Starting phenix.real_space_refine on Tue Feb 3 19:56:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hyw_52519/02_2026/9hyw_52519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hyw_52519/02_2026/9hyw_52519.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/9hyw_52519/02_2026/9hyw_52519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hyw_52519/02_2026/9hyw_52519.map" model { file = "/net/cci-nas-00/data/ceres_data/9hyw_52519/02_2026/9hyw_52519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hyw_52519/02_2026/9hyw_52519.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 18 5.16 5 C 4221 2.51 5 N 1098 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "B" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "E" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "F" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "G" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "I" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Time building chain proxies: 1.68, per 1000 atoms: 0.26 Number of scatterers: 6588 At special positions: 0 Unit cell: (83.49, 74.778, 59.532, 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 18 16.00 O 1251 8.00 N 1098 7.00 C 4221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 266.4 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.299A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS C 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL E 14 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL F 14 " --> pdb=" O LYS G 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.556A pdb=" N VAL G 20 " --> pdb=" O ARG H 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 35 removed outlier: 6.450A pdb=" N ILE D 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA E 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 28 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS E 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 33 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL D 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS E 35 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG D 34 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA G 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS G 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL F 30 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE G 33 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL F 32 " --> pdb=" O PHE G 33 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS G 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG F 34 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 35 removed outlier: 6.450A pdb=" N ILE D 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA E 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 28 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS E 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 33 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL D 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS E 35 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG D 34 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA G 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS G 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL F 30 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE G 33 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL F 32 " --> pdb=" O PHE G 33 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS G 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG F 34 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE H 33 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL G 32 " --> pdb=" O PHE H 33 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LYS H 35 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG G 34 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 62 removed outlier: 5.844A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 62 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR F 59 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU G 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU F 61 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR G 59 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU H 62 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU G 61 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR H 59 " --> pdb=" O THR I 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.292A pdb=" N GLU H 72 " --> pdb=" O ILE I 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 9.285A pdb=" N LYS A 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N TRP B 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR A 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LYS B 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N TRP C 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR B 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N LYS C 76 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N TRP D 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR C 78 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N LYS D 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N TRP E 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR D 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N LYS E 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N TRP F 79 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR E 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N LYS F 76 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TRP G 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR F 78 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS G 76 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N TRP H 79 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TYR G 78 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N LYS H 76 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N TRP I 79 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N TYR H 78 " --> pdb=" O TRP I 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 94 through 98 Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AB1, first strand: chain 'A' and resid 108 through 110 removed outlier: 7.754A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA B 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA C 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA D 108 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA E 108 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA F 108 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA G 108 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA H 108 " --> pdb=" O ALA I 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 7.211A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR F 114 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR G 114 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR H 114 " --> pdb=" O SER I 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 207 hydrogen bonds defined for protein. 615 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: 1.07 Time building geometry restraints manager: 0.77 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: 2084 1.34 - 1.46: 1145 1.46 - 1.57: 3476 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 6732 Sorted by residual: bond pdb=" N VAL E 16 " pdb=" CA VAL E 16 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N VAL H 93 " pdb=" CA VAL H 93 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.22e-02 6.72e+03 1.03e+01 bond pdb=" N ILE I 73 " pdb=" CA ILE I 73 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 9.96e+00 bond pdb=" N VAL D 14 " pdb=" CA VAL D 14 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.93e+00 bond pdb=" N VAL I 93 " pdb=" CA VAL I 93 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.92e+00 ... (remaining 6727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 7804 1.46 - 2.92: 1159 2.92 - 4.38: 173 4.38 - 5.84: 31 5.84 - 7.30: 4 Bond angle restraints: 9171 Sorted by residual: angle pdb=" N SER C 64 " pdb=" CA SER C 64 " pdb=" C SER C 64 " ideal model delta sigma weight residual 107.61 114.55 -6.94 1.74e+00 3.30e-01 1.59e+01 angle pdb=" CA GLU H 63 " pdb=" C GLU H 63 " pdb=" O GLU H 63 " ideal model delta sigma weight residual 122.27 117.74 4.53 1.16e+00 7.43e-01 1.53e+01 angle pdb=" CA GLU E 63 " pdb=" C GLU E 63 " pdb=" O GLU E 63 " ideal model delta sigma weight residual 122.27 117.86 4.41 1.16e+00 7.43e-01 1.45e+01 angle pdb=" N SER D 64 " pdb=" CA SER D 64 " pdb=" C SER D 64 " ideal model delta sigma weight residual 107.49 114.05 -6.56 1.74e+00 3.30e-01 1.42e+01 angle pdb=" CA GLU B 63 " pdb=" C GLU B 63 " pdb=" O GLU B 63 " ideal model delta sigma weight residual 122.27 118.02 4.25 1.16e+00 7.43e-01 1.34e+01 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 3586 17.12 - 34.23: 288 34.23 - 51.35: 83 51.35 - 68.47: 37 68.47 - 85.58: 2 Dihedral angle restraints: 3996 sinusoidal: 1494 harmonic: 2502 Sorted by residual: dihedral pdb=" CA ILE G 26 " pdb=" C ILE G 26 " pdb=" N ASN G 27 " pdb=" CA ASN G 27 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE E 26 " pdb=" C ILE E 26 " pdb=" N ASN E 27 " pdb=" CA ASN E 27 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ILE D 26 " pdb=" C ILE D 26 " pdb=" N ASN D 27 " pdb=" CA ASN D 27 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 3993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 585 0.042 - 0.083: 197 0.083 - 0.125: 226 0.125 - 0.166: 40 0.166 - 0.208: 41 Chirality restraints: 1089 Sorted by residual: chirality pdb=" CA VAL A 14 " pdb=" N VAL A 14 " pdb=" C VAL A 14 " pdb=" CB VAL A 14 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL I 65 " pdb=" N VAL I 65 " pdb=" C VAL I 65 " pdb=" CB VAL I 65 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE I 73 " pdb=" N ILE I 73 " pdb=" C ILE I 73 " pdb=" CB ILE I 73 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 1086 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.97e+00 pdb=" C GLU F 63 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU F 63 " 0.019 2.00e-02 2.50e+03 pdb=" N SER F 64 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 104 " 0.265 9.50e-02 1.11e+02 1.19e-01 8.68e+00 pdb=" NE ARG A 104 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 104 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 104 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 104 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 104 " 0.223 9.50e-02 1.11e+02 1.00e-01 6.14e+00 pdb=" NE ARG E 104 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 104 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 104 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 104 " 0.008 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 533 2.74 - 3.28: 6513 3.28 - 3.82: 11498 3.82 - 4.36: 14547 4.36 - 4.90: 26753 Nonbonded interactions: 59844 Sorted by model distance: nonbonded pdb=" OD2 ASP B 74 " pdb=" OH TYR B 105 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP C 74 " pdb=" OH TYR C 105 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR B 119 " model vdw 2.289 3.040 nonbonded pdb=" O SER F 64 " pdb=" OG SER F 64 " model vdw 2.339 3.040 nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.341 3.040 ... (remaining 59839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.009 0.064 6732 Z= 0.615 Angle : 1.070 7.302 9171 Z= 0.724 Chirality : 0.072 0.208 1089 Planarity : 0.008 0.119 1143 Dihedral : 15.145 85.584 2376 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 18.89 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.17), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 104 TYR 0.027 0.003 TYR H 105 PHE 0.010 0.001 PHE D 33 TRP 0.005 0.001 TRP A 79 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00882 ( 6732) covalent geometry : angle 1.06952 ( 9171) hydrogen bonds : bond 0.14387 ( 169) hydrogen bonds : angle 8.18473 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.245 Fit side-chains REVERT: B 13 MET cc_start: 0.6882 (mtp) cc_final: 0.6644 (mtm) REVERT: D 23 SER cc_start: 0.8990 (m) cc_final: 0.8671 (m) REVERT: D 34 ARG cc_start: 0.7859 (tpt-90) cc_final: 0.7657 (tpp80) REVERT: D 76 LYS cc_start: 0.8506 (mptt) cc_final: 0.8301 (mptt) REVERT: G 13 MET cc_start: 0.6635 (mtp) cc_final: 0.6056 (mtm) REVERT: H 13 MET cc_start: 0.6790 (mtp) cc_final: 0.6461 (mtm) REVERT: H 75 THR cc_start: 0.8953 (p) cc_final: 0.8697 (p) REVERT: I 104 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7642 (ttm110) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.6767 time to fit residues: 104.9885 Evaluate side-chains 120 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 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 = 0.4104 r_free = 0.4104 target = 0.122228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.091684 restraints weight = 7545.656| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.81 r_work: 0.3583 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6732 Z= 0.141 Angle : 0.623 6.407 9171 Z= 0.331 Chirality : 0.051 0.147 1089 Planarity : 0.004 0.025 1143 Dihedral : 5.116 19.614 918 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.50 % Allowed : 24.03 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 104 TYR 0.018 0.002 TYR B 105 PHE 0.012 0.002 PHE C 33 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6732) covalent geometry : angle 0.62314 ( 9171) hydrogen bonds : bond 0.03112 ( 169) hydrogen bonds : angle 4.67933 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.167 Fit side-chains REVERT: B 13 MET cc_start: 0.7674 (mtp) cc_final: 0.7053 (mtm) REVERT: B 62 GLU cc_start: 0.7974 (pt0) cc_final: 0.7664 (pt0) REVERT: D 62 GLU cc_start: 0.8064 (pt0) cc_final: 0.7842 (pt0) REVERT: E 61 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7287 (tt0) REVERT: E 99 ASP cc_start: 0.8284 (t0) cc_final: 0.8012 (t0) REVERT: G 13 MET cc_start: 0.7159 (mtp) cc_final: 0.6413 (mtm) REVERT: H 13 MET cc_start: 0.7161 (mtp) cc_final: 0.6573 (mtm) outliers start: 18 outliers final: 9 residues processed: 137 average time/residue: 0.5516 time to fit residues: 79.0348 Evaluate side-chains 127 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.115608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.084874 restraints weight = 7690.331| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.82 r_work: 0.3447 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6732 Z= 0.242 Angle : 0.698 6.717 9171 Z= 0.370 Chirality : 0.053 0.153 1089 Planarity : 0.004 0.026 1143 Dihedral : 5.646 21.213 918 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.58 % Allowed : 21.67 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 104 TYR 0.031 0.003 TYR C 105 PHE 0.018 0.002 PHE H 33 TRP 0.007 0.001 TRP C 79 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 6732) covalent geometry : angle 0.69785 ( 9171) hydrogen bonds : bond 0.02847 ( 169) hydrogen bonds : angle 4.28386 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.315 Fit side-chains REVERT: B 13 MET cc_start: 0.7810 (mtp) cc_final: 0.7127 (mtm) REVERT: B 62 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: E 58 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8025 (mt) REVERT: E 61 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7182 (tt0) REVERT: G 13 MET cc_start: 0.7228 (mtp) cc_final: 0.6573 (mtm) REVERT: G 82 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (mp) REVERT: H 13 MET cc_start: 0.7246 (mtp) cc_final: 0.6579 (mtm) REVERT: I 69 TYR cc_start: 0.8676 (m-80) cc_final: 0.8472 (m-80) outliers start: 33 outliers final: 15 residues processed: 150 average time/residue: 0.6211 time to fit residues: 97.3831 Evaluate side-chains 138 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 31 HIS H 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.116090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.085803 restraints weight = 7702.785| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.80 r_work: 0.3465 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6732 Z= 0.193 Angle : 0.644 6.626 9171 Z= 0.341 Chirality : 0.052 0.148 1089 Planarity : 0.004 0.026 1143 Dihedral : 5.460 20.333 918 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.86 % Allowed : 22.64 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 104 TYR 0.023 0.003 TYR I 105 PHE 0.011 0.002 PHE B 33 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6732) covalent geometry : angle 0.64427 ( 9171) hydrogen bonds : bond 0.02291 ( 169) hydrogen bonds : angle 4.22993 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.274 Fit side-chains REVERT: B 13 MET cc_start: 0.7830 (mtp) cc_final: 0.7180 (mtm) REVERT: B 62 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: B 76 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8136 (mptt) REVERT: E 61 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7120 (tt0) REVERT: E 64 SER cc_start: 0.8740 (p) cc_final: 0.8451 (p) REVERT: G 13 MET cc_start: 0.7226 (mtp) cc_final: 0.6703 (mtm) REVERT: G 82 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8004 (mp) REVERT: H 13 MET cc_start: 0.7373 (mtp) cc_final: 0.6715 (mtm) REVERT: H 89 GLU cc_start: 0.8370 (tt0) cc_final: 0.7921 (tt0) REVERT: H 90 HIS cc_start: 0.8246 (m90) cc_final: 0.7834 (m90) REVERT: I 69 TYR cc_start: 0.8631 (m-80) cc_final: 0.8416 (m-80) REVERT: I 82 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6711 (mp) outliers start: 35 outliers final: 12 residues processed: 159 average time/residue: 0.5999 time to fit residues: 99.7530 Evaluate side-chains 145 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.086402 restraints weight = 7686.849| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.78 r_work: 0.3466 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6732 Z= 0.177 Angle : 0.635 6.733 9171 Z= 0.335 Chirality : 0.051 0.144 1089 Planarity : 0.004 0.053 1143 Dihedral : 5.345 20.637 918 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.00 % Allowed : 23.61 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 104 TYR 0.022 0.003 TYR I 105 PHE 0.010 0.002 PHE A 33 TRP 0.004 0.001 TRP B 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6732) covalent geometry : angle 0.63454 ( 9171) hydrogen bonds : bond 0.02195 ( 169) hydrogen bonds : angle 4.16453 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.259 Fit side-chains REVERT: A 89 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8436 (mp0) REVERT: B 13 MET cc_start: 0.7853 (mtp) cc_final: 0.7191 (mtm) REVERT: B 34 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7110 (tmt90) REVERT: B 62 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: B 76 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8223 (mptt) REVERT: B 89 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: D 82 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7677 (mp) REVERT: E 61 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7116 (tt0) REVERT: E 64 SER cc_start: 0.8828 (p) cc_final: 0.8580 (p) REVERT: G 13 MET cc_start: 0.7253 (mtp) cc_final: 0.6722 (mtm) REVERT: G 82 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8037 (mp) REVERT: H 13 MET cc_start: 0.7425 (mtp) cc_final: 0.6709 (mtm) REVERT: H 89 GLU cc_start: 0.8401 (tt0) cc_final: 0.7951 (tt0) REVERT: H 90 HIS cc_start: 0.8267 (m90) cc_final: 0.7879 (m90) REVERT: I 69 TYR cc_start: 0.8630 (m-80) cc_final: 0.8390 (m-80) outliers start: 36 outliers final: 16 residues processed: 152 average time/residue: 0.6427 time to fit residues: 102.0077 Evaluate side-chains 149 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 0.0060 chunk 54 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.117065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086890 restraints weight = 7610.795| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.76 r_work: 0.3476 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6732 Z= 0.167 Angle : 0.620 6.734 9171 Z= 0.328 Chirality : 0.051 0.144 1089 Planarity : 0.004 0.041 1143 Dihedral : 5.301 20.881 918 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.31 % Allowed : 24.31 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 104 TYR 0.022 0.002 TYR C 105 PHE 0.009 0.002 PHE E 95 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6732) covalent geometry : angle 0.62032 ( 9171) hydrogen bonds : bond 0.02103 ( 169) hydrogen bonds : angle 4.14911 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.295 Fit side-chains REVERT: A 89 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8382 (mp0) REVERT: B 13 MET cc_start: 0.7874 (mtp) cc_final: 0.7201 (mtm) REVERT: B 34 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7042 (tmt90) REVERT: B 76 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8256 (mptt) REVERT: B 89 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: D 82 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7692 (mp) REVERT: D 89 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: E 61 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7070 (tt0) REVERT: E 64 SER cc_start: 0.8839 (p) cc_final: 0.8547 (p) REVERT: G 13 MET cc_start: 0.7270 (mtp) cc_final: 0.6752 (mtm) REVERT: G 82 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8063 (mp) REVERT: H 13 MET cc_start: 0.7409 (mtp) cc_final: 0.6703 (mtm) REVERT: H 89 GLU cc_start: 0.8425 (tt0) cc_final: 0.7984 (tt0) REVERT: H 90 HIS cc_start: 0.8287 (m90) cc_final: 0.7922 (m90) REVERT: I 69 TYR cc_start: 0.8633 (m-80) cc_final: 0.8389 (m-80) outliers start: 31 outliers final: 16 residues processed: 152 average time/residue: 0.6310 time to fit residues: 100.1759 Evaluate side-chains 153 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.117078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086960 restraints weight = 7540.668| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.75 r_work: 0.3470 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6732 Z= 0.163 Angle : 0.618 6.752 9171 Z= 0.326 Chirality : 0.051 0.143 1089 Planarity : 0.003 0.028 1143 Dihedral : 5.249 21.325 918 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.58 % Allowed : 24.17 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 104 TYR 0.021 0.002 TYR C 105 PHE 0.009 0.002 PHE E 95 TRP 0.003 0.001 TRP B 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6732) covalent geometry : angle 0.61806 ( 9171) hydrogen bonds : bond 0.02075 ( 169) hydrogen bonds : angle 4.11809 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.272 Fit side-chains REVERT: A 89 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8114 (mp0) REVERT: B 13 MET cc_start: 0.7880 (mtp) cc_final: 0.7217 (mtm) REVERT: B 34 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7036 (tmt90) REVERT: B 76 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8253 (mptt) REVERT: D 82 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7723 (mp) REVERT: G 13 MET cc_start: 0.7231 (mtp) cc_final: 0.6713 (mtm) REVERT: G 82 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8082 (mp) REVERT: H 13 MET cc_start: 0.7439 (mtp) cc_final: 0.6709 (mtm) REVERT: H 82 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8108 (mp) REVERT: H 89 GLU cc_start: 0.8436 (tt0) cc_final: 0.7988 (tt0) REVERT: H 90 HIS cc_start: 0.8294 (m90) cc_final: 0.7893 (m90) REVERT: I 69 TYR cc_start: 0.8634 (m-80) cc_final: 0.8382 (m-80) outliers start: 33 outliers final: 16 residues processed: 150 average time/residue: 0.6341 time to fit residues: 99.4413 Evaluate side-chains 151 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN H 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.116702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.086323 restraints weight = 7633.631| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.77 r_work: 0.3457 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6732 Z= 0.180 Angle : 0.629 6.763 9171 Z= 0.333 Chirality : 0.051 0.144 1089 Planarity : 0.003 0.026 1143 Dihedral : 5.333 21.193 918 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.31 % Allowed : 24.86 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 104 TYR 0.024 0.003 TYR I 105 PHE 0.010 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 6732) covalent geometry : angle 0.62924 ( 9171) hydrogen bonds : bond 0.02120 ( 169) hydrogen bonds : angle 4.12731 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.256 Fit side-chains REVERT: A 21 ARG cc_start: 0.8605 (ttt90) cc_final: 0.8313 (ttt90) REVERT: A 89 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8101 (mp0) REVERT: B 13 MET cc_start: 0.7883 (mtp) cc_final: 0.7244 (mtm) REVERT: B 34 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7077 (tmt90) REVERT: B 62 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: B 76 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8260 (mptt) REVERT: D 82 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7696 (mp) REVERT: G 13 MET cc_start: 0.7215 (mtp) cc_final: 0.6715 (mtm) REVERT: H 13 MET cc_start: 0.7441 (mtp) cc_final: 0.6753 (mtm) REVERT: H 89 GLU cc_start: 0.8450 (tt0) cc_final: 0.8071 (tt0) REVERT: H 90 HIS cc_start: 0.8314 (m90) cc_final: 0.7891 (m90) REVERT: I 69 TYR cc_start: 0.8636 (m-80) cc_final: 0.8376 (m-80) outliers start: 31 outliers final: 18 residues processed: 152 average time/residue: 0.6533 time to fit residues: 103.7695 Evaluate side-chains 155 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.116656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086205 restraints weight = 7633.800| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.77 r_work: 0.3455 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6732 Z= 0.180 Angle : 0.629 6.729 9171 Z= 0.333 Chirality : 0.052 0.145 1089 Planarity : 0.003 0.028 1143 Dihedral : 5.351 21.363 918 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.75 % Allowed : 25.42 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 104 TYR 0.023 0.003 TYR I 105 PHE 0.010 0.002 PHE E 95 TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 6732) covalent geometry : angle 0.62935 ( 9171) hydrogen bonds : bond 0.02065 ( 169) hydrogen bonds : angle 4.14666 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.273 Fit side-chains REVERT: A 89 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8083 (mp0) REVERT: B 13 MET cc_start: 0.7835 (mtp) cc_final: 0.7198 (mtm) REVERT: B 34 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7092 (tmt90) REVERT: B 62 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: B 76 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8260 (mptt) REVERT: D 82 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7679 (mp) REVERT: G 13 MET cc_start: 0.7185 (mtp) cc_final: 0.6744 (mtm) REVERT: H 13 MET cc_start: 0.7453 (mtp) cc_final: 0.6736 (mtm) REVERT: H 89 GLU cc_start: 0.8439 (tt0) cc_final: 0.8001 (tt0) REVERT: H 90 HIS cc_start: 0.8315 (m90) cc_final: 0.7945 (m90) REVERT: I 69 TYR cc_start: 0.8640 (m-80) cc_final: 0.8375 (m-80) outliers start: 27 outliers final: 18 residues processed: 149 average time/residue: 0.6488 time to fit residues: 100.9330 Evaluate side-chains 153 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.120651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.090313 restraints weight = 7491.250| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.76 r_work: 0.3538 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6732 Z= 0.119 Angle : 0.578 6.639 9171 Z= 0.304 Chirality : 0.050 0.141 1089 Planarity : 0.003 0.030 1143 Dihedral : 5.031 20.241 918 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.22 % Allowed : 27.36 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.24), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 104 TYR 0.017 0.002 TYR I 105 PHE 0.011 0.001 PHE A 33 TRP 0.001 0.000 TRP E 79 HIS 0.001 0.000 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6732) covalent geometry : angle 0.57799 ( 9171) hydrogen bonds : bond 0.01793 ( 169) hydrogen bonds : angle 4.04932 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.309 Fit side-chains REVERT: A 89 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8113 (mp0) REVERT: B 13 MET cc_start: 0.7817 (mtp) cc_final: 0.7188 (mtm) REVERT: B 62 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: B 76 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8216 (mptt) REVERT: E 58 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8176 (tp) REVERT: G 13 MET cc_start: 0.7192 (mtp) cc_final: 0.6740 (mtm) REVERT: H 13 MET cc_start: 0.7376 (mtp) cc_final: 0.6706 (mtm) REVERT: H 89 GLU cc_start: 0.8389 (tt0) cc_final: 0.7962 (tt0) REVERT: H 90 HIS cc_start: 0.8277 (m90) cc_final: 0.7891 (m90) REVERT: I 15 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7581 (mtpt) REVERT: I 69 TYR cc_start: 0.8600 (m-80) cc_final: 0.8379 (m-80) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.6576 time to fit residues: 104.9225 Evaluate side-chains 149 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 0.0000 chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.115251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.084755 restraints weight = 7546.011| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.74 r_work: 0.3450 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6732 Z= 0.218 Angle : 0.661 6.873 9171 Z= 0.353 Chirality : 0.053 0.163 1089 Planarity : 0.004 0.026 1143 Dihedral : 5.444 21.668 918 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.78 % Allowed : 26.53 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.23), residues: 819 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 104 TYR 0.029 0.003 TYR C 105 PHE 0.011 0.002 PHE B 33 TRP 0.004 0.001 TRP C 79 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 6732) covalent geometry : angle 0.66088 ( 9171) hydrogen bonds : bond 0.02133 ( 169) hydrogen bonds : angle 4.18430 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.25 seconds wall clock time: 47 minutes 16.65 seconds (2836.65 seconds total)