 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 3 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.102108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.095972 restraints weight = 22694.676| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.86 r_work: 0.3989 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6684 Z= 0.446 Angle : 1.042 16.555 9036 Z= 0.509 Chirality : 0.049 0.177 912 Planarity : 0.004 0.052 1164 Dihedral : 5.888 19.414 840 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.60 % Allowed : 32.92 % Favored : 61.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP G 60 HIS 0.003 0.001 HIS A 31 PHE 0.011 0.002 PHE K 30 TYR 0.015 0.001 TYR K 66 ARG 0.011 0.001 ARG E 81 *********************** 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 324 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9042 (mtt180) cc_final: 0.6832 (tmm160) REVERT: A 74 GLU cc_start: 0.3522 (tp30) cc_final: 0.3243 (mm-30) REVERT: A 76 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: B 36 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 38 ASP cc_start: 0.8477 (p0) cc_final: 0.8187 (p0) REVERT: B 41 LYS cc_start: 0.5083 (OUTLIER) cc_final: 0.4209 (pttm) REVERT: B 48 LYS cc_start: 0.8535 (mttt) cc_final: 0.6972 (pmtt) REVERT: B 50 GLU cc_start: 0.8519 (mp0) cc_final: 0.8062 (mp0) REVERT: B 58 LYS cc_start: 0.5098 (OUTLIER) cc_final: 0.4725 (pmtt) REVERT: C 44 GLU cc_start: 0.8862 (tt0) cc_final: 0.8469 (tt0) REVERT: C 45 ARG cc_start: 0.9061 (mtt180) cc_final: 0.7014 (tmm160) REVERT: D 36 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7570 (tm-30) REVERT: D 38 ASP cc_start: 0.8442 (p0) cc_final: 0.7907 (p0) REVERT: D 41 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4288 (pttm) REVERT: D 48 LYS cc_start: 0.8928 (mttt) cc_final: 0.7272 (pmtt) REVERT: D 50 GLU cc_start: 0.8523 (mp0) cc_final: 0.8188 (mp0) REVERT: E 44 GLU cc_start: 0.8850 (tt0) cc_final: 0.8608 (tt0) REVERT: E 48 LYS cc_start: 0.9248 (mtpt) cc_final: 0.9047 (mtpt) REVERT: E 50 GLU cc_start: 0.8770 (mp0) cc_final: 0.8384 (mp0) REVERT: E 74 GLU cc_start: 0.8942 (mp0) cc_final: 0.8567 (mp0) REVERT: E 75 LYS cc_start: 0.8619 (mppt) cc_final: 0.8413 (tptp) REVERT: F 34 ASP cc_start: 0.9144 (t0) cc_final: 0.8800 (t0) REVERT: F 36 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7529 (tm-30) REVERT: F 38 ASP cc_start: 0.8215 (p0) cc_final: 0.7276 (p0) REVERT: F 44 GLU cc_start: 0.8796 (tt0) cc_final: 0.8290 (tm-30) REVERT: F 47 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: F 48 LYS cc_start: 0.8850 (mttt) cc_final: 0.8555 (mtpt) REVERT: F 50 GLU cc_start: 0.8574 (mp0) cc_final: 0.7879 (mp0) REVERT: F 53 ASP cc_start: 0.8848 (t0) cc_final: 0.8584 (t0) REVERT: F 73 THR cc_start: 0.9323 (m) cc_final: 0.8994 (t) REVERT: G 48 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8621 (mtpm) REVERT: G 50 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: H 34 ASP cc_start: 0.9102 (t0) cc_final: 0.8823 (t0) REVERT: H 36 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7524 (tm-30) REVERT: H 38 ASP cc_start: 0.8319 (p0) cc_final: 0.7198 (p0) REVERT: H 44 GLU cc_start: 0.8781 (tt0) cc_final: 0.8245 (pm20) REVERT: H 48 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8374 (ttmm) REVERT: H 53 ASP cc_start: 0.8908 (t0) cc_final: 0.8601 (t0) REVERT: I 44 GLU cc_start: 0.8797 (tt0) cc_final: 0.8213 (tm-30) REVERT: J 27 MET cc_start: 0.7126 (ttt) cc_final: 0.6563 (ttt) REVERT: J 34 ASP cc_start: 0.9203 (t0) cc_final: 0.8967 (t0) REVERT: J 36 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7844 (tm-30) REVERT: J 38 ASP cc_start: 0.8383 (p0) cc_final: 0.7714 (p0) REVERT: J 48 LYS cc_start: 0.8864 (mttt) cc_final: 0.7986 (mmpt) REVERT: J 50 GLU cc_start: 0.8275 (mp0) cc_final: 0.8003 (mp0) REVERT: J 53 ASP cc_start: 0.8810 (t0) cc_final: 0.8224 (t0) REVERT: K 44 GLU cc_start: 0.8697 (tt0) cc_final: 0.8128 (tm-30) REVERT: L 27 MET cc_start: 0.7122 (ttt) cc_final: 0.6557 (ttt) REVERT: L 36 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8015 (tm-30) REVERT: L 38 ASP cc_start: 0.8575 (p0) cc_final: 0.8023 (p0) REVERT: L 53 ASP cc_start: 0.8838 (t0) cc_final: 0.8292 (t0) outliers start: 41 outliers final: 26 residues processed: 296 average time/residue: 1.2391 time to fit residues: 382.9646 Evaluate side-chains 304 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 52 SER 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 48 LYS 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 E residue 69 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 47 GLU 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 34 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.101973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.095978 restraints weight = 22211.293| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.77 r_work: 0.4006 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6684 Z= 0.378 Angle : 1.068 15.935 9036 Z= 0.512 Chirality : 0.048 0.168 912 Planarity : 0.004 0.053 1164 Dihedral : 5.904 18.513 840 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.78 % Allowed : 34.43 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP G 60 HIS 0.004 0.001 HIS A 31 PHE 0.016 0.002 PHE J 22 TYR 0.031 0.002 TYR C 66 ARG 0.012 0.001 ARG E 81 ********************** 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 316 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5776 (pmtt) cc_final: 0.5311 (pmtt) REVERT: A 45 ARG cc_start: 0.9006 (mtt180) cc_final: 0.6937 (tmm160) REVERT: A 76 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7801 (t0) REVERT: B 41 LYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4036 (pttm) REVERT: B 48 LYS cc_start: 0.8400 (mttt) cc_final: 0.6802 (pmtt) REVERT: B 50 GLU cc_start: 0.8521 (mp0) cc_final: 0.8164 (mp0) REVERT: B 58 LYS cc_start: 0.4728 (OUTLIER) cc_final: 0.4414 (pmtt) REVERT: C 44 GLU cc_start: 0.8860 (tt0) cc_final: 0.8444 (tt0) REVERT: C 45 ARG cc_start: 0.9066 (mtt180) cc_final: 0.7030 (tmm160) REVERT: C 58 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5593 (pmtt) REVERT: D 36 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 38 ASP cc_start: 0.8446 (p0) cc_final: 0.7941 (p0) REVERT: D 41 LYS cc_start: 0.5240 (OUTLIER) cc_final: 0.4469 (pttm) REVERT: D 48 LYS cc_start: 0.8763 (mttt) cc_final: 0.7119 (pmtt) REVERT: D 50 GLU cc_start: 0.8501 (mp0) cc_final: 0.8145 (mp0) REVERT: E 44 GLU cc_start: 0.8810 (tt0) cc_final: 0.8591 (tt0) REVERT: E 47 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8469 (tm-30) REVERT: E 48 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8424 (mtpt) REVERT: E 50 GLU cc_start: 0.8701 (mp0) cc_final: 0.8285 (mp0) REVERT: F 34 ASP cc_start: 0.9132 (t0) cc_final: 0.8796 (t0) REVERT: F 36 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7530 (tm-30) REVERT: F 38 ASP cc_start: 0.8274 (p0) cc_final: 0.7339 (p0) REVERT: F 47 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: F 48 LYS cc_start: 0.8759 (mttt) cc_final: 0.8509 (mtpt) REVERT: F 53 ASP cc_start: 0.8865 (t0) cc_final: 0.8581 (t0) REVERT: F 73 THR cc_start: 0.9326 (m) cc_final: 0.9008 (t) REVERT: G 48 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8149 (mtpp) REVERT: G 50 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: H 34 ASP cc_start: 0.9102 (t0) cc_final: 0.8827 (t0) REVERT: H 36 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7476 (tm-30) REVERT: H 38 ASP cc_start: 0.8197 (p0) cc_final: 0.7115 (p0) REVERT: H 44 GLU cc_start: 0.8727 (tt0) cc_final: 0.8268 (pm20) REVERT: H 47 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8219 (tp30) REVERT: H 48 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8441 (ttmm) REVERT: H 53 ASP cc_start: 0.8882 (t0) cc_final: 0.8547 (t0) REVERT: I 44 GLU cc_start: 0.8750 (tt0) cc_final: 0.8210 (tm-30) REVERT: J 27 MET cc_start: 0.7107 (ttt) cc_final: 0.6535 (ttt) REVERT: J 34 ASP cc_start: 0.9169 (t0) cc_final: 0.8936 (t0) REVERT: J 36 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7848 (tm-30) REVERT: J 38 ASP cc_start: 0.8557 (p0) cc_final: 0.7901 (p0) REVERT: J 48 LYS cc_start: 0.8878 (mttt) cc_final: 0.8001 (mmpt) REVERT: J 50 GLU cc_start: 0.8294 (mp0) cc_final: 0.7982 (mp0) REVERT: J 53 ASP cc_start: 0.8836 (t0) cc_final: 0.8230 (t0) REVERT: K 33 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8788 (t) REVERT: K 44 GLU cc_start: 0.8660 (tt0) cc_final: 0.8152 (tm-30) REVERT: L 27 MET cc_start: 0.7095 (ttt) cc_final: 0.6529 (ttt) REVERT: L 36 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7754 (tm-30) REVERT: L 38 ASP cc_start: 0.8377 (p0) cc_final: 0.7793 (p0) REVERT: L 48 LYS cc_start: 0.8951 (mtmt) cc_final: 0.7882 (mmpt) REVERT: L 53 ASP cc_start: 0.8828 (t0) cc_final: 0.8307 (t0) outliers start: 35 outliers final: 24 residues processed: 291 average time/residue: 1.1692 time to fit residues: 355.7893 Evaluate side-chains 307 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 52 SER 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 48 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 SER 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 E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain F residue 47 GLU 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 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 K residue 33 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 overall best weight: 7.0988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.101832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.095812 restraints weight = 22663.960| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 3.82 r_work: 0.4009 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6684 Z= 0.374 Angle : 1.067 16.627 9036 Z= 0.515 Chirality : 0.049 0.173 912 Planarity : 0.004 0.052 1164 Dihedral : 5.925 19.833 840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.64 % Allowed : 34.84 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 60 HIS 0.004 0.001 HIS A 31 PHE 0.009 0.001 PHE K 30 TYR 0.031 0.001 TYR C 66 ARG 0.012 0.001 ARG E 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7636.97 seconds wall clock time: 130 minutes 0.07 seconds (7800.07 seconds total)