Starting phenix.real_space_refine on Thu Oct 29 09:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nas_12246/10_2026/7nas_12246_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nas_12246/10_2026/7nas_12246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nas_12246/10_2026/7nas_12246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nas_12246/10_2026/7nas_12246.map" model { file = "/net/cci-nas-00/data/ceres_data/7nas_12246/10_2026/7nas_12246_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nas_12246/10_2026/7nas_12246_neut.cif" } resolution = 3.31 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= 0.004 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: 6 Type Number sf(0) Gaussians P 974 5.49 5 Mg 43 5.21 5 S 46 5.16 5 C 16464 2.51 5 N 6037 2.21 5 O 8826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32390 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 20936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 20936 Classifications: {'RNA': 973, 'RNAv2': 1} Modifications used: {'rna2p_pur': 77, 'rna2p_pyr': 50, 'rna3p': 5, 'rna3p_pur': 484, 'rna3p_pyr': 358} Link IDs: {'rna2p': 126, 'rna3p': 847} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Unusual residues: {' MG': 43} Classifications: {'undetermined': 43} Link IDs: {None: 42} Time building chain proxies: 6.23, per 1000 atoms: 0.19 Number of scatterers: 32390 At special positions: 0 Unit cell: (146.475, 214.83, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 974 15.00 Mg 43 11.99 O 8826 8.00 N 6037 7.00 C 16464 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: 2.82 Conformation dependent library (CDL) restraints added in 579.0 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2702 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 42.2% alpha, 19.3% beta 299 base pairs and 491 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.923A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.569A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.036A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.534A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.293A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 163 removed outlier: 3.764A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.586A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.898A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 139 Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 17 removed outlier: 4.934A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 32 removed outlier: 5.020A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 removed outlier: 3.671A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'H' and resid 5 through 21 removed outlier: 4.064A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 43 removed outlier: 3.507A pdb=" N ALA H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.853A pdb=" N GLY K 51 " --> pdb=" O GLY K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 59 through 72 removed outlier: 3.593A pdb=" N ALA K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 92 through 101 removed outlier: 3.740A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 removed outlier: 3.748A pdb=" N ARG L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.092A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 4.046A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'R' and resid 25 through 33 removed outlier: 3.677A pdb=" N LEU R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.596A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.517A pdb=" N SER T 14 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET T 28 " --> pdb=" O ARG T 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 34 " --> pdb=" O THR T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 11 through 25 Processing helix chain 'U' and resid 27 through 35 removed outlier: 4.110A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 67 removed outlier: 3.628A pdb=" N GLU U 44 " --> pdb=" O LYS U 40 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG U 47 " --> pdb=" O THR U 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 19 Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 47 through 65 removed outlier: 3.650A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.718A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.693A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 21 removed outlier: 6.920A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL E 18 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR E 34 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 20 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER E 32 " --> pdb=" O ARG E 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AA5, first strand: chain 'F' and resid 3 through 4 removed outlier: 4.391A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 92 " --> pdb=" O HIS F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 38 through 45 removed outlier: 5.718A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 28 removed outlier: 4.202A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 removed outlier: 5.658A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 41 through 46 Processing sheet with id=AB1, first strand: chain 'X' and resid 22 through 29 removed outlier: 6.328A pdb=" N TYR X 39 " --> pdb=" O VAL X 24 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE X 26 " --> pdb=" O ARG X 37 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG X 37 " --> pdb=" O ILE X 26 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE X 28 " --> pdb=" O THR X 35 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR X 35 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU X 74 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N TYR L 95 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR L 64 " --> pdb=" O TYR L 95 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR L 97 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR L 66 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 50 through 52 removed outlier: 3.619A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 12 through 17 removed outlier: 6.559A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 12 through 17 removed outlier: 6.559A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'X' and resid 83 through 84 removed outlier: 3.629A pdb=" N LYS X 143 " --> pdb=" O VAL X 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 116 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL X 120 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET X 124 " --> pdb=" O VAL X 120 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 702 hydrogen bonds 954 hydrogen bond angles 0 basepair planarities 299 basepair parallelities 491 stacking parallelities Total time for adding SS restraints: 9.49 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5774 1.33 - 1.45: 13876 1.45 - 1.57: 13344 1.57 - 1.70: 1945 1.70 - 1.82: 79 Bond restraints: 35018 Sorted by residual: bond pdb=" C2' A A 523 " pdb=" O2' A A 523 " ideal model delta sigma weight residual 1.420 1.487 -0.067 1.00e-02 1.00e+04 4.55e+01 bond pdb=" C SER X 77 " pdb=" N SER X 78 " ideal model delta sigma weight residual 1.333 1.263 0.070 1.59e-02 3.96e+03 1.91e+01 bond pdb=" N9 A A 768 " pdb=" C4 A A 768 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.60e+01 bond pdb=" N9 A A 860 " pdb=" C4 A A 860 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.59e+01 bond pdb=" C5 MA6 A1518 " pdb=" C4 MA6 A1518 " ideal model delta sigma weight residual 1.394 1.472 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 35013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 51004 2.87 - 5.74: 1057 5.74 - 8.60: 45 8.60 - 11.47: 7 11.47 - 14.34: 3 Bond angle restraints: 52116 Sorted by residual: angle pdb=" N ASN U 9 " pdb=" CA ASN U 9 " pdb=" C ASN U 9 " ideal model delta sigma weight residual 114.12 101.73 12.39 1.39e+00 5.18e-01 7.95e+01 angle pdb=" C VAL X 24 " pdb=" N GLY X 25 " pdb=" CA GLY X 25 " ideal model delta sigma weight residual 121.65 115.87 5.78 6.80e-01 2.16e+00 7.22e+01 angle pdb=" O4' A A 523 " pdb=" C1' A A 523 " pdb=" N9 A A 523 " ideal model delta sigma weight residual 108.50 104.27 4.23 7.00e-01 2.04e+00 3.65e+01 angle pdb=" C TYR X 39 " pdb=" N ILE X 40 " pdb=" CA ILE X 40 " ideal model delta sigma weight residual 122.68 131.75 -9.07 1.58e+00 4.01e-01 3.29e+01 angle pdb=" O5' A A 523 " pdb=" C5' A A 523 " pdb=" C4' A A 523 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.20e+01 ... (remaining 52111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 19730 35.85 - 71.71: 2429 71.71 - 107.56: 295 107.56 - 143.41: 6 143.41 - 179.26: 7 Dihedral angle restraints: 22467 sinusoidal: 18288 harmonic: 4179 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 52.16 147.84 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 55.88 144.12 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' U A1540 " pdb=" C1' U A1540 " pdb=" N1 U A1540 " pdb=" C2 U A1540 " ideal model delta sinusoidal sigma weight residual -128.00 51.26 -179.26 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 22464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5600 0.104 - 0.209: 988 0.209 - 0.313: 21 0.313 - 0.417: 1 0.417 - 0.522: 3 Chirality restraints: 6613 Sorted by residual: chirality pdb=" CA D2T L 89 " pdb=" N D2T L 89 " pdb=" C D2T L 89 " pdb=" CB D2T L 89 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" C2' A A 523 " pdb=" C3' A A 523 " pdb=" O2' A A 523 " pdb=" C1' A A 523 " both_signs ideal model delta sigma weight residual False -2.62 -3.07 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C3' A A 523 " pdb=" C4' A A 523 " pdb=" O3' A A 523 " pdb=" C2' A A 523 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 6610 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " -0.123 2.00e-02 2.50e+03 2.03e-01 4.14e+02 pdb=" N6 MA6 A1519 " 0.352 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " -0.117 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " -0.123 2.00e-02 2.50e+03 2.00e-01 4.02e+02 pdb=" N6 MA6 A1518 " 0.347 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " -0.115 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.048 2.00e-02 2.50e+03 8.99e-02 2.62e+02 pdb=" N9 2MG A1516 " 0.007 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.044 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.061 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.013 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.008 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.049 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.040 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.086 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.128 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.083 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.030 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.247 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 195 2.28 - 2.94: 15402 2.94 - 3.59: 62674 3.59 - 4.25: 101177 4.25 - 4.90: 134609 Nonbonded interactions: 314057 Sorted by model distance: nonbonded pdb=" OP2 C A 175 " pdb="MG MG A1631 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A A 572 " pdb="MG MG A1626 " model vdw 1.678 2.170 nonbonded pdb=" OP1 U A 387 " pdb="MG MG A1604 " model vdw 1.682 2.170 nonbonded pdb=" CB LEU X 36 " pdb=" CD2 LEU X 74 " model vdw 1.724 3.860 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1642 " model vdw 1.728 2.170 ... (remaining 314052 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 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 0.078 35018 Z= 0.847 Angle : 0.954 14.339 52116 Z= 0.770 Chirality : 0.064 0.522 6613 Planarity : 0.007 0.203 2992 Dihedral : 23.550 179.264 19765 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Cbeta Deviations : 0.22 % 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: -3.73 (0.19), residues: 1425 helix: -2.64 (0.18), residues: 528 sheet: -2.28 (0.30), residues: 280 loop : -2.22 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 74 TYR 0.012 0.002 TYR K 77 PHE 0.015 0.002 PHE X 94 TRP 0.008 0.002 TRP Q 73 HIS 0.009 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.85 (35018) covalent geometry : angle 0.95380 / 0.77 (52116) hydrogen bonds : bond 0.31604 / 33.76 ( 1219) hydrogen bonds : angle 9.47619 / 12.27 ( 2406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 ASN cc_start: 0.9471 (m110) cc_final: 0.9208 (m110) REVERT: D 124 MET cc_start: 0.8676 (mtm) cc_final: 0.8355 (mtm) REVERT: D 164 GLN cc_start: 0.8997 (mp10) cc_final: 0.8763 (mp10) REVERT: D 206 LYS cc_start: 0.9308 (ptmt) cc_final: 0.9048 (ttmm) REVERT: E 10 GLU cc_start: 0.8429 (pp20) cc_final: 0.8000 (pp20) REVERT: E 12 GLN cc_start: 0.9032 (tt0) cc_final: 0.8639 (mp10) REVERT: E 13 GLU cc_start: 0.8768 (mp0) cc_final: 0.8479 (mp0) REVERT: E 45 ARG cc_start: 0.8718 (ttt90) cc_final: 0.7921 (ttt90) REVERT: E 60 ILE cc_start: 0.9549 (tt) cc_final: 0.9223 (pt) REVERT: E 71 MET cc_start: 0.7950 (mtp) cc_final: 0.7677 (ttp) REVERT: E 116 GLU cc_start: 0.9263 (tp30) cc_final: 0.9000 (tm-30) REVERT: F 6 ILE cc_start: 0.9232 (mp) cc_final: 0.8996 (mp) REVERT: F 9 MET cc_start: 0.8655 (mtm) cc_final: 0.8431 (mtm) REVERT: F 56 LYS cc_start: 0.9027 (tptp) cc_final: 0.8764 (tppt) REVERT: F 72 ASP cc_start: 0.9233 (m-30) cc_final: 0.8984 (m-30) REVERT: F 74 LEU cc_start: 0.9545 (tp) cc_final: 0.9294 (tp) REVERT: F 82 ASP cc_start: 0.9185 (p0) cc_final: 0.8957 (p0) REVERT: F 88 MET cc_start: 0.8298 (tmm) cc_final: 0.8072 (tmm) REVERT: H 43 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8807 (mm-30) REVERT: H 60 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8583 (tm-30) REVERT: H 111 MET cc_start: 0.8661 (pmm) cc_final: 0.8106 (pmm) REVERT: K 31 ILE cc_start: 0.9643 (mt) cc_final: 0.9377 (tp) REVERT: L 49 LEU cc_start: 0.8537 (mt) cc_final: 0.7926 (mm) REVERT: L 81 LEU cc_start: 0.9636 (tp) cc_final: 0.9379 (tp) REVERT: O 58 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8646 (ttt180) REVERT: Q 34 TYR cc_start: 0.9212 (m-80) cc_final: 0.8655 (m-10) REVERT: Q 80 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7910 (tm-30) REVERT: R 42 SER cc_start: 0.9430 (p) cc_final: 0.9106 (p) REVERT: T 12 ILE cc_start: 0.9686 (mt) cc_final: 0.9470 (mt) REVERT: U 10 GLU cc_start: 0.6931 (pt0) cc_final: 0.6494 (pm20) REVERT: U 12 PHE cc_start: 0.6597 (t80) cc_final: 0.6163 (t80) REVERT: U 20 LYS cc_start: 0.9323 (ttmt) cc_final: 0.9027 (ttpp) REVERT: U 46 LYS cc_start: 0.9749 (ptmt) cc_final: 0.9442 (mmtm) REVERT: U 54 LYS cc_start: 0.9505 (ttpp) cc_final: 0.9290 (ttpp) REVERT: X 41 ASP cc_start: 0.8249 (t0) cc_final: 0.7935 (t70) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2398 time to fit residues: 139.8024 Evaluate side-chains 303 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN D 100 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN R 31 ASN T 3 ASN T 70 ASN T 78 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.029360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.022842 restraints weight = 297503.468| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.60 r_work: 0.2472 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35018 Z= 0.157 Angle : 0.623 13.782 52116 Z= 0.345 Chirality : 0.041 0.445 6613 Planarity : 0.005 0.057 2992 Dihedral : 24.111 178.690 16907 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.41 % Allowed : 18.73 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.21), residues: 1425 helix: -1.05 (0.20), residues: 547 sheet: -1.87 (0.32), residues: 252 loop : -1.64 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 88 TYR 0.021 0.002 TYR R 70 PHE 0.021 0.002 PHE F 8 TRP 0.019 0.004 TRP F 42 HIS 0.007 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (35018) covalent geometry : angle 0.62266 / 0.34 (52116) hydrogen bonds : bond 0.14600 / 15.56 ( 1219) hydrogen bonds : angle 5.09057 / 6.44 ( 2406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 362 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9379 (mt0) cc_final: 0.9045 (mt0) REVERT: D 73 ARG cc_start: 0.9452 (ptm-80) cc_final: 0.9189 (ttp80) REVERT: D 74 ASN cc_start: 0.9349 (m110) cc_final: 0.9010 (m110) REVERT: D 103 TYR cc_start: 0.9502 (t80) cc_final: 0.9231 (t80) REVERT: D 124 MET cc_start: 0.9027 (mtm) cc_final: 0.8723 (mtm) REVERT: D 164 GLN cc_start: 0.9170 (mp10) cc_final: 0.8845 (mp10) REVERT: D 206 LYS cc_start: 0.9386 (ptmt) cc_final: 0.9144 (ttmm) REVERT: E 10 GLU cc_start: 0.8513 (pp20) cc_final: 0.8213 (pp20) REVERT: E 12 GLN cc_start: 0.9183 (tt0) cc_final: 0.8807 (mp10) REVERT: E 13 GLU cc_start: 0.9019 (mp0) cc_final: 0.8674 (mp0) REVERT: E 24 THR cc_start: 0.9118 (m) cc_final: 0.8771 (p) REVERT: E 36 LEU cc_start: 0.9481 (tp) cc_final: 0.9270 (tt) REVERT: E 45 ARG cc_start: 0.8988 (ttt90) cc_final: 0.8427 (ttt90) REVERT: E 64 MET cc_start: 0.9568 (OUTLIER) cc_final: 0.9340 (tpp) REVERT: E 66 LYS cc_start: 0.9269 (mtmm) cc_final: 0.8789 (mtmm) REVERT: E 97 GLN cc_start: 0.9174 (pt0) cc_final: 0.8891 (pt0) REVERT: E 111 MET cc_start: 0.9132 (mtp) cc_final: 0.8896 (ttm) REVERT: E 142 ASP cc_start: 0.9381 (p0) cc_final: 0.9068 (p0) REVERT: F 5 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8679 (mm-30) REVERT: F 88 MET cc_start: 0.8565 (tmm) cc_final: 0.8247 (tmm) REVERT: H 43 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8965 (mm-30) REVERT: H 80 ARG cc_start: 0.9406 (ptt90) cc_final: 0.8655 (ptt90) REVERT: H 111 MET cc_start: 0.9041 (pmm) cc_final: 0.8775 (pmm) REVERT: K 31 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9422 (tp) REVERT: L 103 ASP cc_start: 0.8418 (t0) cc_final: 0.8153 (t0) REVERT: O 62 GLN cc_start: 0.9555 (tp-100) cc_final: 0.9296 (tp-100) REVERT: Q 34 TYR cc_start: 0.9233 (m-80) cc_final: 0.8734 (m-10) REVERT: Q 80 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8342 (tm-30) REVERT: R 38 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9024 (mtpp) REVERT: T 12 ILE cc_start: 0.9657 (mt) cc_final: 0.9413 (mm) REVERT: U 12 PHE cc_start: 0.6520 (t80) cc_final: 0.5835 (t80) REVERT: U 39 GLU cc_start: 0.8830 (tt0) cc_final: 0.8291 (tt0) REVERT: U 46 LYS cc_start: 0.9693 (ptmt) cc_final: 0.9314 (mmtp) REVERT: X 41 ASP cc_start: 0.8635 (t0) cc_final: 0.8269 (t0) REVERT: X 53 ASP cc_start: 0.9502 (OUTLIER) cc_final: 0.9009 (p0) outliers start: 29 outliers final: 12 residues processed: 372 average time/residue: 0.2223 time to fit residues: 125.8572 Evaluate side-chains 323 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 307 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 121 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [185, 0, 187, 68, 19, 11, 159, 46, 116, 205, 72] chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 116 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN D 74 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN O 38 HIS P 63 GLN R 54 GLN T 78 ASN U 56 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.022618 restraints weight = 301011.913| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.55 r_work: 0.2463 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35018 Z= 0.217 Angle : 0.606 9.419 52116 Z= 0.335 Chirality : 0.040 0.439 6613 Planarity : 0.005 0.067 2992 Dihedral : 23.918 179.183 16907 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.25 % Allowed : 22.56 % Favored : 74.19 % 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: -1.86 (0.21), residues: 1425 helix: -0.62 (0.21), residues: 541 sheet: -1.70 (0.32), residues: 258 loop : -1.44 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 45 TYR 0.018 0.002 TYR D 75 PHE 0.017 0.002 PHE E 33 TRP 0.045 0.003 TRP F 42 HIS 0.005 0.001 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.22 (35018) covalent geometry : angle 0.60559 / 0.33 (52116) hydrogen bonds : bond 0.12285 / 13.19 ( 1219) hydrogen bonds : angle 4.78071 / 6.02 ( 2406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9345 (mt0) cc_final: 0.9113 (mt0) REVERT: D 73 ARG cc_start: 0.9527 (ptm-80) cc_final: 0.9199 (ttp80) REVERT: D 74 ASN cc_start: 0.9439 (m-40) cc_final: 0.9003 (m-40) REVERT: D 124 MET cc_start: 0.9060 (mtm) cc_final: 0.8731 (mtm) REVERT: D 164 GLN cc_start: 0.9153 (mp10) cc_final: 0.8811 (mp10) REVERT: D 206 LYS cc_start: 0.9444 (ptmt) cc_final: 0.9227 (ttmm) REVERT: E 10 GLU cc_start: 0.8520 (pp20) cc_final: 0.8232 (pp20) REVERT: E 13 GLU cc_start: 0.8992 (mp0) cc_final: 0.8646 (mp0) REVERT: E 64 MET cc_start: 0.9546 (tpp) cc_final: 0.9141 (tpp) REVERT: E 66 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8677 (mtmm) REVERT: E 97 GLN cc_start: 0.9226 (pt0) cc_final: 0.8971 (pt0) REVERT: E 142 ASP cc_start: 0.9319 (p0) cc_final: 0.9101 (p0) REVERT: F 9 MET cc_start: 0.8994 (mtm) cc_final: 0.8744 (mtm) REVERT: F 88 MET cc_start: 0.8602 (tmm) cc_final: 0.8253 (tmm) REVERT: H 43 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8882 (mm-30) REVERT: H 111 MET cc_start: 0.9015 (pmm) cc_final: 0.8739 (pmm) REVERT: K 31 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9420 (tp) REVERT: K 38 GLN cc_start: 0.9345 (mp10) cc_final: 0.8969 (mp10) REVERT: K 86 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8703 (p) REVERT: L 43 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6573 (tppt) REVERT: L 62 GLU cc_start: 0.8913 (tt0) cc_final: 0.8381 (tp30) REVERT: L 103 ASP cc_start: 0.8638 (t0) cc_final: 0.8388 (t0) REVERT: O 62 GLN cc_start: 0.9598 (tp-100) cc_final: 0.9271 (tp-100) REVERT: P 25 ARG cc_start: 0.9017 (mpp80) cc_final: 0.8590 (mtm-85) REVERT: P 56 ARG cc_start: 0.9280 (tpp80) cc_final: 0.8750 (tpp80) REVERT: Q 34 TYR cc_start: 0.9274 (m-10) cc_final: 0.8830 (m-10) REVERT: Q 52 GLU cc_start: 0.8717 (pt0) cc_final: 0.8497 (pp20) REVERT: Q 80 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8314 (tm-30) REVERT: R 38 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9087 (mtpp) REVERT: T 29 ARG cc_start: 0.8981 (ptp-110) cc_final: 0.8762 (ptp-110) REVERT: U 12 PHE cc_start: 0.6615 (t80) cc_final: 0.5964 (t80) REVERT: U 20 LYS cc_start: 0.9442 (ttmm) cc_final: 0.9144 (ttpp) REVERT: U 36 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8321 (mp0) REVERT: U 46 LYS cc_start: 0.9704 (ptmt) cc_final: 0.9347 (mmtp) REVERT: U 54 LYS cc_start: 0.9405 (ptmt) cc_final: 0.9119 (pttp) REVERT: X 41 ASP cc_start: 0.8716 (t0) cc_final: 0.8314 (t0) REVERT: X 74 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8787 (pp) outliers start: 39 outliers final: 23 residues processed: 358 average time/residue: 0.2231 time to fit residues: 122.4898 Evaluate side-chains 333 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 306 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain T residue 78 ASN Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [215, 49, 192, 31, 3, 61, 182, 223, 161, 142, 211] chunk 215 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 192 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN K 64 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.022342 restraints weight = 301800.551| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.53 r_work: 0.2447 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35018 Z= 0.292 Angle : 0.658 10.092 52116 Z= 0.357 Chirality : 0.044 0.448 6613 Planarity : 0.006 0.079 2992 Dihedral : 23.866 179.421 16907 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.16 % Allowed : 24.90 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.81 (0.21), residues: 1425 helix: -0.60 (0.21), residues: 548 sheet: -1.57 (0.32), residues: 252 loop : -1.46 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 86 TYR 0.023 0.002 TYR D 75 PHE 0.019 0.002 PHE U 19 TRP 0.050 0.004 TRP F 42 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.29 (35018) covalent geometry : angle 0.65770 / 0.36 (52116) hydrogen bonds : bond 0.11937 / 12.73 ( 1219) hydrogen bonds : angle 4.76553 / 6.03 ( 2406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9347 (mt0) cc_final: 0.9113 (mt0) REVERT: D 73 ARG cc_start: 0.9556 (ptm-80) cc_final: 0.9216 (ttp80) REVERT: D 74 ASN cc_start: 0.9482 (m-40) cc_final: 0.9002 (m110) REVERT: D 124 MET cc_start: 0.9108 (mtm) cc_final: 0.8697 (mtm) REVERT: D 164 GLN cc_start: 0.9130 (mp10) cc_final: 0.8777 (mp10) REVERT: D 206 LYS cc_start: 0.9518 (ptmt) cc_final: 0.9305 (ttmm) REVERT: E 10 GLU cc_start: 0.8735 (pp20) cc_final: 0.8277 (pp20) REVERT: E 64 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9251 (tpp) REVERT: E 66 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8777 (mtmm) REVERT: E 97 GLN cc_start: 0.9223 (pt0) cc_final: 0.8966 (pt0) REVERT: F 5 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8564 (mm-30) REVERT: F 9 MET cc_start: 0.9047 (mtm) cc_final: 0.8820 (mtm) REVERT: F 88 MET cc_start: 0.8589 (tmm) cc_final: 0.8182 (tmm) REVERT: H 43 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8906 (mm-30) REVERT: H 111 MET cc_start: 0.9003 (pmm) cc_final: 0.8699 (pmm) REVERT: K 31 ILE cc_start: 0.9676 (OUTLIER) cc_final: 0.9420 (tp) REVERT: K 64 GLN cc_start: 0.9654 (OUTLIER) cc_final: 0.9248 (pp30) REVERT: L 62 GLU cc_start: 0.8935 (tt0) cc_final: 0.8391 (tp30) REVERT: L 103 ASP cc_start: 0.8680 (t0) cc_final: 0.8411 (t0) REVERT: O 10 LYS cc_start: 0.9426 (pttm) cc_final: 0.9200 (pttm) REVERT: O 62 GLN cc_start: 0.9589 (tp-100) cc_final: 0.8963 (tp-100) REVERT: O 65 LYS cc_start: 0.9675 (mtmm) cc_final: 0.9335 (mtmm) REVERT: Q 30 LYS cc_start: 0.9451 (ttpp) cc_final: 0.9046 (ttpp) REVERT: Q 34 TYR cc_start: 0.9293 (m-10) cc_final: 0.9028 (m-10) REVERT: Q 52 GLU cc_start: 0.8717 (pt0) cc_final: 0.8461 (pp20) REVERT: Q 80 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8228 (tm-30) REVERT: R 19 GLN cc_start: 0.8763 (pm20) cc_final: 0.8253 (pp30) REVERT: U 12 PHE cc_start: 0.6724 (t80) cc_final: 0.5992 (t80) REVERT: U 20 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9163 (ttpp) REVERT: U 46 LYS cc_start: 0.9707 (ptmt) cc_final: 0.9275 (mmtm) REVERT: U 54 LYS cc_start: 0.9422 (ptmt) cc_final: 0.9133 (pttp) REVERT: X 41 ASP cc_start: 0.8765 (t0) cc_final: 0.8399 (t0) REVERT: X 53 ASP cc_start: 0.9526 (m-30) cc_final: 0.9105 (p0) REVERT: X 74 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8721 (pp) outliers start: 50 outliers final: 34 residues processed: 328 average time/residue: 0.2234 time to fit residues: 113.7595 Evaluate side-chains 332 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [25, 86, 191, 189, 98, 56, 22, 146, 190, 185, 76] chunk 25 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.028937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.022464 restraints weight = 301740.021| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 2.51 r_work: 0.2453 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35018 Z= 0.261 Angle : 0.627 9.875 52116 Z= 0.343 Chirality : 0.042 0.462 6613 Planarity : 0.005 0.056 2992 Dihedral : 23.862 179.343 16907 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.75 % Allowed : 24.90 % Favored : 70.36 % 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: -1.69 (0.21), residues: 1425 helix: -0.51 (0.21), residues: 549 sheet: -1.48 (0.31), residues: 252 loop : -1.39 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 45 TYR 0.024 0.002 TYR D 75 PHE 0.021 0.002 PHE E 33 TRP 0.061 0.004 TRP F 42 HIS 0.005 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.26 (35018) covalent geometry : angle 0.62683 / 0.34 (52116) hydrogen bonds : bond 0.11554 / 12.28 ( 1219) hydrogen bonds : angle 4.68208 / 5.92 ( 2406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9329 (mt0) cc_final: 0.9108 (mt0) REVERT: D 73 ARG cc_start: 0.9561 (ptm-80) cc_final: 0.9031 (ttp80) REVERT: D 74 ASN cc_start: 0.9482 (m-40) cc_final: 0.9233 (m110) REVERT: D 124 MET cc_start: 0.9079 (mtm) cc_final: 0.8658 (mtm) REVERT: D 164 GLN cc_start: 0.9135 (mp10) cc_final: 0.8770 (mp10) REVERT: D 206 LYS cc_start: 0.9517 (ptmt) cc_final: 0.9216 (ttmm) REVERT: E 10 GLU cc_start: 0.8676 (pp20) cc_final: 0.8106 (pp20) REVERT: E 13 GLU cc_start: 0.8918 (mp0) cc_final: 0.8668 (mp0) REVERT: E 26 LYS cc_start: 0.9426 (tptp) cc_final: 0.9218 (tppt) REVERT: E 64 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9225 (tpp) REVERT: E 66 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8848 (mtmm) REVERT: E 97 GLN cc_start: 0.9229 (pt0) cc_final: 0.8988 (pt0) REVERT: F 9 MET cc_start: 0.9049 (mtm) cc_final: 0.8799 (mtm) REVERT: F 88 MET cc_start: 0.8614 (tmm) cc_final: 0.8180 (tmm) REVERT: H 42 GLU cc_start: 0.8864 (pp20) cc_final: 0.8650 (pp20) REVERT: H 43 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8857 (mm-30) REVERT: H 111 MET cc_start: 0.9007 (pmm) cc_final: 0.8701 (pmm) REVERT: K 31 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9413 (tp) REVERT: K 38 GLN cc_start: 0.9399 (mp10) cc_final: 0.9085 (mp10) REVERT: L 62 GLU cc_start: 0.8906 (tt0) cc_final: 0.8324 (tp30) REVERT: L 103 ASP cc_start: 0.8737 (t0) cc_final: 0.8497 (t0) REVERT: O 28 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: O 62 GLN cc_start: 0.9571 (tp-100) cc_final: 0.8941 (tp-100) REVERT: O 65 LYS cc_start: 0.9663 (mtmm) cc_final: 0.9326 (mtmm) REVERT: Q 30 LYS cc_start: 0.9390 (ttpp) cc_final: 0.9055 (ttpp) REVERT: Q 80 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8269 (tm-30) REVERT: R 30 LYS cc_start: 0.9313 (mtmm) cc_final: 0.9008 (mtmm) REVERT: R 38 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9143 (mtpp) REVERT: U 12 PHE cc_start: 0.6586 (t80) cc_final: 0.5621 (t80) REVERT: U 16 LEU cc_start: 0.9320 (mt) cc_final: 0.9085 (mm) REVERT: U 20 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9177 (ttpp) REVERT: U 54 LYS cc_start: 0.9401 (ptmt) cc_final: 0.9100 (pttp) REVERT: X 41 ASP cc_start: 0.8685 (t0) cc_final: 0.8369 (t0) outliers start: 57 outliers final: 40 residues processed: 341 average time/residue: 0.2210 time to fit residues: 115.7560 Evaluate side-chains 337 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 293 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [32, 173, 71, 227, 39, 126, 67, 189, 205, 26, 192] chunk 32 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 227 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.029003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.022550 restraints weight = 299839.854| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 2.51 r_work: 0.2454 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35018 Z= 0.248 Angle : 0.625 10.334 52116 Z= 0.341 Chirality : 0.041 0.462 6613 Planarity : 0.005 0.077 2992 Dihedral : 23.831 179.269 16907 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.83 % Allowed : 26.89 % Favored : 68.28 % 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: -1.61 (0.21), residues: 1425 helix: -0.42 (0.21), residues: 551 sheet: -1.46 (0.31), residues: 253 loop : -1.36 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 77 TYR 0.031 0.002 TYR D 75 PHE 0.016 0.002 PHE X 150 TRP 0.071 0.004 TRP F 42 HIS 0.005 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.25 (35018) covalent geometry : angle 0.62488 / 0.34 (52116) hydrogen bonds : bond 0.11274 / 11.99 ( 1219) hydrogen bonds : angle 4.64696 / 5.88 ( 2406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9326 (mt0) cc_final: 0.9107 (mt0) REVERT: D 73 ARG cc_start: 0.9557 (ptm-80) cc_final: 0.9204 (ttp80) REVERT: D 74 ASN cc_start: 0.9458 (m-40) cc_final: 0.9157 (m110) REVERT: D 124 MET cc_start: 0.9110 (mtm) cc_final: 0.8698 (mtm) REVERT: D 164 GLN cc_start: 0.9149 (mp10) cc_final: 0.8781 (mp10) REVERT: D 206 LYS cc_start: 0.9519 (ptmt) cc_final: 0.9222 (ttmm) REVERT: E 13 GLU cc_start: 0.8973 (mp0) cc_final: 0.8701 (mp0) REVERT: E 64 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9145 (tpp) REVERT: E 97 GLN cc_start: 0.9225 (pt0) cc_final: 0.8974 (pt0) REVERT: F 5 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 9 MET cc_start: 0.9073 (mtm) cc_final: 0.8807 (mtm) REVERT: F 88 MET cc_start: 0.8662 (tmm) cc_final: 0.8216 (tmm) REVERT: H 42 GLU cc_start: 0.8894 (pp20) cc_final: 0.8646 (pp20) REVERT: H 43 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8863 (mm-30) REVERT: H 111 MET cc_start: 0.9016 (pmm) cc_final: 0.8714 (pmm) REVERT: K 31 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9394 (tp) REVERT: K 38 GLN cc_start: 0.9379 (mp10) cc_final: 0.9053 (mp10) REVERT: K 64 GLN cc_start: 0.9669 (OUTLIER) cc_final: 0.9299 (pp30) REVERT: L 62 GLU cc_start: 0.8925 (tt0) cc_final: 0.8317 (tp30) REVERT: L 103 ASP cc_start: 0.8740 (t0) cc_final: 0.8505 (t0) REVERT: O 28 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: O 62 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9237 (tp-100) REVERT: Q 30 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9092 (ttpp) REVERT: Q 77 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8381 (ptm160) REVERT: Q 80 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8290 (tm-30) REVERT: R 16 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9100 (mp0) REVERT: R 19 GLN cc_start: 0.8758 (pm20) cc_final: 0.8284 (pp30) REVERT: R 38 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9140 (mtpp) REVERT: U 12 PHE cc_start: 0.6648 (t80) cc_final: 0.5603 (t80) REVERT: U 16 LEU cc_start: 0.9308 (mt) cc_final: 0.9085 (mm) REVERT: U 20 LYS cc_start: 0.9471 (ttmm) cc_final: 0.9194 (ttpp) REVERT: U 40 LYS cc_start: 0.9559 (ttmt) cc_final: 0.9326 (tttt) REVERT: U 54 LYS cc_start: 0.9422 (ptmt) cc_final: 0.9129 (pttp) REVERT: X 23 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8653 (tt) REVERT: X 53 ASP cc_start: 0.9538 (m-30) cc_final: 0.9081 (p0) REVERT: X 105 MET cc_start: 0.7963 (ptp) cc_final: 0.7721 (ptp) outliers start: 58 outliers final: 42 residues processed: 335 average time/residue: 0.2162 time to fit residues: 112.8818 Evaluate side-chains 340 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [109, 191, 220, 178, 52, 142, 230, 31, 72, 87, 99] chunk 109 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 178 optimal weight: 0.0060 chunk 52 optimal weight: 30.0000 chunk 142 optimal weight: 0.0570 chunk 230 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 overall best weight: 2.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** 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 = 0.2943 r_free = 0.2943 target = 0.029587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.023108 restraints weight = 296871.079| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 2.52 r_work: 0.2482 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35018 Z= 0.149 Angle : 0.573 11.862 52116 Z= 0.318 Chirality : 0.036 0.467 6613 Planarity : 0.005 0.062 2992 Dihedral : 23.822 179.264 16907 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.50 % Allowed : 28.23 % Favored : 68.28 % 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: -1.42 (0.22), residues: 1425 helix: -0.31 (0.21), residues: 548 sheet: -1.42 (0.31), residues: 260 loop : -1.16 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 45 TYR 0.035 0.002 TYR D 75 PHE 0.018 0.002 PHE K 61 TRP 0.052 0.004 TRP F 42 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (35018) covalent geometry : angle 0.57284 / 0.32 (52116) hydrogen bonds : bond 0.10682 / 11.33 ( 1219) hydrogen bonds : angle 4.55033 / 5.77 ( 2406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9538 (ptm-80) cc_final: 0.9275 (ttp80) REVERT: D 74 ASN cc_start: 0.9441 (m-40) cc_final: 0.9201 (m-40) REVERT: D 124 MET cc_start: 0.9094 (mtm) cc_final: 0.8765 (mtm) REVERT: D 164 GLN cc_start: 0.9242 (mp10) cc_final: 0.8867 (mp10) REVERT: D 206 LYS cc_start: 0.9461 (ptmt) cc_final: 0.9242 (ttmm) REVERT: E 45 ARG cc_start: 0.9061 (ttt90) cc_final: 0.8647 (ttt90) REVERT: E 64 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9127 (tpp) REVERT: E 71 MET cc_start: 0.8511 (tpp) cc_final: 0.6931 (mmm) REVERT: E 97 GLN cc_start: 0.9192 (pt0) cc_final: 0.8968 (pt0) REVERT: E 103 THR cc_start: 0.9637 (m) cc_final: 0.9400 (p) REVERT: F 5 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8567 (mm-30) REVERT: F 79 ARG cc_start: 0.8904 (mtp180) cc_final: 0.8589 (mtp85) REVERT: F 88 MET cc_start: 0.8647 (tmm) cc_final: 0.8186 (tmm) REVERT: H 42 GLU cc_start: 0.8864 (pp20) cc_final: 0.8622 (pp20) REVERT: H 43 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8812 (mm-30) REVERT: H 58 GLU cc_start: 0.8448 (pp20) cc_final: 0.8228 (tm-30) REVERT: H 80 ARG cc_start: 0.9289 (ptt90) cc_final: 0.8329 (ptt90) REVERT: H 111 MET cc_start: 0.9020 (pmm) cc_final: 0.8729 (pmm) REVERT: K 31 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9412 (tp) REVERT: K 38 GLN cc_start: 0.9387 (mp10) cc_final: 0.9070 (mp10) REVERT: L 62 GLU cc_start: 0.8945 (tt0) cc_final: 0.8326 (tp30) REVERT: L 103 ASP cc_start: 0.8803 (t0) cc_final: 0.8594 (t0) REVERT: L 112 GLN cc_start: 0.8922 (mt0) cc_final: 0.8704 (mp10) REVERT: O 28 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: O 62 GLN cc_start: 0.9562 (tp-100) cc_final: 0.9217 (tp-100) REVERT: P 48 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7884 (tm-30) REVERT: Q 30 LYS cc_start: 0.9404 (ttpp) cc_final: 0.9120 (ttpp) REVERT: Q 80 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8333 (tm-30) REVERT: R 19 GLN cc_start: 0.8766 (pm20) cc_final: 0.8275 (pp30) REVERT: T 18 ARG cc_start: 0.9418 (ttp80) cc_final: 0.9213 (ttp80) REVERT: T 28 MET cc_start: 0.9038 (tmm) cc_final: 0.8712 (ppp) REVERT: U 12 PHE cc_start: 0.6780 (t80) cc_final: 0.5872 (t80) REVERT: U 36 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8385 (mp0) REVERT: U 46 LYS cc_start: 0.9679 (ptmt) cc_final: 0.9284 (mmtm) REVERT: U 54 LYS cc_start: 0.9403 (ptmt) cc_final: 0.9105 (pttp) REVERT: X 53 ASP cc_start: 0.9535 (m-30) cc_final: 0.9041 (p0) REVERT: X 105 MET cc_start: 0.7812 (ptp) cc_final: 0.7583 (ptp) outliers start: 42 outliers final: 32 residues processed: 346 average time/residue: 0.2251 time to fit residues: 120.5137 Evaluate side-chains 338 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [68, 152, 45, 149, 197, 133, 201, 93, 124, 31, 57] chunk 68 optimal weight: 40.0000 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 201 optimal weight: 0.0570 chunk 93 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 ASN ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.022654 restraints weight = 299102.590| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 2.50 r_work: 0.2459 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35018 Z= 0.258 Angle : 0.638 11.319 52116 Z= 0.346 Chirality : 0.041 0.458 6613 Planarity : 0.005 0.053 2992 Dihedral : 23.754 179.628 16907 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.00 % Allowed : 27.64 % Favored : 67.36 % 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: -1.48 (0.22), residues: 1425 helix: -0.38 (0.21), residues: 554 sheet: -1.43 (0.30), residues: 261 loop : -1.18 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 45 TYR 0.027 0.002 TYR D 75 PHE 0.016 0.002 PHE X 150 TRP 0.047 0.004 TRP F 42 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.26 (35018) covalent geometry : angle 0.63820 / 0.35 (52116) hydrogen bonds : bond 0.10916 / 11.61 ( 1219) hydrogen bonds : angle 4.65919 / 5.89 ( 2406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9558 (ptm-80) cc_final: 0.9209 (ttp80) REVERT: D 74 ASN cc_start: 0.9459 (m-40) cc_final: 0.9144 (m110) REVERT: D 124 MET cc_start: 0.9118 (mtm) cc_final: 0.8712 (mtm) REVERT: D 164 GLN cc_start: 0.9199 (mp10) cc_final: 0.8815 (mp10) REVERT: D 206 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9233 (ttmm) REVERT: E 26 LYS cc_start: 0.9315 (tppt) cc_final: 0.9086 (tppt) REVERT: E 45 ARG cc_start: 0.9120 (ttt90) cc_final: 0.8886 (ttt90) REVERT: E 64 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.9137 (tpp) REVERT: E 71 MET cc_start: 0.8668 (tpp) cc_final: 0.7239 (mmm) REVERT: F 1 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8189 (tmm) REVERT: F 9 MET cc_start: 0.9139 (mtm) cc_final: 0.8855 (mtm) REVERT: F 59 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: F 79 ARG cc_start: 0.8938 (mtp180) cc_final: 0.8616 (mtp85) REVERT: F 88 MET cc_start: 0.8696 (tmm) cc_final: 0.8211 (tmm) REVERT: H 42 GLU cc_start: 0.8903 (pp20) cc_final: 0.8659 (pp20) REVERT: H 43 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8854 (mm-30) REVERT: H 80 ARG cc_start: 0.9299 (ptt90) cc_final: 0.8369 (ptt90) REVERT: H 111 MET cc_start: 0.9008 (pmm) cc_final: 0.8714 (pmm) REVERT: K 31 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9392 (tp) REVERT: K 38 GLN cc_start: 0.9396 (mp10) cc_final: 0.9079 (mp10) REVERT: L 62 GLU cc_start: 0.8908 (tt0) cc_final: 0.8316 (tp30) REVERT: L 103 ASP cc_start: 0.8853 (t0) cc_final: 0.8620 (t0) REVERT: O 28 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8262 (mp10) REVERT: O 62 GLN cc_start: 0.9594 (tp-100) cc_final: 0.9252 (tp-100) REVERT: Q 30 LYS cc_start: 0.9413 (ttpp) cc_final: 0.9125 (ttpp) REVERT: Q 80 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8128 (tm-30) REVERT: R 19 GLN cc_start: 0.8817 (pm20) cc_final: 0.8280 (pp30) REVERT: R 26 ILE cc_start: 0.9386 (tp) cc_final: 0.9074 (tp) REVERT: R 30 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.8952 (mtmm) REVERT: T 18 ARG cc_start: 0.9433 (ttp80) cc_final: 0.9212 (ttp80) REVERT: U 12 PHE cc_start: 0.6697 (t80) cc_final: 0.5676 (t80) REVERT: U 16 LEU cc_start: 0.9301 (mt) cc_final: 0.9070 (mm) REVERT: U 36 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8368 (mp0) REVERT: U 54 LYS cc_start: 0.9415 (ptmt) cc_final: 0.9113 (pttp) REVERT: X 53 ASP cc_start: 0.9549 (m-30) cc_final: 0.9058 (p0) REVERT: X 105 MET cc_start: 0.7875 (ptp) cc_final: 0.7625 (ptp) outliers start: 60 outliers final: 45 residues processed: 344 average time/residue: 0.2198 time to fit residues: 117.7447 Evaluate side-chains 352 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [211, 159, 53, 141, 153, 134, 147, 140, 9, 149, 105] chunk 211 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 chunk 141 optimal weight: 7.9990 chunk 153 optimal weight: 0.0770 chunk 134 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 9 optimal weight: 40.0000 chunk 149 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** 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 = 0.2946 r_free = 0.2946 target = 0.029675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.023203 restraints weight = 294938.301| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.50 r_work: 0.2486 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 35018 Z= 0.153 Angle : 0.590 12.228 52116 Z= 0.325 Chirality : 0.036 0.471 6613 Planarity : 0.005 0.050 2992 Dihedral : 23.777 179.277 16907 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.16 % Allowed : 28.89 % 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 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: -1.29 (0.22), residues: 1425 helix: -0.30 (0.21), residues: 547 sheet: -1.25 (0.31), residues: 259 loop : -1.03 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 45 TYR 0.030 0.002 TYR D 75 PHE 0.019 0.002 PHE X 150 TRP 0.047 0.003 TRP F 42 HIS 0.004 0.001 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (35018) covalent geometry : angle 0.59029 / 0.33 (52116) hydrogen bonds : bond 0.10472 / 11.10 ( 1219) hydrogen bonds : angle 4.56829 / 5.80 ( 2406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9540 (ptm-80) cc_final: 0.9159 (ttp80) REVERT: D 74 ASN cc_start: 0.9453 (m-40) cc_final: 0.9003 (m110) REVERT: D 124 MET cc_start: 0.9086 (mtm) cc_final: 0.8754 (mtm) REVERT: D 164 GLN cc_start: 0.9245 (mp10) cc_final: 0.8873 (mp10) REVERT: D 206 LYS cc_start: 0.9475 (ptmt) cc_final: 0.9215 (ttmm) REVERT: E 45 ARG cc_start: 0.9095 (ttt90) cc_final: 0.8819 (ttt90) REVERT: E 64 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9106 (tpp) REVERT: E 71 MET cc_start: 0.8676 (tpp) cc_final: 0.7610 (mmm) REVERT: E 78 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9104 (p0) REVERT: E 103 THR cc_start: 0.9639 (m) cc_final: 0.9410 (p) REVERT: E 152 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8899 (ptm) REVERT: F 1 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8127 (tmm) REVERT: F 9 MET cc_start: 0.9100 (mtm) cc_final: 0.8812 (mtm) REVERT: F 59 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: F 79 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8584 (mtp85) REVERT: F 88 MET cc_start: 0.8696 (tmm) cc_final: 0.8189 (tmm) REVERT: H 42 GLU cc_start: 0.8864 (pp20) cc_final: 0.8633 (pp20) REVERT: H 43 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8813 (mm-30) REVERT: H 80 ARG cc_start: 0.9314 (ptt90) cc_final: 0.8389 (ptt90) REVERT: H 111 MET cc_start: 0.9029 (pmm) cc_final: 0.8729 (pmm) REVERT: K 31 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9395 (tp) REVERT: K 38 GLN cc_start: 0.9400 (mp10) cc_final: 0.9080 (mp10) REVERT: L 62 GLU cc_start: 0.8951 (tt0) cc_final: 0.8372 (tp30) REVERT: L 112 GLN cc_start: 0.8916 (mt0) cc_final: 0.8707 (mp10) REVERT: O 28 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: O 62 GLN cc_start: 0.9568 (tp-100) cc_final: 0.9224 (tp-100) REVERT: P 25 ARG cc_start: 0.8964 (mpp80) cc_final: 0.8517 (mpp80) REVERT: Q 30 LYS cc_start: 0.9401 (ttpp) cc_final: 0.9113 (ttpp) REVERT: Q 80 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8260 (tm-30) REVERT: R 19 GLN cc_start: 0.8854 (pm20) cc_final: 0.8299 (pp30) REVERT: R 26 ILE cc_start: 0.9400 (tp) cc_final: 0.9033 (tp) REVERT: R 30 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.8892 (mtmm) REVERT: R 73 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8056 (ptp90) REVERT: T 18 ARG cc_start: 0.9420 (ttp80) cc_final: 0.9203 (ttp80) REVERT: U 12 PHE cc_start: 0.6878 (t80) cc_final: 0.6000 (t80) REVERT: U 36 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8379 (mp0) REVERT: U 54 LYS cc_start: 0.9410 (ptmt) cc_final: 0.9113 (pttp) REVERT: X 53 ASP cc_start: 0.9559 (m-30) cc_final: 0.9057 (p0) REVERT: X 105 MET cc_start: 0.7962 (ptp) cc_final: 0.7739 (ptp) outliers start: 50 outliers final: 38 residues processed: 340 average time/residue: 0.2185 time to fit residues: 115.9235 Evaluate side-chains 350 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [90, 38, 163, 149, 162, 207, 60, 177, 165, 160, 125] chunk 90 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.029540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023059 restraints weight = 299764.435| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 2.53 r_work: 0.2477 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35018 Z= 0.197 Angle : 0.619 13.183 52116 Z= 0.339 Chirality : 0.038 0.463 6613 Planarity : 0.005 0.062 2992 Dihedral : 23.714 179.584 16907 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.08 % Allowed : 29.14 % Favored : 66.78 % 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: -1.25 (0.22), residues: 1425 helix: -0.30 (0.22), residues: 548 sheet: -1.20 (0.31), residues: 261 loop : -0.99 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 45 TYR 0.027 0.002 TYR D 75 PHE 0.018 0.002 PHE X 150 TRP 0.067 0.004 TRP F 42 HIS 0.004 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 (35018) covalent geometry : angle 0.61936 / 0.34 (52116) hydrogen bonds : bond 0.10452 / 11.10 ( 1219) hydrogen bonds : angle 4.61915 / 5.86 ( 2406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9544 (ptm-80) cc_final: 0.9168 (ttp80) REVERT: D 74 ASN cc_start: 0.9454 (m-40) cc_final: 0.9009 (m110) REVERT: D 124 MET cc_start: 0.9117 (mtm) cc_final: 0.8710 (mtm) REVERT: D 164 GLN cc_start: 0.9237 (mp10) cc_final: 0.8864 (mp10) REVERT: D 206 LYS cc_start: 0.9500 (ptmt) cc_final: 0.9247 (ttmm) REVERT: E 64 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9152 (tpp) REVERT: E 103 THR cc_start: 0.9629 (m) cc_final: 0.9395 (p) REVERT: F 1 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: F 5 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8637 (mm-30) REVERT: F 9 MET cc_start: 0.9123 (mtm) cc_final: 0.8862 (mtm) REVERT: F 79 ARG cc_start: 0.8952 (mtp180) cc_final: 0.8636 (mtp85) REVERT: F 88 MET cc_start: 0.8711 (tmm) cc_final: 0.8199 (tmm) REVERT: H 42 GLU cc_start: 0.8874 (pp20) cc_final: 0.8648 (pp20) REVERT: H 43 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8848 (mm-30) REVERT: H 80 ARG cc_start: 0.9336 (ptt90) cc_final: 0.8394 (ptt90) REVERT: H 111 MET cc_start: 0.9006 (pmm) cc_final: 0.8721 (pmm) REVERT: K 31 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9384 (tp) REVERT: K 38 GLN cc_start: 0.9405 (mp10) cc_final: 0.9083 (mp10) REVERT: L 62 GLU cc_start: 0.8957 (tt0) cc_final: 0.8373 (tp30) REVERT: L 112 GLN cc_start: 0.9015 (mt0) cc_final: 0.8751 (mp10) REVERT: O 28 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: O 62 GLN cc_start: 0.9572 (tp-100) cc_final: 0.9228 (tp-100) REVERT: P 25 ARG cc_start: 0.8967 (mpp80) cc_final: 0.8523 (mpp80) REVERT: Q 30 LYS cc_start: 0.9418 (ttpp) cc_final: 0.9110 (ttpp) REVERT: Q 80 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8168 (tm-30) REVERT: R 19 GLN cc_start: 0.8890 (pm20) cc_final: 0.8399 (pp30) REVERT: R 26 ILE cc_start: 0.9444 (tp) cc_final: 0.9006 (tp) REVERT: R 30 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.8929 (mtmt) REVERT: R 73 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7969 (mpp-170) REVERT: T 18 ARG cc_start: 0.9430 (ttp80) cc_final: 0.9214 (ttp80) REVERT: U 12 PHE cc_start: 0.6872 (t80) cc_final: 0.5836 (t80) REVERT: U 16 LEU cc_start: 0.9289 (mt) cc_final: 0.9086 (mm) REVERT: U 36 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8363 (mp0) REVERT: U 46 LYS cc_start: 0.9687 (ptmt) cc_final: 0.9295 (mmtm) REVERT: U 54 LYS cc_start: 0.9393 (ptmt) cc_final: 0.9097 (pttp) REVERT: X 53 ASP cc_start: 0.9525 (m-30) cc_final: 0.9013 (p0) REVERT: X 105 MET cc_start: 0.7844 (ptp) cc_final: 0.7608 (ptp) outliers start: 49 outliers final: 41 residues processed: 332 average time/residue: 0.2233 time to fit residues: 114.9512 Evaluate side-chains 344 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [181, 74, 26, 170, 114, 193, 117, 133, 69, 76, 126] chunk 181 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 114 optimal weight: 0.0570 chunk 193 optimal weight: 0.0870 chunk 117 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 69 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.030230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.023786 restraints weight = 290925.173| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 2.50 r_work: 0.2512 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35018 Z= 0.130 Angle : 0.584 12.617 52116 Z= 0.321 Chirality : 0.035 0.470 6613 Planarity : 0.005 0.079 2992 Dihedral : 23.704 179.222 16907 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.50 % Allowed : 29.81 % Favored : 66.69 % 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: -1.06 (0.22), residues: 1425 helix: -0.16 (0.21), residues: 552 sheet: -1.03 (0.32), residues: 261 loop : -0.91 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 45 TYR 0.026 0.002 TYR D 75 PHE 0.020 0.001 PHE X 150 TRP 0.064 0.004 TRP F 42 HIS 0.004 0.001 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (35018) covalent geometry : angle 0.58439 / 0.32 (52116) hydrogen bonds : bond 0.10162 / 10.78 ( 1219) hydrogen bonds : angle 4.53175 / 5.77 ( 2406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7208.82 seconds wall clock time: 124 minutes 46.96 seconds (7486.96 seconds total)