Starting phenix.real_space_refine on Thu Jul 24 15:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7q_15224/07_2025/8a7q_15224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7q_15224/07_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_15224/07_2025/8a7q_15224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7q_15224/07_2025/8a7q_15224.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7q_15224/07_2025/8a7q_15224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7q_15224/07_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-5711/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: 4.81, per 1000 atoms: 0.74 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: 1.35 Conformation dependent library (CDL) restraints added in 871.9 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: 0.94 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: 1.94 Time building geometry restraints manager: 1.66 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: 1.700 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.550 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:15.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6696 Z= 0.289 Angle : 0.673 4.426 9060 Z= 0.451 Chirality : 0.055 0.217 912 Planarity : 0.003 0.022 1164 Dihedral : 11.640 85.115 2400 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.26326 ( 93) hydrogen bonds : angle 10.67194 ( 279) SS BOND : bond 0.00155 ( 12) SS BOND : angle 0.58244 ( 24) covalent geometry : bond 0.00417 ( 6684) covalent geometry : angle 0.67348 ( 9036) *********************** 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 : 0.737 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: 1.2093 time to fit residues: 477.3798 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 : 0.801 ------------------------------------------------------------------------------- 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: 10.0000 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: 40.0000 chunk 65 optimal weight: 9.9990 overall best weight: 9.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN B 24 ASN C 83 ASN D 24 ASN E 24 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS H 24 ASN 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 = 0.4236 r_free = 0.4236 target = 0.103631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.097521 restraints weight = 21387.997| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.82 r_work: 0.3991 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 6696 Z= 0.282 Angle : 0.830 7.145 9060 Z= 0.435 Chirality : 0.048 0.160 912 Planarity : 0.004 0.040 1164 Dihedral : 5.174 14.214 840 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.15 % Allowed : 25.82 % Favored : 68.03 % 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 0.005 0.001 HIS A 31 PHE 0.016 0.002 PHE H 22 TYR 0.017 0.002 TYR B 66 ARG 0.008 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 93) hydrogen bonds : angle 7.92902 ( 279) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.45418 ( 24) covalent geometry : bond 0.00658 ( 6684) covalent geometry : angle 0.83100 ( 9036) *********************** 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 365 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.5427 (pm20) cc_final: 0.4984 (pm20) REVERT: A 45 ARG cc_start: 0.9114 (mtt180) cc_final: 0.7106 (tmm160) REVERT: B 36 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 38 ASP cc_start: 0.8555 (p0) cc_final: 0.8090 (p0) REVERT: B 41 LYS cc_start: 0.5346 (OUTLIER) cc_final: 0.3857 (mppt) REVERT: B 48 LYS cc_start: 0.8888 (mttt) cc_final: 0.7432 (pmtt) REVERT: B 50 GLU cc_start: 0.8443 (mp0) cc_final: 0.8148 (mp0) REVERT: B 58 LYS cc_start: 0.5457 (OUTLIER) cc_final: 0.4326 (pmtt) REVERT: C 36 GLU cc_start: 0.5303 (pm20) cc_final: 0.4645 (pm20) REVERT: C 44 GLU cc_start: 0.8875 (tt0) cc_final: 0.8478 (tt0) REVERT: C 45 ARG cc_start: 0.9144 (mtt180) cc_final: 0.7129 (tmm160) REVERT: C 76 ASP cc_start: 0.8274 (m-30) cc_final: 0.7860 (m-30) REVERT: D 36 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 38 ASP cc_start: 0.8510 (p0) cc_final: 0.7818 (p0) REVERT: D 41 LYS cc_start: 0.5621 (OUTLIER) cc_final: 0.4113 (mppt) REVERT: D 48 LYS cc_start: 0.8862 (mttt) cc_final: 0.7246 (pmtt) REVERT: D 50 GLU cc_start: 0.8399 (mp0) cc_final: 0.8156 (mp0) REVERT: D 74 GLU cc_start: 0.4405 (mm-30) cc_final: 0.4137 (tp30) REVERT: D 77 GLU cc_start: 0.4366 (pm20) cc_final: 0.4147 (pm20) REVERT: E 50 GLU cc_start: 0.8391 (mp0) cc_final: 0.8175 (mp0) REVERT: E 58 LYS cc_start: 0.9283 (mmmt) cc_final: 0.9070 (mmtt) REVERT: F 34 ASP cc_start: 0.9048 (t0) cc_final: 0.8777 (t0) REVERT: F 36 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7848 (tm-30) REVERT: F 38 ASP cc_start: 0.8512 (p0) cc_final: 0.8287 (p0) REVERT: F 50 GLU cc_start: 0.8459 (mp0) cc_final: 0.8160 (mp0) REVERT: F 53 ASP cc_start: 0.8809 (t0) cc_final: 0.8530 (t0) REVERT: F 73 THR cc_start: 0.9446 (m) cc_final: 0.9133 (t) REVERT: F 76 ASP cc_start: 0.8440 (m-30) cc_final: 0.8120 (m-30) REVERT: G 58 LYS cc_start: 0.9283 (mmmt) cc_final: 0.9075 (mmtt) REVERT: H 34 ASP cc_start: 0.9014 (t0) cc_final: 0.8666 (t0) REVERT: H 36 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7355 (tm-30) REVERT: H 38 ASP cc_start: 0.8516 (p0) cc_final: 0.7382 (p0) REVERT: H 53 ASP cc_start: 0.8786 (t0) cc_final: 0.8492 (t0) REVERT: I 33 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8698 (t) REVERT: I 48 LYS cc_start: 0.4840 (OUTLIER) cc_final: 0.3652 (mmpt) REVERT: J 27 MET cc_start: 0.7434 (ttt) cc_final: 0.6757 (ttt) REVERT: J 34 ASP cc_start: 0.9202 (t0) cc_final: 0.8942 (t0) REVERT: J 36 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7944 (tm-30) REVERT: J 38 ASP cc_start: 0.8522 (p0) cc_final: 0.7920 (p0) REVERT: J 48 LYS cc_start: 0.8763 (mttt) cc_final: 0.7982 (mmpt) REVERT: J 53 ASP cc_start: 0.8851 (t0) cc_final: 0.8239 (t0) REVERT: K 33 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8678 (t) REVERT: K 48 LYS cc_start: 0.5113 (OUTLIER) cc_final: 0.3938 (mmpt) REVERT: L 27 MET cc_start: 0.7466 (ttt) cc_final: 0.6732 (ttt) REVERT: L 36 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7877 (tm-30) REVERT: L 38 ASP cc_start: 0.8377 (p0) cc_final: 0.7759 (p0) REVERT: L 48 LYS cc_start: 0.8750 (mttt) cc_final: 0.7964 (mmpt) REVERT: L 53 ASP cc_start: 0.8894 (t0) cc_final: 0.8341 (t0) outliers start: 45 outliers final: 13 residues processed: 329 average time/residue: 1.2107 time to fit residues: 416.9459 Evaluate side-chains 303 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain D residue 73 THR 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 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 K 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.102124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.096165 restraints weight = 21686.094| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.79 r_work: 0.3992 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6696 Z= 0.241 Angle : 0.801 10.411 9060 Z= 0.412 Chirality : 0.047 0.169 912 Planarity : 0.004 0.031 1164 Dihedral : 5.244 15.727 840 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.42 % Allowed : 26.64 % Favored : 66.94 % 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: -4.72 (0.19), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.14), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 60 HIS 0.005 0.001 HIS C 31 PHE 0.012 0.002 PHE K 22 TYR 0.009 0.001 TYR G 78 ARG 0.008 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 93) hydrogen bonds : angle 7.28382 ( 279) SS BOND : bond 0.00227 ( 12) SS BOND : angle 0.28102 ( 24) covalent geometry : bond 0.00566 ( 6684) covalent geometry : angle 0.80148 ( 9036) *********************** 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 362 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9162 (mtt180) cc_final: 0.7056 (tmm160) REVERT: B 36 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7682 (tm-30) REVERT: B 38 ASP cc_start: 0.8580 (p0) cc_final: 0.8170 (p0) REVERT: B 41 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.3374 (pttm) REVERT: B 48 LYS cc_start: 0.8907 (mttt) cc_final: 0.7501 (pmtt) REVERT: B 50 GLU cc_start: 0.8432 (mp0) cc_final: 0.8102 (mp0) REVERT: B 58 LYS cc_start: 0.4246 (OUTLIER) cc_final: 0.3379 (pmtt) REVERT: C 44 GLU cc_start: 0.8866 (tt0) cc_final: 0.8440 (tt0) REVERT: C 45 ARG cc_start: 0.9050 (mtt180) cc_final: 0.7128 (tmm160) REVERT: D 36 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 38 ASP cc_start: 0.8540 (p0) cc_final: 0.8004 (OUTLIER) REVERT: D 41 LYS cc_start: 0.5236 (OUTLIER) cc_final: 0.3492 (pttm) REVERT: D 47 GLU cc_start: 0.5617 (pm20) cc_final: 0.5209 (pm20) REVERT: D 48 LYS cc_start: 0.8684 (mttt) cc_final: 0.7389 (pmtt) REVERT: D 50 GLU cc_start: 0.8393 (mp0) cc_final: 0.8150 (mp0) REVERT: E 50 GLU cc_start: 0.8469 (mp0) cc_final: 0.8047 (mp0) REVERT: E 58 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9111 (mmtt) REVERT: E 74 GLU cc_start: 0.9052 (pm20) cc_final: 0.8790 (mp0) REVERT: F 34 ASP cc_start: 0.9090 (t0) cc_final: 0.8785 (t0) REVERT: F 36 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7964 (tm-30) REVERT: F 38 ASP cc_start: 0.8485 (p0) cc_final: 0.8169 (p0) REVERT: F 41 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8673 (ttmm) REVERT: F 47 GLU cc_start: 0.8605 (tp30) cc_final: 0.8163 (tp30) REVERT: F 53 ASP cc_start: 0.8834 (t0) cc_final: 0.8496 (t0) REVERT: F 73 THR cc_start: 0.9439 (m) cc_final: 0.9093 (t) REVERT: G 48 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8853 (ptpp) REVERT: G 58 LYS cc_start: 0.9370 (mmmt) cc_final: 0.9110 (mmtt) REVERT: G 74 GLU cc_start: 0.8772 (pm20) cc_final: 0.8481 (pm20) REVERT: G 75 LYS cc_start: 0.8569 (mppt) cc_final: 0.8224 (tptp) REVERT: H 34 ASP cc_start: 0.8979 (t0) cc_final: 0.8677 (t0) REVERT: H 36 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7570 (tm-30) REVERT: H 38 ASP cc_start: 0.8530 (p0) cc_final: 0.7483 (p0) REVERT: H 47 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7710 (tm-30) REVERT: H 50 GLU cc_start: 0.8634 (mp0) cc_final: 0.8247 (mp0) REVERT: H 53 ASP cc_start: 0.8851 (t0) cc_final: 0.8507 (t0) REVERT: I 44 GLU cc_start: 0.8775 (tt0) cc_final: 0.8059 (tm-30) REVERT: I 47 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: I 48 LYS cc_start: 0.4617 (OUTLIER) cc_final: 0.3409 (mmpt) REVERT: J 27 MET cc_start: 0.7314 (ttt) cc_final: 0.6654 (ttt) REVERT: J 34 ASP cc_start: 0.9193 (t0) cc_final: 0.8957 (t0) REVERT: J 36 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8016 (tm-30) REVERT: J 38 ASP cc_start: 0.8580 (p0) cc_final: 0.7879 (p0) REVERT: J 48 LYS cc_start: 0.8764 (mttt) cc_final: 0.7921 (mmpt) REVERT: J 50 GLU cc_start: 0.8197 (mp0) cc_final: 0.7912 (mp0) REVERT: J 53 ASP cc_start: 0.8830 (t0) cc_final: 0.8232 (t0) REVERT: J 76 ASP cc_start: 0.7646 (m-30) cc_final: 0.6348 (m-30) REVERT: K 38 ASP cc_start: 0.8728 (p0) cc_final: 0.7667 (p0) REVERT: K 44 GLU cc_start: 0.8729 (tt0) cc_final: 0.8061 (tm-30) REVERT: K 48 LYS cc_start: 0.4758 (OUTLIER) cc_final: 0.3662 (mmpt) REVERT: L 27 MET cc_start: 0.7325 (ttt) cc_final: 0.6663 (ttt) REVERT: L 36 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7932 (tm-30) REVERT: L 38 ASP cc_start: 0.8499 (p0) cc_final: 0.7874 (p0) REVERT: L 48 LYS cc_start: 0.8804 (mttt) cc_final: 0.7974 (mmpt) REVERT: L 50 GLU cc_start: 0.8268 (mp0) cc_final: 0.7973 (mp0) REVERT: L 53 ASP cc_start: 0.8906 (t0) cc_final: 0.8360 (t0) outliers start: 47 outliers final: 23 residues processed: 327 average time/residue: 1.1275 time to fit residues: 385.8982 Evaluate side-chains 311 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.102367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.096486 restraints weight = 21924.662| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.78 r_work: 0.4006 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6696 Z= 0.206 Angle : 0.784 11.778 9060 Z= 0.397 Chirality : 0.046 0.136 912 Planarity : 0.004 0.036 1164 Dihedral : 5.285 16.566 840 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.74 % Allowed : 28.14 % 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: -4.69 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 60 HIS 0.006 0.001 HIS A 31 PHE 0.023 0.002 PHE A 22 TYR 0.024 0.001 TYR D 66 ARG 0.009 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 93) hydrogen bonds : angle 6.84923 ( 279) SS BOND : bond 0.00222 ( 12) SS BOND : angle 0.25568 ( 24) covalent geometry : bond 0.00489 ( 6684) covalent geometry : angle 0.78481 ( 9036) *********************** 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 351 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 309 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9316 (tt) cc_final: 0.9104 (tt) REVERT: A 45 ARG cc_start: 0.9139 (mtt180) cc_final: 0.7003 (tmm160) REVERT: B 36 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 38 ASP cc_start: 0.8603 (p0) cc_final: 0.8228 (p0) REVERT: B 41 LYS cc_start: 0.5292 (OUTLIER) cc_final: 0.4095 (pttm) REVERT: B 48 LYS cc_start: 0.8888 (mttt) cc_final: 0.7407 (pmtt) REVERT: B 50 GLU cc_start: 0.8438 (mp0) cc_final: 0.8155 (mp0) REVERT: B 58 LYS cc_start: 0.4402 (OUTLIER) cc_final: 0.3467 (pmtt) REVERT: C 44 GLU cc_start: 0.8876 (tt0) cc_final: 0.8597 (tt0) REVERT: C 45 ARG cc_start: 0.9059 (mtt180) cc_final: 0.7125 (tmm160) REVERT: D 36 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 38 ASP cc_start: 0.8502 (p0) cc_final: 0.7944 (p0) REVERT: D 41 LYS cc_start: 0.5491 (OUTLIER) cc_final: 0.4242 (pttm) REVERT: D 48 LYS cc_start: 0.8604 (mttt) cc_final: 0.7371 (pmtt) REVERT: D 50 GLU cc_start: 0.8379 (mp0) cc_final: 0.8082 (mp0) REVERT: E 38 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7964 (t70) REVERT: E 48 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8580 (mtpm) REVERT: E 58 LYS cc_start: 0.9308 (mmmt) cc_final: 0.9057 (mmtt) REVERT: E 74 GLU cc_start: 0.9055 (pm20) cc_final: 0.8650 (pm20) REVERT: F 34 ASP cc_start: 0.9106 (t0) cc_final: 0.8797 (t0) REVERT: F 36 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7978 (tm-30) REVERT: F 38 ASP cc_start: 0.8347 (p0) cc_final: 0.8070 (p0) REVERT: F 41 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8765 (ttmm) REVERT: F 47 GLU cc_start: 0.8420 (tp30) cc_final: 0.7949 (tm-30) REVERT: F 48 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8415 (ttmt) REVERT: F 53 ASP cc_start: 0.8873 (t0) cc_final: 0.8472 (t0) REVERT: F 73 THR cc_start: 0.9395 (m) cc_final: 0.9085 (t) REVERT: G 47 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8399 (tm-30) REVERT: G 48 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8796 (ptpp) REVERT: G 50 GLU cc_start: 0.9021 (mp0) cc_final: 0.8119 (mp0) REVERT: G 58 LYS cc_start: 0.9313 (mmmt) cc_final: 0.9058 (mmtt) REVERT: H 34 ASP cc_start: 0.8995 (t0) cc_final: 0.8678 (t0) REVERT: H 36 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7494 (tm-30) REVERT: H 38 ASP cc_start: 0.8378 (p0) cc_final: 0.7288 (p0) REVERT: H 47 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7695 (tm-30) REVERT: H 48 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8564 (ttpt) REVERT: H 50 GLU cc_start: 0.8499 (mp0) cc_final: 0.8170 (mp0) REVERT: H 53 ASP cc_start: 0.8886 (t0) cc_final: 0.8499 (t0) REVERT: I 33 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8851 (t) REVERT: I 38 ASP cc_start: 0.8454 (p0) cc_final: 0.7343 (p0) REVERT: I 44 GLU cc_start: 0.8754 (tt0) cc_final: 0.8060 (tm-30) REVERT: I 47 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: I 48 LYS cc_start: 0.4531 (OUTLIER) cc_final: 0.3358 (mmpt) REVERT: I 74 GLU cc_start: 0.8472 (pm20) cc_final: 0.8173 (mp0) REVERT: J 27 MET cc_start: 0.7258 (ttt) cc_final: 0.6579 (ttt) REVERT: J 34 ASP cc_start: 0.9192 (t0) cc_final: 0.8939 (t0) REVERT: J 36 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8021 (tm-30) REVERT: J 38 ASP cc_start: 0.8633 (p0) cc_final: 0.7913 (p0) REVERT: J 48 LYS cc_start: 0.8846 (mttt) cc_final: 0.7975 (mmpt) REVERT: J 50 GLU cc_start: 0.8283 (mp0) cc_final: 0.7894 (mp0) REVERT: J 53 ASP cc_start: 0.8893 (t0) cc_final: 0.8311 (t0) REVERT: K 33 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8799 (t) REVERT: K 44 GLU cc_start: 0.8729 (tt0) cc_final: 0.8153 (tm-30) REVERT: K 48 LYS cc_start: 0.4626 (OUTLIER) cc_final: 0.3495 (mmpt) REVERT: L 27 MET cc_start: 0.7230 (ttt) cc_final: 0.6561 (ttt) REVERT: L 36 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7979 (tm-30) REVERT: L 38 ASP cc_start: 0.8582 (p0) cc_final: 0.7916 (p0) REVERT: L 48 LYS cc_start: 0.8866 (mttt) cc_final: 0.8006 (mmpt) REVERT: L 50 GLU cc_start: 0.8302 (mp0) cc_final: 0.7890 (mp0) REVERT: L 53 ASP cc_start: 0.8888 (t0) cc_final: 0.8316 (t0) outliers start: 42 outliers final: 21 residues processed: 323 average time/residue: 1.1555 time to fit residues: 390.0598 Evaluate side-chains 315 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER 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 49 VAL 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 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain 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 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: 9.9990 chunk 60 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.101489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.095558 restraints weight = 22304.483| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.73 r_work: 0.3988 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6696 Z= 0.269 Angle : 0.872 13.467 9060 Z= 0.438 Chirality : 0.049 0.233 912 Planarity : 0.004 0.035 1164 Dihedral : 5.552 19.348 840 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 7.38 % Allowed : 28.14 % Favored : 64.48 % 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: -4.67 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS C 31 PHE 0.025 0.002 PHE C 22 TYR 0.013 0.001 TYR E 66 ARG 0.009 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 93) hydrogen bonds : angle 7.07767 ( 279) SS BOND : bond 0.00305 ( 12) SS BOND : angle 0.27586 ( 24) covalent geometry : bond 0.00635 ( 6684) covalent geometry : angle 0.87339 ( 9036) *********************** 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 342 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7790 (ttt) cc_final: 0.7588 (ttt) REVERT: A 45 ARG cc_start: 0.9139 (mtt180) cc_final: 0.6963 (tmm160) REVERT: A 74 GLU cc_start: 0.3406 (tp30) cc_final: 0.3159 (mm-30) REVERT: B 41 LYS cc_start: 0.5244 (OUTLIER) cc_final: 0.4309 (pttm) REVERT: B 48 LYS cc_start: 0.8962 (mttt) cc_final: 0.7515 (pmtt) REVERT: B 50 GLU cc_start: 0.8474 (mp0) cc_final: 0.8134 (mp0) REVERT: B 58 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.3378 (pmtt) REVERT: C 44 GLU cc_start: 0.8813 (tt0) cc_final: 0.8461 (tt0) REVERT: C 45 ARG cc_start: 0.9044 (mtt180) cc_final: 0.7025 (tmm160) REVERT: D 36 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7612 (tm-30) REVERT: D 38 ASP cc_start: 0.8465 (p0) cc_final: 0.7913 (p0) REVERT: D 41 LYS cc_start: 0.5120 (OUTLIER) cc_final: 0.3917 (pttm) REVERT: D 48 LYS cc_start: 0.8584 (mttt) cc_final: 0.7274 (pmtt) REVERT: D 50 GLU cc_start: 0.8451 (mp0) cc_final: 0.8151 (mp0) REVERT: E 48 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8545 (pptt) REVERT: E 50 GLU cc_start: 0.8803 (mp0) cc_final: 0.8160 (mp0) REVERT: E 58 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9142 (mmtt) REVERT: F 34 ASP cc_start: 0.9121 (t0) cc_final: 0.8792 (t0) REVERT: F 36 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8109 (tm-30) REVERT: F 41 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8791 (ttmm) REVERT: F 47 GLU cc_start: 0.8507 (tp30) cc_final: 0.8012 (tm-30) REVERT: F 53 ASP cc_start: 0.8879 (t0) cc_final: 0.8497 (t0) REVERT: F 73 THR cc_start: 0.9355 (m) cc_final: 0.9074 (t) REVERT: G 47 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8425 (tm-30) REVERT: G 50 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8750 (mp0) REVERT: G 58 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9120 (mmtt) REVERT: G 74 GLU cc_start: 0.8775 (pm20) cc_final: 0.8547 (pm20) REVERT: G 75 LYS cc_start: 0.8557 (mppt) cc_final: 0.8322 (tptp) REVERT: H 34 ASP cc_start: 0.8995 (t0) cc_final: 0.8672 (t0) REVERT: H 36 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7513 (tm-30) REVERT: H 38 ASP cc_start: 0.8374 (p0) cc_final: 0.7202 (p0) REVERT: H 41 LYS cc_start: 0.9078 (ttmp) cc_final: 0.8575 (ttmm) REVERT: H 47 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7764 (tm-30) REVERT: H 50 GLU cc_start: 0.8518 (mp0) cc_final: 0.8165 (mp0) REVERT: H 53 ASP cc_start: 0.8880 (t0) cc_final: 0.8549 (t0) REVERT: I 33 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8756 (t) REVERT: I 38 ASP cc_start: 0.8745 (p0) cc_final: 0.8035 (p0) REVERT: I 44 GLU cc_start: 0.8715 (tt0) cc_final: 0.8118 (tm-30) REVERT: I 48 LYS cc_start: 0.4713 (OUTLIER) cc_final: 0.3568 (mmpt) REVERT: J 27 MET cc_start: 0.7265 (ttt) cc_final: 0.6640 (ttt) REVERT: J 34 ASP cc_start: 0.9208 (t0) cc_final: 0.8959 (t0) REVERT: J 36 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7497 (tm-30) REVERT: J 38 ASP cc_start: 0.8652 (p0) cc_final: 0.7539 (p0) REVERT: J 48 LYS cc_start: 0.8850 (mttt) cc_final: 0.7936 (mmpt) REVERT: J 53 ASP cc_start: 0.8857 (t0) cc_final: 0.8226 (t0) REVERT: K 44 GLU cc_start: 0.8734 (tt0) cc_final: 0.8201 (tm-30) REVERT: K 48 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3037 (mmpt) REVERT: L 27 MET cc_start: 0.7276 (ttt) cc_final: 0.6627 (ttt) REVERT: L 36 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7881 (tm-30) REVERT: L 38 ASP cc_start: 0.8606 (p0) cc_final: 0.7848 (p0) REVERT: L 48 LYS cc_start: 0.8860 (mttt) cc_final: 0.7949 (mmpt) REVERT: L 53 ASP cc_start: 0.8831 (t0) cc_final: 0.8266 (t0) outliers start: 54 outliers final: 25 residues processed: 308 average time/residue: 1.2617 time to fit residues: 405.4658 Evaluate side-chains 305 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 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 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 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 46 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 47 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** 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 = 0.4230 r_free = 0.4230 target = 0.101610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.095795 restraints weight = 21909.378| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.68 r_work: 0.4011 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6696 Z= 0.222 Angle : 0.896 16.027 9060 Z= 0.439 Chirality : 0.048 0.297 912 Planarity : 0.004 0.040 1164 Dihedral : 5.540 16.821 840 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.28 % Allowed : 28.69 % Favored : 65.03 % 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 0.002 0.000 TRP I 60 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.002 PHE A 22 TYR 0.027 0.002 TYR A 66 ARG 0.010 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 93) hydrogen bonds : angle 6.73059 ( 279) SS BOND : bond 0.00256 ( 12) SS BOND : angle 0.35489 ( 24) covalent geometry : bond 0.00531 ( 6684) covalent geometry : angle 0.89714 ( 9036) *********************** 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 340 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7751 (ttt) cc_final: 0.7546 (ttt) REVERT: A 41 LYS cc_start: 0.5302 (pmtt) cc_final: 0.2856 (pptt) REVERT: A 45 ARG cc_start: 0.9078 (mtt180) cc_final: 0.6887 (tmm160) REVERT: A 74 GLU cc_start: 0.3077 (tp30) cc_final: 0.2861 (mm-30) REVERT: B 41 LYS cc_start: 0.5388 (OUTLIER) cc_final: 0.4471 (pttm) REVERT: B 48 LYS cc_start: 0.8914 (mttt) cc_final: 0.7082 (pmtt) REVERT: B 50 GLU cc_start: 0.8428 (mp0) cc_final: 0.8131 (mp0) REVERT: C 44 GLU cc_start: 0.8789 (tt0) cc_final: 0.8530 (tt0) REVERT: C 45 ARG cc_start: 0.9030 (mtt180) cc_final: 0.7111 (tmm160) REVERT: D 36 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7413 (tm-30) REVERT: D 38 ASP cc_start: 0.8561 (p0) cc_final: 0.7937 (p0) REVERT: D 41 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.3990 (pttm) REVERT: D 48 LYS cc_start: 0.8443 (mttt) cc_final: 0.7233 (pmtt) REVERT: D 50 GLU cc_start: 0.8404 (mp0) cc_final: 0.8198 (mp0) REVERT: E 48 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8547 (pptt) REVERT: E 50 GLU cc_start: 0.8835 (mp0) cc_final: 0.8607 (mp0) REVERT: F 34 ASP cc_start: 0.9138 (t0) cc_final: 0.8821 (t0) REVERT: F 36 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 38 ASP cc_start: 0.8565 (p0) cc_final: 0.8182 (p0) REVERT: F 41 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8775 (ttmm) REVERT: F 45 ARG cc_start: 0.9229 (mtt90) cc_final: 0.8993 (mtt-85) REVERT: F 48 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8524 (ttmt) REVERT: F 53 ASP cc_start: 0.8917 (t0) cc_final: 0.8510 (t0) REVERT: F 73 THR cc_start: 0.9331 (m) cc_final: 0.9031 (t) REVERT: G 36 GLU cc_start: 0.8911 (tt0) cc_final: 0.8460 (tt0) REVERT: G 38 ASP cc_start: 0.8534 (t0) cc_final: 0.8303 (t0) REVERT: G 41 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8348 (mttp) REVERT: G 47 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: G 74 GLU cc_start: 0.8748 (pm20) cc_final: 0.8542 (pm20) REVERT: G 75 LYS cc_start: 0.8539 (mppt) cc_final: 0.8322 (tptp) REVERT: H 34 ASP cc_start: 0.9032 (t0) cc_final: 0.8709 (t0) REVERT: H 36 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 38 ASP cc_start: 0.8263 (p0) cc_final: 0.7015 (p0) REVERT: H 41 LYS cc_start: 0.9102 (ttmp) cc_final: 0.8600 (ttmm) REVERT: H 48 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8462 (ttmt) REVERT: H 53 ASP cc_start: 0.8867 (t0) cc_final: 0.8511 (t0) REVERT: I 44 GLU cc_start: 0.8696 (tt0) cc_final: 0.8178 (tm-30) REVERT: I 48 LYS cc_start: 0.4268 (OUTLIER) cc_final: 0.3053 (mmpt) REVERT: I 74 GLU cc_start: 0.8352 (pm20) cc_final: 0.8041 (mp0) REVERT: J 27 MET cc_start: 0.7193 (ttt) cc_final: 0.6570 (ttt) REVERT: J 34 ASP cc_start: 0.9227 (t0) cc_final: 0.9002 (t0) REVERT: J 36 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7603 (tm-30) REVERT: J 38 ASP cc_start: 0.8713 (p0) cc_final: 0.7573 (p0) REVERT: J 48 LYS cc_start: 0.8852 (mttt) cc_final: 0.7966 (mmpt) REVERT: J 50 GLU cc_start: 0.8279 (mp0) cc_final: 0.7889 (mp0) REVERT: J 53 ASP cc_start: 0.8894 (t0) cc_final: 0.8282 (t0) REVERT: K 44 GLU cc_start: 0.8660 (tt0) cc_final: 0.8169 (tm-30) REVERT: K 48 LYS cc_start: 0.4464 (OUTLIER) cc_final: 0.3357 (mmpt) REVERT: L 27 MET cc_start: 0.7218 (ttt) cc_final: 0.6591 (ttt) REVERT: L 36 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7806 (tm-30) REVERT: L 38 ASP cc_start: 0.8533 (p0) cc_final: 0.7781 (p0) REVERT: L 50 GLU cc_start: 0.8273 (mp0) cc_final: 0.8012 (mp0) REVERT: L 53 ASP cc_start: 0.8820 (t0) cc_final: 0.8262 (t0) outliers start: 46 outliers final: 27 residues processed: 310 average time/residue: 1.7057 time to fit residues: 550.9594 Evaluate side-chains 311 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 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 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 E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 47 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 39 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 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** ** 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 = 0.4249 r_free = 0.4249 target = 0.101872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.095868 restraints weight = 21726.702| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 3.82 r_work: 0.4016 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6696 Z= 0.201 Angle : 0.910 13.611 9060 Z= 0.448 Chirality : 0.048 0.173 912 Planarity : 0.004 0.046 1164 Dihedral : 5.576 21.193 840 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.60 % Allowed : 32.24 % Favored : 62.16 % 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 0.002 0.000 TRP I 60 HIS 0.003 0.001 HIS A 31 PHE 0.008 0.001 PHE H 62 TYR 0.011 0.001 TYR G 66 ARG 0.011 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 93) hydrogen bonds : angle 6.59261 ( 279) SS BOND : bond 0.00218 ( 12) SS BOND : angle 0.39707 ( 24) covalent geometry : bond 0.00485 ( 6684) covalent geometry : angle 0.91138 ( 9036) *********************** 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 331 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9087 (mtt180) cc_final: 0.7033 (tmm160) REVERT: A 74 GLU cc_start: 0.3084 (tp30) cc_final: 0.2819 (mm-30) REVERT: B 36 GLU cc_start: 0.4561 (pm20) cc_final: 0.4121 (tm-30) REVERT: B 38 ASP cc_start: 0.8738 (p0) cc_final: 0.8053 (p0) REVERT: B 41 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.4411 (pttm) REVERT: B 48 LYS cc_start: 0.8739 (mttt) cc_final: 0.7097 (pmtt) REVERT: B 50 GLU cc_start: 0.8493 (mp0) cc_final: 0.8170 (mp0) REVERT: C 44 GLU cc_start: 0.8801 (tt0) cc_final: 0.8570 (tt0) REVERT: C 45 ARG cc_start: 0.9014 (mtt180) cc_final: 0.7137 (tmm160) REVERT: D 36 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7433 (tm-30) REVERT: D 38 ASP cc_start: 0.8472 (p0) cc_final: 0.7941 (p0) REVERT: E 48 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8463 (mtpp) REVERT: F 34 ASP cc_start: 0.9117 (t0) cc_final: 0.8786 (t0) REVERT: F 36 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7764 (tm-30) REVERT: F 38 ASP cc_start: 0.8411 (p0) cc_final: 0.7551 (p0) REVERT: F 44 GLU cc_start: 0.8738 (tt0) cc_final: 0.8453 (tm-30) REVERT: F 48 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8514 (ttmt) REVERT: F 50 GLU cc_start: 0.8590 (mp0) cc_final: 0.8376 (mp0) REVERT: F 53 ASP cc_start: 0.8901 (t0) cc_final: 0.8547 (t0) REVERT: F 73 THR cc_start: 0.9346 (m) cc_final: 0.9038 (t) REVERT: H 34 ASP cc_start: 0.9053 (t0) cc_final: 0.8728 (t0) REVERT: H 36 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7318 (tm-30) REVERT: H 38 ASP cc_start: 0.8208 (p0) cc_final: 0.7090 (p0) REVERT: H 48 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8437 (ttmt) REVERT: H 53 ASP cc_start: 0.8887 (t0) cc_final: 0.8530 (t0) REVERT: I 36 GLU cc_start: 0.8649 (tt0) cc_final: 0.8447 (tm-30) REVERT: I 44 GLU cc_start: 0.8672 (tt0) cc_final: 0.8135 (tm-30) REVERT: I 47 GLU cc_start: 0.8307 (tp30) cc_final: 0.7942 (tp30) REVERT: I 74 GLU cc_start: 0.8217 (pm20) cc_final: 0.7848 (pm20) REVERT: J 27 MET cc_start: 0.7095 (ttt) cc_final: 0.6493 (ttt) REVERT: J 34 ASP cc_start: 0.9155 (t0) cc_final: 0.8919 (t0) REVERT: J 36 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8090 (tm-30) REVERT: J 38 ASP cc_start: 0.8672 (p0) cc_final: 0.7962 (p0) REVERT: J 48 LYS cc_start: 0.8904 (mttt) cc_final: 0.8031 (mmpt) REVERT: J 50 GLU cc_start: 0.8212 (mp0) cc_final: 0.7862 (mp0) REVERT: J 53 ASP cc_start: 0.8863 (t0) cc_final: 0.8249 (t0) REVERT: K 44 GLU cc_start: 0.8625 (tt0) cc_final: 0.8132 (tm-30) REVERT: K 48 LYS cc_start: 0.4537 (OUTLIER) cc_final: 0.3572 (mmpt) REVERT: L 27 MET cc_start: 0.7178 (ttt) cc_final: 0.6536 (ttt) REVERT: L 36 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7829 (tm-30) REVERT: L 38 ASP cc_start: 0.8438 (p0) cc_final: 0.7677 (p0) REVERT: L 48 LYS cc_start: 0.8928 (mtmt) cc_final: 0.7800 (mmpt) REVERT: L 53 ASP cc_start: 0.8818 (t0) cc_final: 0.8273 (t0) outliers start: 41 outliers final: 30 residues processed: 303 average time/residue: 2.1294 time to fit residues: 676.5767 Evaluate side-chains 311 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 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 52 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 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 ** 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 = 0.4263 r_free = 0.4263 target = 0.102933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.097039 restraints weight = 21952.529| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 3.74 r_work: 0.4039 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6696 Z= 0.191 Angle : 0.979 16.798 9060 Z= 0.465 Chirality : 0.048 0.219 912 Planarity : 0.004 0.048 1164 Dihedral : 5.630 24.564 840 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.33 % Allowed : 31.97 % 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: -4.72 (0.21), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP I 60 HIS 0.003 0.001 HIS A 31 PHE 0.022 0.001 PHE A 22 TYR 0.025 0.001 TYR A 66 ARG 0.011 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 93) hydrogen bonds : angle 6.53842 ( 279) SS BOND : bond 0.00193 ( 12) SS BOND : angle 0.41831 ( 24) covalent geometry : bond 0.00464 ( 6684) covalent geometry : angle 0.98041 ( 9036) *********************** 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 335 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5042 (pmtt) cc_final: 0.2694 (pptt) REVERT: A 45 ARG cc_start: 0.9030 (mtt180) cc_final: 0.6854 (tmm160) REVERT: A 69 GLU cc_start: 0.4262 (pm20) cc_final: 0.3794 (pm20) REVERT: B 36 GLU cc_start: 0.4426 (pm20) cc_final: 0.3746 (tm-30) REVERT: B 38 ASP cc_start: 0.8693 (p0) cc_final: 0.7951 (p0) REVERT: B 48 LYS cc_start: 0.8687 (mttt) cc_final: 0.7076 (pmtt) REVERT: B 50 GLU cc_start: 0.8493 (mp0) cc_final: 0.8195 (mp0) REVERT: C 44 GLU cc_start: 0.8739 (tt0) cc_final: 0.8482 (tt0) REVERT: C 45 ARG cc_start: 0.9011 (mtt180) cc_final: 0.7112 (tmm160) REVERT: C 69 GLU cc_start: 0.4164 (pm20) cc_final: 0.3786 (pm20) REVERT: D 36 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7409 (tm-30) REVERT: D 38 ASP cc_start: 0.8441 (p0) cc_final: 0.7890 (p0) REVERT: D 58 LYS cc_start: 0.4891 (OUTLIER) cc_final: 0.4021 (pmtt) REVERT: E 47 GLU cc_start: 0.8731 (tp30) cc_final: 0.8255 (tt0) REVERT: E 48 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8628 (mtpp) REVERT: E 59 ASP cc_start: 0.9011 (m-30) cc_final: 0.8777 (m-30) REVERT: E 74 GLU cc_start: 0.8892 (mp0) cc_final: 0.8632 (mp0) REVERT: F 34 ASP cc_start: 0.9122 (t0) cc_final: 0.8814 (t0) REVERT: F 36 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7754 (tm-30) REVERT: F 38 ASP cc_start: 0.8368 (p0) cc_final: 0.7545 (p0) REVERT: F 44 GLU cc_start: 0.8661 (tt0) cc_final: 0.8431 (tm-30) REVERT: F 47 GLU cc_start: 0.8539 (tp30) cc_final: 0.8056 (tm-30) REVERT: F 48 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8655 (ttmt) REVERT: F 53 ASP cc_start: 0.8919 (t0) cc_final: 0.8595 (t0) REVERT: F 73 THR cc_start: 0.9317 (m) cc_final: 0.9002 (t) REVERT: G 38 ASP cc_start: 0.8718 (t0) cc_final: 0.8468 (t0) REVERT: G 44 GLU cc_start: 0.8871 (tt0) cc_final: 0.8580 (tt0) REVERT: G 47 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8387 (tm-30) REVERT: G 50 GLU cc_start: 0.8838 (mp0) cc_final: 0.8587 (mp0) REVERT: G 59 ASP cc_start: 0.9010 (m-30) cc_final: 0.8800 (m-30) REVERT: G 74 GLU cc_start: 0.8721 (pm20) cc_final: 0.8514 (pm20) REVERT: H 36 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7294 (tm-30) REVERT: H 38 ASP cc_start: 0.8158 (p0) cc_final: 0.7023 (p0) REVERT: H 48 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8272 (ttmt) REVERT: H 53 ASP cc_start: 0.8892 (t0) cc_final: 0.8525 (t0) REVERT: I 44 GLU cc_start: 0.8701 (tt0) cc_final: 0.8173 (tm-30) REVERT: I 74 GLU cc_start: 0.8264 (pm20) cc_final: 0.7904 (pm20) REVERT: J 27 MET cc_start: 0.7101 (ttt) cc_final: 0.6520 (ttt) REVERT: J 34 ASP cc_start: 0.9168 (t0) cc_final: 0.8944 (t0) REVERT: J 36 GLU cc_start: 0.8616 (tm-30) cc_final: 0.7966 (tm-30) REVERT: J 38 ASP cc_start: 0.8649 (p0) cc_final: 0.7868 (p0) REVERT: J 50 GLU cc_start: 0.8261 (mp0) cc_final: 0.7988 (mp0) REVERT: J 53 ASP cc_start: 0.8916 (t0) cc_final: 0.8322 (t0) REVERT: K 44 GLU cc_start: 0.8624 (tt0) cc_final: 0.8155 (tm-30) REVERT: K 48 LYS cc_start: 0.4554 (OUTLIER) cc_final: 0.3568 (mmpt) REVERT: L 27 MET cc_start: 0.7151 (ttt) cc_final: 0.6524 (ttt) REVERT: L 36 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7702 (tm-30) REVERT: L 38 ASP cc_start: 0.8419 (p0) cc_final: 0.7714 (p0) REVERT: L 48 LYS cc_start: 0.8907 (mtmt) cc_final: 0.7746 (mmpt) REVERT: L 50 GLU cc_start: 0.8335 (mp0) cc_final: 0.7999 (mp0) REVERT: L 53 ASP cc_start: 0.8844 (t0) cc_final: 0.8295 (t0) outliers start: 39 outliers final: 29 residues processed: 307 average time/residue: 1.6847 time to fit residues: 539.7035 Evaluate side-chains 312 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER 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 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 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 Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 GLU 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: 10.0000 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.102558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.096564 restraints weight = 22400.854| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.79 r_work: 0.4031 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6696 Z= 0.204 Angle : 1.000 16.149 9060 Z= 0.480 Chirality : 0.048 0.183 912 Planarity : 0.004 0.051 1164 Dihedral : 5.685 21.676 840 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.92 % Allowed : 31.97 % Favored : 63.11 % 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 0.002 0.000 TRP L 60 HIS 0.004 0.001 HIS A 31 PHE 0.024 0.001 PHE A 22 TYR 0.009 0.001 TYR F 78 ARG 0.011 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 93) hydrogen bonds : angle 6.51128 ( 279) SS BOND : bond 0.00207 ( 12) SS BOND : angle 0.44741 ( 24) covalent geometry : bond 0.00494 ( 6684) covalent geometry : angle 1.00076 ( 9036) *********************** 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: 36 poor density : 288 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9081 (mtt180) cc_final: 0.6960 (tmm160) REVERT: B 36 GLU cc_start: 0.4331 (pm20) cc_final: 0.3544 (mm-30) REVERT: B 38 ASP cc_start: 0.8683 (p0) cc_final: 0.8355 (m-30) REVERT: B 48 LYS cc_start: 0.8621 (mttt) cc_final: 0.7052 (pmtt) REVERT: B 50 GLU cc_start: 0.8551 (mp0) cc_final: 0.8215 (mp0) REVERT: C 44 GLU cc_start: 0.8808 (tt0) cc_final: 0.8548 (tt0) REVERT: C 45 ARG cc_start: 0.9043 (mtt180) cc_final: 0.7135 (tmm160) REVERT: C 58 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5719 (pmtt) REVERT: C 69 GLU cc_start: 0.4100 (pm20) cc_final: 0.3628 (pm20) REVERT: D 36 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7424 (tm-30) REVERT: D 38 ASP cc_start: 0.8379 (p0) cc_final: 0.7853 (p0) REVERT: D 41 LYS cc_start: 0.5308 (OUTLIER) cc_final: 0.4193 (pttm) REVERT: D 58 LYS cc_start: 0.4742 (OUTLIER) cc_final: 0.3894 (pmtt) REVERT: D 76 ASP cc_start: 0.7726 (m-30) cc_final: 0.7249 (m-30) REVERT: E 48 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8539 (mtpp) REVERT: E 59 ASP cc_start: 0.9048 (m-30) cc_final: 0.8827 (m-30) REVERT: F 34 ASP cc_start: 0.9133 (t0) cc_final: 0.8825 (t0) REVERT: F 36 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7520 (tm-30) REVERT: F 38 ASP cc_start: 0.8344 (p0) cc_final: 0.6790 (p0) REVERT: F 47 GLU cc_start: 0.8614 (tp30) cc_final: 0.8155 (tm-30) REVERT: F 48 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8686 (ttmt) REVERT: F 53 ASP cc_start: 0.8864 (t0) cc_final: 0.8539 (t0) REVERT: F 73 THR cc_start: 0.9337 (m) cc_final: 0.9007 (t) REVERT: G 44 GLU cc_start: 0.8822 (tt0) cc_final: 0.8437 (tt0) REVERT: G 45 ARG cc_start: 0.9505 (mtt-85) cc_final: 0.9095 (mtt-85) REVERT: G 47 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8449 (tm-30) REVERT: G 50 GLU cc_start: 0.8869 (mp0) cc_final: 0.8606 (mp0) REVERT: G 59 ASP cc_start: 0.9050 (m-30) cc_final: 0.8830 (m-30) REVERT: H 34 ASP cc_start: 0.9109 (t0) cc_final: 0.8853 (t0) REVERT: H 36 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7310 (tm-30) REVERT: H 38 ASP cc_start: 0.8143 (p0) cc_final: 0.7129 (p0) REVERT: H 48 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8391 (mtpt) REVERT: H 50 GLU cc_start: 0.8678 (mp0) cc_final: 0.8387 (mp0) REVERT: H 53 ASP cc_start: 0.8888 (t0) cc_final: 0.8520 (t0) REVERT: H 76 ASP cc_start: 0.8771 (m-30) cc_final: 0.8312 (m-30) REVERT: I 44 GLU cc_start: 0.8623 (tt0) cc_final: 0.8160 (tm-30) REVERT: I 47 GLU cc_start: 0.8276 (tp30) cc_final: 0.8039 (tp30) REVERT: I 48 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.4177 (tptp) REVERT: I 74 GLU cc_start: 0.8255 (pm20) cc_final: 0.7874 (pm20) REVERT: J 27 MET cc_start: 0.7079 (ttt) cc_final: 0.6499 (ttt) REVERT: J 34 ASP cc_start: 0.9168 (t0) cc_final: 0.8945 (t0) REVERT: J 36 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8068 (tm-30) REVERT: J 38 ASP cc_start: 0.8621 (p0) cc_final: 0.7946 (p0) REVERT: J 50 GLU cc_start: 0.8265 (mp0) cc_final: 0.8062 (mp0) REVERT: J 53 ASP cc_start: 0.8889 (t0) cc_final: 0.8262 (t0) REVERT: K 44 GLU cc_start: 0.8676 (tt0) cc_final: 0.8198 (tm-30) REVERT: K 48 LYS cc_start: 0.4630 (OUTLIER) cc_final: 0.3645 (mmpt) REVERT: L 27 MET cc_start: 0.7128 (ttt) cc_final: 0.6524 (ttt) REVERT: L 36 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7412 (tm-30) REVERT: L 38 ASP cc_start: 0.8293 (p0) cc_final: 0.7371 (p0) REVERT: L 48 LYS cc_start: 0.8878 (mtmt) cc_final: 0.7735 (mmpt) REVERT: L 53 ASP cc_start: 0.8855 (t0) cc_final: 0.8315 (t0) outliers start: 36 outliers final: 27 residues processed: 300 average time/residue: 1.1529 time to fit residues: 361.7454 Evaluate side-chains 313 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 281 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain B residue 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 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 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 E residue 69 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 39 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.104808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.098668 restraints weight = 21881.107| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.80 r_work: 0.4074 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6696 Z= 0.172 Angle : 1.032 17.264 9060 Z= 0.486 Chirality : 0.048 0.261 912 Planarity : 0.004 0.051 1164 Dihedral : 5.545 23.132 840 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.60 % Allowed : 36.34 % Favored : 61.07 % 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 0.004 0.000 TRP I 60 HIS 0.003 0.001 HIS A 31 PHE 0.024 0.001 PHE A 22 TYR 0.024 0.001 TYR D 66 ARG 0.011 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 93) hydrogen bonds : angle 6.19563 ( 279) SS BOND : bond 0.00141 ( 12) SS BOND : angle 0.39760 ( 24) covalent geometry : bond 0.00423 ( 6684) covalent geometry : angle 1.03351 ( 9036) ********************** 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 322 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.9060 (mtt180) cc_final: 0.6938 (tmm160) REVERT: A 69 GLU cc_start: 0.4519 (pm20) cc_final: 0.4079 (pm20) REVERT: A 76 ASP cc_start: 0.8061 (m-30) cc_final: 0.7425 (t0) REVERT: B 36 GLU cc_start: 0.4265 (pm20) cc_final: 0.3542 (mm-30) REVERT: B 48 LYS cc_start: 0.8565 (mttt) cc_final: 0.7041 (pmtt) REVERT: B 50 GLU cc_start: 0.8558 (mp0) cc_final: 0.8231 (mp0) REVERT: C 44 GLU cc_start: 0.8792 (tt0) cc_final: 0.8583 (tt0) REVERT: C 45 ARG cc_start: 0.8986 (mtt180) cc_final: 0.7138 (tmm160) REVERT: C 69 GLU cc_start: 0.3995 (pm20) cc_final: 0.3598 (pm20) REVERT: D 36 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 38 ASP cc_start: 0.8153 (p0) cc_final: 0.7754 (p0) REVERT: D 58 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.3956 (pmtt) REVERT: E 44 GLU cc_start: 0.8819 (tt0) cc_final: 0.8578 (tt0) REVERT: E 47 GLU cc_start: 0.8550 (tp30) cc_final: 0.8069 (tt0) REVERT: E 48 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8655 (mtpp) REVERT: F 34 ASP cc_start: 0.9112 (t0) cc_final: 0.8814 (t0) REVERT: F 36 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7489 (tm-30) REVERT: F 38 ASP cc_start: 0.8286 (p0) cc_final: 0.6662 (p0) REVERT: F 47 GLU cc_start: 0.8597 (tp30) cc_final: 0.8255 (tm-30) REVERT: F 53 ASP cc_start: 0.8879 (t0) cc_final: 0.8525 (t0) REVERT: F 73 THR cc_start: 0.9290 (m) cc_final: 0.8950 (t) REVERT: G 47 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8403 (tm-30) REVERT: G 50 GLU cc_start: 0.8890 (mp0) cc_final: 0.8577 (mp0) REVERT: H 34 ASP cc_start: 0.9099 (t0) cc_final: 0.8822 (t0) REVERT: H 36 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7276 (tm-30) REVERT: H 38 ASP cc_start: 0.7997 (p0) cc_final: 0.7114 (p0) REVERT: H 44 GLU cc_start: 0.8856 (tt0) cc_final: 0.8620 (tt0) REVERT: H 50 GLU cc_start: 0.8656 (mp0) cc_final: 0.8397 (mp0) REVERT: H 53 ASP cc_start: 0.8932 (t0) cc_final: 0.8557 (t0) REVERT: I 44 GLU cc_start: 0.8870 (tt0) cc_final: 0.8262 (tm-30) REVERT: I 48 LYS cc_start: 0.4479 (OUTLIER) cc_final: 0.4247 (tptp) REVERT: I 74 GLU cc_start: 0.8276 (pm20) cc_final: 0.7959 (pm20) REVERT: J 27 MET cc_start: 0.7098 (ttt) cc_final: 0.6506 (ttt) REVERT: J 34 ASP cc_start: 0.9218 (t0) cc_final: 0.9006 (t0) REVERT: J 36 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8067 (tm-30) REVERT: J 38 ASP cc_start: 0.8610 (p0) cc_final: 0.7919 (p0) REVERT: J 48 LYS cc_start: 0.8965 (mtmt) cc_final: 0.7849 (mmpt) REVERT: J 50 GLU cc_start: 0.8290 (mp0) cc_final: 0.7996 (mp0) REVERT: J 53 ASP cc_start: 0.8891 (t0) cc_final: 0.8341 (t0) REVERT: K 33 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8787 (t) REVERT: K 36 GLU cc_start: 0.8473 (tt0) cc_final: 0.8073 (tm-30) REVERT: K 39 LEU cc_start: 0.8682 (tm) cc_final: 0.8464 (tm) REVERT: K 44 GLU cc_start: 0.8678 (tt0) cc_final: 0.8206 (tm-30) REVERT: K 48 LYS cc_start: 0.4819 (OUTLIER) cc_final: 0.3767 (mmpt) REVERT: L 27 MET cc_start: 0.7127 (ttt) cc_final: 0.6516 (ttt) REVERT: L 36 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7406 (tm-30) REVERT: L 38 ASP cc_start: 0.8103 (p0) cc_final: 0.7134 (p0) REVERT: L 44 GLU cc_start: 0.9047 (tt0) cc_final: 0.8720 (tt0) REVERT: L 48 LYS cc_start: 0.8954 (mtmt) cc_final: 0.7731 (mmpt) REVERT: L 50 GLU cc_start: 0.8306 (mp0) cc_final: 0.8038 (mp0) REVERT: L 53 ASP cc_start: 0.8829 (t0) cc_final: 0.8291 (t0) outliers start: 19 outliers final: 12 residues processed: 308 average time/residue: 1.1472 time to fit residues: 369.6021 Evaluate side-chains 299 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 283 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 58 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain G residue 33 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.103075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.097071 restraints weight = 22713.478| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.76 r_work: 0.4034 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6696 Z= 0.211 Angle : 1.065 15.972 9060 Z= 0.507 Chirality : 0.050 0.283 912 Planarity : 0.004 0.050 1164 Dihedral : 5.634 22.039 840 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.87 % Allowed : 37.57 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.000 TRP G 60 HIS 0.004 0.001 HIS A 31 PHE 0.008 0.001 PHE H 62 TYR 0.023 0.001 TYR C 66 ARG 0.011 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 93) hydrogen bonds : angle 6.40402 ( 279) SS BOND : bond 0.00197 ( 12) SS BOND : angle 0.41389 ( 24) covalent geometry : bond 0.00512 ( 6684) covalent geometry : angle 1.06581 ( 9036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8521.74 seconds wall clock time: 152 minutes 36.01 seconds (9156.01 seconds total)