Starting phenix.real_space_refine on Wed Aug 5 07:24:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e93_47752/08_2026/9e93_47752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e93_47752/08_2026/9e93_47752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e93_47752/08_2026/9e93_47752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e93_47752/08_2026/9e93_47752.map" model { file = "/net/cci-nas-00/data/ceres_data/9e93_47752/08_2026/9e93_47752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e93_47752/08_2026/9e93_47752.cif" } resolution = 3.58 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= -0.026 sd= 0.342 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 Zn 4 6.06 5 P 36 5.49 5 S 50 5.16 5 C 5427 2.51 5 N 1587 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8773 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 173 Classifications: {'DNA': 2, 'RNA': 8} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1, ' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1508 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "H" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 173 Classifications: {'DNA': 2, 'RNA': 8} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1, ' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1508 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "o" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1138 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1367 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "s" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1147 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1367 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1066 SG CYS A 85 72.287 55.628 49.334 1.00 67.15 S ATOM 1084 SG CYS A 88 73.419 55.035 47.951 1.00 65.88 S ATOM 2941 SG CYS E 85 41.143 56.096 49.407 1.00 65.73 S ATOM 2959 SG CYS E 88 39.736 56.696 48.097 1.00 63.94 S ATOM 5812 SG CYS p 114 60.812 88.006 60.028 1.00 94.13 S ATOM 5959 SG CYS p 133 63.366 88.061 59.934 1.00 95.31 S ATOM 8326 SG CYS t 114 52.648 25.185 60.311 1.00 94.09 S ATOM 8473 SG CYS t 133 49.640 24.842 59.811 1.00 94.64 S Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 8773 At special positions: 0 Unit cell: (112.59, 110.97, 95.58, 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) Zn 4 29.99 S 50 16.00 P 36 15.00 O 1669 8.00 N 1587 7.00 C 5427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 166.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 300 " pdb="ZN ZN A 300 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 300 " - pdb=" SG CYS A 85 " pdb="ZN ZN A 300 " - pdb=" SG CYS A 88 " pdb=" ZN E 300 " pdb="ZN ZN E 300 " - pdb=" SG CYS E 85 " pdb="ZN ZN E 300 " - pdb=" SG CYS E 88 " pdb="ZN ZN E 300 " - pdb=" ND1 HIS E 54 " pdb=" ZN p 201 " pdb="ZN ZN p 201 " - pdb=" SG CYS p 133 " pdb="ZN ZN p 201 " - pdb=" NE2 HIS p 108 " pdb="ZN ZN p 201 " - pdb=" SG CYS p 114 " pdb=" ZN t 201 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 114 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 133 " pdb="ZN ZN t 201 " - pdb=" NE2 HIS t 108 " 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 41.0% alpha, 26.1% beta 16 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 158 through 182 removed outlier: 4.010A pdb=" N MET A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 85 through 99 Processing helix chain 'E' and resid 116 through 129 Processing helix chain 'E' and resid 137 through 149 Processing helix chain 'E' and resid 158 through 182 removed outlier: 3.849A pdb=" N MET E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'o' and resid 8 through 15 removed outlier: 3.675A pdb=" N GLU o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 24 removed outlier: 3.894A pdb=" N ARG o 19 " --> pdb=" O GLU o 15 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU o 24 " --> pdb=" O LYS o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 50 removed outlier: 4.517A pdb=" N ALA o 42 " --> pdb=" O GLU o 38 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG o 43 " --> pdb=" O GLU o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 129 through 135 Processing helix chain 'o' and resid 136 through 149 removed outlier: 3.889A pdb=" N GLN o 140 " --> pdb=" O ASP o 136 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 31 Processing helix chain 'p' and resid 99 through 112 removed outlier: 3.750A pdb=" N HIS p 110 " --> pdb=" O LEU p 106 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE p 112 " --> pdb=" O HIS p 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 118 through 126 removed outlier: 3.550A pdb=" N THR p 123 " --> pdb=" O ALA p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 135 through 139 removed outlier: 3.873A pdb=" N HIS p 139 " --> pdb=" O GLN p 136 " (cutoff:3.500A) Processing helix chain 'p' and resid 144 through 154 Processing helix chain 'p' and resid 165 through 170 removed outlier: 3.649A pdb=" N LEU p 169 " --> pdb=" O SER p 165 " (cutoff:3.500A) Processing helix chain 's' and resid 8 through 13 Processing helix chain 's' and resid 15 through 24 Processing helix chain 's' and resid 36 through 50 removed outlier: 4.017A pdb=" N ALA s 42 " --> pdb=" O GLU s 38 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG s 43 " --> pdb=" O GLU s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 129 through 135 Processing helix chain 's' and resid 136 through 147 removed outlier: 3.954A pdb=" N GLN s 140 " --> pdb=" O ASP s 136 " (cutoff:3.500A) Processing helix chain 't' and resid 14 through 30 Processing helix chain 't' and resid 99 through 110 removed outlier: 3.931A pdb=" N HIS t 110 " --> pdb=" O LEU t 106 " (cutoff:3.500A) Processing helix chain 't' and resid 118 through 125 Processing helix chain 't' and resid 146 through 154 Processing helix chain 't' and resid 165 through 171 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 48 removed outlier: 3.624A pdb=" N GLY A 45 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 29 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 81 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 75 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 48 removed outlier: 3.624A pdb=" N GLY A 45 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 29 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 81 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 75 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER A 109 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU A 80 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.859A pdb=" N GLY E 45 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 32 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 75 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR E 74 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ARG E 105 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL E 76 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE E 107 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS E 78 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER E 109 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU E 80 " --> pdb=" O SER E 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'o' and resid 27 through 28 Processing sheet with id=AA5, first strand: chain 'o' and resid 64 through 70 removed outlier: 20.859A pdb=" N TRP p 5 " --> pdb=" O LYS p 91 " (cutoff:3.500A) removed outlier: 18.335A pdb=" N LYS p 91 " --> pdb=" O TRP p 5 " (cutoff:3.500A) removed outlier: 14.273A pdb=" N VAL p 7 " --> pdb=" O TRP p 89 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N TRP p 89 " --> pdb=" O VAL p 7 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE p 9 " --> pdb=" O ILE p 87 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE p 87 " --> pdb=" O ILE p 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN p 83 " --> pdb=" O VAL p 13 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY p 84 " --> pdb=" O TYR p 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS p 63 " --> pdb=" O ARG p 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'o' and resid 64 through 70 removed outlier: 20.859A pdb=" N TRP p 5 " --> pdb=" O LYS p 91 " (cutoff:3.500A) removed outlier: 18.335A pdb=" N LYS p 91 " --> pdb=" O TRP p 5 " (cutoff:3.500A) removed outlier: 14.273A pdb=" N VAL p 7 " --> pdb=" O TRP p 89 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N TRP p 89 " --> pdb=" O VAL p 7 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE p 9 " --> pdb=" O ILE p 87 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE p 87 " --> pdb=" O ILE p 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN p 83 " --> pdb=" O VAL p 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 86 through 87 removed outlier: 4.035A pdb=" N TYR o 96 " --> pdb=" O ASP o 87 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL o 95 " --> pdb=" O ILE o 114 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS o 124 " --> pdb=" O LYS o 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 's' and resid 27 through 28 removed outlier: 3.821A pdb=" N ASP s 120 " --> pdb=" O ASP s 115 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS s 98 " --> pdb=" O TYR s 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR s 85 " --> pdb=" O LYS s 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 's' and resid 56 through 58 removed outlier: 3.542A pdb=" N MET t 8 " --> pdb=" O GLN s 67 " (cutoff:3.500A) removed outlier: 19.980A pdb=" N TRP t 5 " --> pdb=" O LYS t 91 " (cutoff:3.500A) removed outlier: 17.563A pdb=" N LYS t 91 " --> pdb=" O TRP t 5 " (cutoff:3.500A) removed outlier: 14.290A pdb=" N VAL t 7 " --> pdb=" O TRP t 89 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N TRP t 89 " --> pdb=" O VAL t 7 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE t 9 " --> pdb=" O ILE t 87 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE t 87 " --> pdb=" O ILE t 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN t 83 " --> pdb=" O VAL t 13 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TRP t 70 " --> pdb=" O ILE t 51 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE t 51 " --> pdb=" O TRP t 70 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU t 54 " --> pdb=" O ARG t 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 's' and resid 56 through 58 removed outlier: 3.542A pdb=" N MET t 8 " --> pdb=" O GLN s 67 " (cutoff:3.500A) removed outlier: 19.980A pdb=" N TRP t 5 " --> pdb=" O LYS t 91 " (cutoff:3.500A) removed outlier: 17.563A pdb=" N LYS t 91 " --> pdb=" O TRP t 5 " (cutoff:3.500A) removed outlier: 14.290A pdb=" N VAL t 7 " --> pdb=" O TRP t 89 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N TRP t 89 " --> pdb=" O VAL t 7 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE t 9 " --> pdb=" O ILE t 87 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE t 87 " --> pdb=" O ILE t 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN t 83 " --> pdb=" O VAL t 13 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2737 1.34 - 1.46: 1618 1.46 - 1.58: 4558 1.58 - 1.69: 70 1.69 - 1.81: 66 Bond restraints: 9049 Sorted by residual: bond pdb=" C SER t 130 " pdb=" N PRO t 131 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.36e-01 bond pdb=" C1' G D 7 " pdb=" N9 G D 7 " ideal model delta sigma weight residual 1.483 1.474 0.009 1.50e-02 4.44e+03 3.82e-01 bond pdb=" CG PRO A 22 " pdb=" CD PRO A 22 " ideal model delta sigma weight residual 1.512 1.495 0.017 2.70e-02 1.37e+03 3.79e-01 bond pdb=" P A H 10 " pdb=" O5' A H 10 " ideal model delta sigma weight residual 1.593 1.599 -0.006 1.00e-02 1.00e+04 3.73e-01 bond pdb=" C1' G H 7 " pdb=" N9 G H 7 " ideal model delta sigma weight residual 1.483 1.474 0.009 1.50e-02 4.44e+03 3.57e-01 ... (remaining 9044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 12004 1.10 - 2.20: 231 2.20 - 3.30: 118 3.30 - 4.40: 6 4.40 - 5.50: 9 Bond angle restraints: 12368 Sorted by residual: angle pdb=" O5' U H 2 " pdb=" C5' U H 2 " pdb=" C4' U H 2 " ideal model delta sigma weight residual 109.40 112.22 -2.82 8.00e-01 1.56e+00 1.25e+01 angle pdb=" O5' A H 3 " pdb=" C5' A H 3 " pdb=" C4' A H 3 " ideal model delta sigma weight residual 109.40 111.98 -2.58 8.00e-01 1.56e+00 1.04e+01 angle pdb=" O5' G G 7 " pdb=" C5' G G 7 " pdb=" C4' G G 7 " ideal model delta sigma weight residual 109.40 111.91 -2.51 8.00e-01 1.56e+00 9.82e+00 angle pdb=" O5' G C 7 " pdb=" C5' G C 7 " pdb=" C4' G C 7 " ideal model delta sigma weight residual 109.40 111.87 -2.47 8.00e-01 1.56e+00 9.53e+00 angle pdb=" O5' G G 8 " pdb=" C5' G G 8 " pdb=" C4' G G 8 " ideal model delta sigma weight residual 109.40 111.81 -2.41 8.00e-01 1.56e+00 9.07e+00 ... (remaining 12363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 4995 15.03 - 30.06: 317 30.06 - 45.10: 96 45.10 - 60.13: 57 60.13 - 75.16: 43 Dihedral angle restraints: 5508 sinusoidal: 2669 harmonic: 2839 Sorted by residual: dihedral pdb=" CA GLU o 130 " pdb=" CB GLU o 130 " pdb=" CG GLU o 130 " pdb=" CD GLU o 130 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CA ILE t 128 " pdb=" CB ILE t 128 " pdb=" CG1 ILE t 128 " pdb=" CD1 ILE t 128 " ideal model delta sinusoidal sigma weight residual 60.00 113.23 -53.23 3 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" N LEU p 169 " pdb=" CA LEU p 169 " pdb=" CB LEU p 169 " pdb=" CG LEU p 169 " ideal model delta sinusoidal sigma weight residual -60.00 -110.76 50.76 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 979 0.034 - 0.068: 206 0.068 - 0.102: 67 0.102 - 0.135: 57 0.135 - 0.169: 10 Chirality restraints: 1319 Sorted by residual: chirality pdb=" CB ILE t 159 " pdb=" CA ILE t 159 " pdb=" CG1 ILE t 159 " pdb=" CG2 ILE t 159 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" C2' G G 7 " pdb=" C3' G G 7 " pdb=" O2' G G 7 " pdb=" C1' G G 7 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" C2' G C 7 " pdb=" C3' G C 7 " pdb=" O2' G C 7 " pdb=" C1' G C 7 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1316 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U H 2 " -0.024 2.00e-02 2.50e+03 2.41e-02 1.30e+01 pdb=" N1 U H 2 " 0.059 2.00e-02 2.50e+03 pdb=" C2 U H 2 " -0.032 2.00e-02 2.50e+03 pdb=" O2 U H 2 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U H 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U H 2 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U H 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U H 2 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U H 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS t 160 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO t 161 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO t 161 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO t 161 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS p 160 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO p 161 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO p 161 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO p 161 " -0.039 5.00e-02 4.00e+02 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1666 2.78 - 3.31: 8100 3.31 - 3.84: 14522 3.84 - 4.37: 16512 4.37 - 4.90: 27896 Nonbonded interactions: 68696 Sorted by model distance: nonbonded pdb=" OE2 GLU E 121 " pdb=" OH TYR p 30 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR E 35 " pdb=" O GLN E 75 " model vdw 2.323 3.040 nonbonded pdb=" O PHE s 32 " pdb=" NH1 ARG s 40 " model vdw 2.326 3.120 nonbonded pdb=" O ASN E 15 " pdb=" ND2 ASN E 169 " model vdw 2.348 3.120 nonbonded pdb=" O ASP o 7 " pdb=" OG SER o 10 " model vdw 2.413 3.040 ... (remaining 68691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'o' selection = (chain 's' and resid 7 through 153) } ncs_group { reference = chain 'p' selection = chain 't' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.002 0.028 9061 Z= 0.084 Angle : 0.452 5.503 12368 Z= 0.272 Chirality : 0.041 0.169 1319 Planarity : 0.007 0.079 1466 Dihedral : 13.952 75.160 3662 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.34 (0.28), residues: 945 helix: 1.60 (0.28), residues: 363 sheet: -0.48 (0.40), residues: 171 loop : -0.66 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG t 121 TYR 0.009 0.001 TYR t 94 PHE 0.007 0.001 PHE E 59 TRP 0.009 0.001 TRP t 70 HIS 0.004 0.000 HIS t 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00162 / 0.08 ( 9049) covalent geometry : angle 0.45223 / 0.27 (12368) hydrogen bonds : bond 0.17560 / 18.91 ( 407) hydrogen bonds : angle 7.68717 / 7.30 ( 1225) metal coordination : bond 0.00274 / 0.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.345 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: A 133 VAL cc_start: 0.7586 (t) cc_final: 0.7156 (p) REVERT: E 136 MET cc_start: 0.7744 (mtp) cc_final: 0.7122 (mtp) REVERT: E 158 ASP cc_start: 0.7701 (p0) cc_final: 0.7392 (p0) REVERT: o 120 ASP cc_start: 0.7706 (t0) cc_final: 0.7385 (t0) REVERT: p 12 GLN cc_start: 0.8701 (mp10) cc_final: 0.8459 (mp10) REVERT: s 118 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7625 (ttp80) REVERT: s 141 GLN cc_start: 0.8090 (mt0) cc_final: 0.7843 (mt0) REVERT: t 16 MET cc_start: 0.7777 (mtm) cc_final: 0.7486 (mtm) REVERT: t 83 GLN cc_start: 0.7905 (mt0) cc_final: 0.7546 (mt0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1471 time to fit residues: 65.9299 Evaluate side-chains 263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN A 37 GLN A 38 ASN A 97 GLN E 49 ASN E 101 HIS o 8 GLN o 45 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 139 HIS s 37 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072327 restraints weight = 28727.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074227 restraints weight = 15474.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075487 restraints weight = 9975.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.076318 restraints weight = 7286.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076914 restraints weight = 5801.460| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9061 Z= 0.196 Angle : 0.671 10.545 12368 Z= 0.349 Chirality : 0.042 0.170 1319 Planarity : 0.006 0.059 1466 Dihedral : 13.726 73.544 1623 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.24 % Allowed : 13.90 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.23 (0.27), residues: 945 helix: 1.35 (0.27), residues: 363 sheet: -0.33 (0.43), residues: 154 loop : -0.65 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG s 49 TYR 0.024 0.002 TYR t 94 PHE 0.015 0.002 PHE E 148 TRP 0.017 0.002 TRP s 113 HIS 0.008 0.001 HIS p 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 9049) covalent geometry : angle 0.67126 / 0.35 (12368) hydrogen bonds : bond 0.04082 / 4.31 ( 407) hydrogen bonds : angle 5.59760 / 5.56 ( 1225) metal coordination : bond 0.00503 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.215 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: E 136 MET cc_start: 0.8174 (mtp) cc_final: 0.7861 (mtt) REVERT: E 158 ASP cc_start: 0.7967 (p0) cc_final: 0.7767 (p0) REVERT: p 15 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7595 (tpp80) REVERT: p 83 GLN cc_start: 0.8183 (mm110) cc_final: 0.7937 (mm110) REVERT: p 121 ARG cc_start: 0.7741 (mmp-170) cc_final: 0.7488 (mmp80) REVERT: s 120 ASP cc_start: 0.7903 (t0) cc_final: 0.7203 (t0) REVERT: t 45 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7077 (tt0) REVERT: t 83 GLN cc_start: 0.8021 (mt0) cc_final: 0.7774 (mt0) outliers start: 28 outliers final: 22 residues processed: 283 average time/residue: 0.1365 time to fit residues: 47.3933 Evaluate side-chains 274 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 28 LYS Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 80 HIS Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 37 HIS Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain t residue 67 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 140 ASN p 158 GLN s 37 HIS s 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071458 restraints weight = 28363.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073326 restraints weight = 15315.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074550 restraints weight = 9920.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.075378 restraints weight = 7250.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075925 restraints weight = 5766.157| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 9061 Z= 0.154 Angle : 0.612 6.658 12368 Z= 0.315 Chirality : 0.039 0.189 1319 Planarity : 0.006 0.060 1466 Dihedral : 13.761 73.636 1623 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.36 % Allowed : 16.45 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.14 (0.27), residues: 945 helix: 1.32 (0.27), residues: 362 sheet: -0.69 (0.39), residues: 183 loop : -0.57 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 20 TYR 0.022 0.002 TYR A 32 PHE 0.015 0.002 PHE E 148 TRP 0.018 0.002 TRP s 113 HIS 0.008 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 9049) covalent geometry : angle 0.61192 / 0.31 (12368) hydrogen bonds : bond 0.03802 / 3.97 ( 407) hydrogen bonds : angle 5.26469 / 5.23 ( 1225) metal coordination : bond 0.00288 / 0.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.328 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: A 74 TYR cc_start: 0.7300 (m-10) cc_final: 0.7024 (m-10) REVERT: E 136 MET cc_start: 0.8353 (mtp) cc_final: 0.8020 (mtt) REVERT: o 24 GLU cc_start: 0.7298 (mp0) cc_final: 0.6534 (tm-30) REVERT: o 45 GLN cc_start: 0.7628 (tp40) cc_final: 0.7093 (tp-100) REVERT: o 144 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 29 outliers final: 20 residues processed: 275 average time/residue: 0.1242 time to fit residues: 42.5129 Evaluate side-chains 269 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 80 HIS Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 23 ARG Chi-restraints excluded: chain s residue 37 HIS Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 95 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN A 37 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 139 HIS ** s 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068718 restraints weight = 29209.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070591 restraints weight = 15672.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071784 restraints weight = 10091.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072580 restraints weight = 7409.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073127 restraints weight = 5948.815| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9061 Z= 0.175 Angle : 0.642 7.768 12368 Z= 0.330 Chirality : 0.041 0.230 1319 Planarity : 0.005 0.051 1466 Dihedral : 13.760 73.829 1623 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.06 % Allowed : 16.57 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.06 (0.27), residues: 945 helix: 0.86 (0.26), residues: 379 sheet: -0.66 (0.38), residues: 185 loop : -0.50 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG o 43 TYR 0.021 0.002 TYR A 32 PHE 0.018 0.002 PHE o 18 TRP 0.021 0.002 TRP s 113 HIS 0.015 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9049) covalent geometry : angle 0.64216 / 0.33 (12368) hydrogen bonds : bond 0.03906 / 4.15 ( 407) hydrogen bonds : angle 5.02229 / 4.99 ( 1225) metal coordination : bond 0.00320 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 0.215 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: A 72 GLN cc_start: 0.7689 (pm20) cc_final: 0.7398 (pm20) REVERT: A 165 GLU cc_start: 0.7624 (tp30) cc_final: 0.7397 (tp30) REVERT: E 51 LYS cc_start: 0.7695 (tppt) cc_final: 0.7191 (tppt) REVERT: E 146 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7771 (tm-30) REVERT: o 20 LYS cc_start: 0.7348 (tmtt) cc_final: 0.6464 (tmtt) REVERT: o 43 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6674 (ptm160) REVERT: o 109 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7925 (mt) REVERT: o 144 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7568 (mm-30) REVERT: o 147 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8041 (ttp80) REVERT: s 140 GLN cc_start: 0.7360 (pm20) cc_final: 0.7000 (pm20) REVERT: s 144 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7515 (mt-10) outliers start: 35 outliers final: 28 residues processed: 273 average time/residue: 0.1263 time to fit residues: 42.9408 Evaluate side-chains 263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 43 ARG Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 80 HIS Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 23 ARG Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 141 GLN t 12 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.078410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068414 restraints weight = 28943.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070286 restraints weight = 15485.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071481 restraints weight = 9993.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072261 restraints weight = 7339.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072831 restraints weight = 5895.399| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9061 Z= 0.153 Angle : 0.634 7.556 12368 Z= 0.322 Chirality : 0.040 0.225 1319 Planarity : 0.005 0.052 1466 Dihedral : 13.785 73.558 1623 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.17 % Allowed : 18.42 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.01 (0.27), residues: 945 helix: 0.96 (0.26), residues: 369 sheet: -0.49 (0.41), residues: 171 loop : -0.55 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG s 9 TYR 0.018 0.002 TYR E 32 PHE 0.010 0.001 PHE t 112 TRP 0.022 0.002 TRP s 113 HIS 0.005 0.001 HIS p 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9049) covalent geometry : angle 0.63377 / 0.32 (12368) hydrogen bonds : bond 0.03559 / 3.75 ( 407) hydrogen bonds : angle 4.92728 / 4.89 ( 1225) metal coordination : bond 0.00232 / 0.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.198 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: A 72 GLN cc_start: 0.7645 (pm20) cc_final: 0.7393 (pm20) REVERT: E 68 LEU cc_start: 0.8568 (mt) cc_final: 0.8361 (mp) REVERT: E 146 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7809 (tm-30) REVERT: o 43 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6725 (ptm160) REVERT: o 109 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7948 (mt) REVERT: o 118 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7491 (ptm160) REVERT: o 144 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7522 (mm-30) REVERT: p 139 HIS cc_start: 0.6310 (p-80) cc_final: 0.5992 (p-80) REVERT: t 14 ASP cc_start: 0.7096 (m-30) cc_final: 0.6870 (m-30) outliers start: 36 outliers final: 27 residues processed: 272 average time/residue: 0.1260 time to fit residues: 42.4995 Evaluate side-chains 271 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 43 ARG Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN o 45 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 37 HIS ** s 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066921 restraints weight = 28745.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068758 restraints weight = 15247.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069968 restraints weight = 9851.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070759 restraints weight = 7178.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071267 restraints weight = 5756.255| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9061 Z= 0.178 Angle : 0.670 8.221 12368 Z= 0.342 Chirality : 0.041 0.215 1319 Planarity : 0.005 0.061 1466 Dihedral : 13.790 73.451 1623 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.94 % Allowed : 19.12 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.22 (0.27), residues: 945 helix: 0.54 (0.26), residues: 383 sheet: -0.60 (0.39), residues: 181 loop : -0.46 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG s 49 TYR 0.019 0.002 TYR A 32 PHE 0.013 0.002 PHE E 148 TRP 0.027 0.002 TRP s 113 HIS 0.004 0.001 HIS p 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9049) covalent geometry : angle 0.67033 / 0.34 (12368) hydrogen bonds : bond 0.03836 / 4.09 ( 407) hydrogen bonds : angle 4.92775 / 4.90 ( 1225) metal coordination : bond 0.00306 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.333 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: A 72 GLN cc_start: 0.7669 (pm20) cc_final: 0.7379 (pm20) REVERT: E 146 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7843 (tm-30) REVERT: o 43 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6771 (ptm160) REVERT: o 118 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7540 (ptm160) REVERT: o 144 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7475 (mm-30) REVERT: p 90 ARG cc_start: 0.8490 (ptp90) cc_final: 0.8231 (ptm160) REVERT: p 139 HIS cc_start: 0.6736 (p-80) cc_final: 0.6523 (p-80) REVERT: s 113 TRP cc_start: 0.8599 (p-90) cc_final: 0.8263 (p-90) REVERT: t 14 ASP cc_start: 0.7061 (m-30) cc_final: 0.6815 (m-30) outliers start: 34 outliers final: 29 residues processed: 266 average time/residue: 0.1363 time to fit residues: 44.9258 Evaluate side-chains 271 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 43 ARG Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 37 HIS Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 109 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 140 ASN s 37 HIS ** s 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.075817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.065997 restraints weight = 28445.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067835 restraints weight = 15241.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.069004 restraints weight = 9821.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069738 restraints weight = 7213.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070273 restraints weight = 5834.538| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9061 Z= 0.182 Angle : 0.674 8.366 12368 Z= 0.345 Chirality : 0.041 0.211 1319 Planarity : 0.005 0.052 1466 Dihedral : 13.794 73.438 1623 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.06 % Allowed : 20.63 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.21 (0.27), residues: 945 helix: 0.49 (0.26), residues: 381 sheet: -0.49 (0.39), residues: 178 loop : -0.44 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG o 49 TYR 0.018 0.002 TYR t 147 PHE 0.028 0.002 PHE E 148 TRP 0.026 0.002 TRP E 115 HIS 0.015 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 9049) covalent geometry : angle 0.67437 / 0.35 (12368) hydrogen bonds : bond 0.03836 / 4.07 ( 407) hydrogen bonds : angle 4.92572 / 4.89 ( 1225) metal coordination : bond 0.00482 / 0.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.365 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: A 69 ASP cc_start: 0.7112 (t0) cc_final: 0.6902 (t0) REVERT: A 72 GLN cc_start: 0.7612 (pm20) cc_final: 0.7400 (pm20) REVERT: E 136 MET cc_start: 0.8720 (mtt) cc_final: 0.8200 (mtt) REVERT: o 118 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7596 (ptm160) REVERT: o 144 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7475 (mm-30) REVERT: p 14 ASP cc_start: 0.7266 (t0) cc_final: 0.6485 (t0) REVERT: p 29 MET cc_start: 0.8598 (mmt) cc_final: 0.8334 (mmm) REVERT: s 9 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6933 (mmm160) REVERT: s 113 TRP cc_start: 0.8665 (p-90) cc_final: 0.8373 (p-90) REVERT: s 141 GLN cc_start: 0.7854 (mp10) cc_final: 0.7588 (mp10) REVERT: t 14 ASP cc_start: 0.7096 (m-30) cc_final: 0.6804 (m-30) outliers start: 35 outliers final: 28 residues processed: 263 average time/residue: 0.1326 time to fit residues: 43.4175 Evaluate side-chains 262 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 109 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 158 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 = 0.3432 r_free = 0.3432 target = 0.075582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065720 restraints weight = 28300.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067537 restraints weight = 15137.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068725 restraints weight = 9792.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069514 restraints weight = 7183.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070001 restraints weight = 5759.677| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9061 Z= 0.169 Angle : 0.695 8.555 12368 Z= 0.355 Chirality : 0.042 0.210 1319 Planarity : 0.005 0.063 1466 Dihedral : 13.842 74.078 1623 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.06 % Allowed : 21.78 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.27 (0.27), residues: 945 helix: 0.37 (0.26), residues: 379 sheet: -0.42 (0.39), residues: 176 loop : -0.46 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG o 131 TYR 0.018 0.002 TYR t 147 PHE 0.024 0.002 PHE s 127 TRP 0.033 0.002 TRP E 115 HIS 0.004 0.001 HIS p 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9049) covalent geometry : angle 0.69488 / 0.36 (12368) hydrogen bonds : bond 0.03963 / 4.14 ( 407) hydrogen bonds : angle 4.91020 / 4.88 ( 1225) metal coordination : bond 0.00291 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.366 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: A 72 GLN cc_start: 0.7595 (pm20) cc_final: 0.7394 (pm20) REVERT: E 69 ASP cc_start: 0.7917 (p0) cc_final: 0.7633 (p0) REVERT: E 136 MET cc_start: 0.8682 (mtt) cc_final: 0.8152 (mtt) REVERT: o 118 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7601 (ptm160) REVERT: o 144 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7429 (mm-30) REVERT: s 52 ARG cc_start: 0.7354 (ttp80) cc_final: 0.6953 (tmm160) REVERT: s 113 TRP cc_start: 0.8673 (p-90) cc_final: 0.8370 (p-90) REVERT: s 141 GLN cc_start: 0.7823 (mp10) cc_final: 0.7492 (mp10) REVERT: t 14 ASP cc_start: 0.6921 (m-30) cc_final: 0.6689 (m-30) outliers start: 35 outliers final: 32 residues processed: 256 average time/residue: 0.1357 time to fit residues: 43.3318 Evaluate side-chains 269 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 109 ILE Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 57 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 90 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 HIS o 140 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 122 ASN p 158 GLN s 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.066047 restraints weight = 28304.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067824 restraints weight = 15191.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069002 restraints weight = 9789.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069787 restraints weight = 7169.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070325 restraints weight = 5750.879| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9061 Z= 0.154 Angle : 0.717 9.787 12368 Z= 0.366 Chirality : 0.041 0.206 1319 Planarity : 0.007 0.192 1466 Dihedral : 13.899 73.572 1623 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.94 % Allowed : 23.41 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.27 (0.28), residues: 945 helix: 0.31 (0.26), residues: 381 sheet: -0.39 (0.40), residues: 176 loop : -0.39 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG o 19 TYR 0.024 0.002 TYR E 74 PHE 0.027 0.002 PHE o 32 TRP 0.042 0.002 TRP E 115 HIS 0.006 0.001 HIS o 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 9049) covalent geometry : angle 0.71739 / 0.37 (12368) hydrogen bonds : bond 0.03684 / 3.88 ( 407) hydrogen bonds : angle 4.89471 / 4.85 ( 1225) metal coordination : bond 0.00231 / 0.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.321 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: A 69 ASP cc_start: 0.6966 (t0) cc_final: 0.6763 (t0) REVERT: E 136 MET cc_start: 0.8620 (mtt) cc_final: 0.8074 (mtt) REVERT: o 13 GLU cc_start: 0.7705 (mm-30) cc_final: 0.6857 (mm-30) REVERT: o 19 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7270 (mtm-85) REVERT: o 118 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7608 (ptm160) REVERT: o 144 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7393 (mm-30) REVERT: p 29 MET cc_start: 0.8611 (mmt) cc_final: 0.8359 (mmm) REVERT: s 90 ARG cc_start: 0.7622 (ptp-170) cc_final: 0.7340 (ttp80) REVERT: s 113 TRP cc_start: 0.8639 (p-90) cc_final: 0.8382 (p-90) REVERT: s 141 GLN cc_start: 0.7843 (mp10) cc_final: 0.7540 (mp10) REVERT: t 14 ASP cc_start: 0.6904 (m-30) cc_final: 0.6673 (m-30) REVERT: t 83 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7351 (mt0) outliers start: 34 outliers final: 30 residues processed: 256 average time/residue: 0.1344 time to fit residues: 43.2589 Evaluate side-chains 268 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain t residue 16 MET Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 83 GLN Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 1 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 HIS ** p 97 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 = 0.3431 r_free = 0.3431 target = 0.075290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065532 restraints weight = 28418.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067325 restraints weight = 15255.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.068527 restraints weight = 9852.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069290 restraints weight = 7183.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069850 restraints weight = 5775.327| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9061 Z= 0.170 Angle : 0.744 10.387 12368 Z= 0.381 Chirality : 0.041 0.214 1319 Planarity : 0.007 0.166 1466 Dihedral : 13.876 73.507 1623 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.06 % Allowed : 23.29 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.29 (0.27), residues: 945 helix: 0.35 (0.27), residues: 377 sheet: -0.35 (0.40), residues: 176 loop : -0.49 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG o 131 TYR 0.018 0.002 TYR A 32 PHE 0.021 0.002 PHE o 32 TRP 0.053 0.002 TRP E 115 HIS 0.007 0.001 HIS o 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9049) covalent geometry : angle 0.74427 / 0.38 (12368) hydrogen bonds : bond 0.03874 / 4.02 ( 407) hydrogen bonds : angle 4.88468 / 4.88 ( 1225) metal coordination : bond 0.00225 / 0.17 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.332 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: E 136 MET cc_start: 0.8631 (mtt) cc_final: 0.8075 (mtt) REVERT: o 13 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7196 (mm-30) REVERT: o 118 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7623 (ptm160) REVERT: o 144 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7385 (mm-30) REVERT: p 29 MET cc_start: 0.8618 (mmt) cc_final: 0.8375 (mmm) REVERT: s 113 TRP cc_start: 0.8635 (p-90) cc_final: 0.8365 (p-90) REVERT: s 141 GLN cc_start: 0.7857 (mp10) cc_final: 0.7121 (mp10) REVERT: t 14 ASP cc_start: 0.6887 (m-30) cc_final: 0.6653 (m-30) outliers start: 35 outliers final: 32 residues processed: 261 average time/residue: 0.1399 time to fit residues: 45.7030 Evaluate side-chains 272 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 73 TRP Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 159 ILE Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain p residue 169 LEU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 46 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 93 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 0.0980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 HIS ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063840 restraints weight = 28535.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065588 restraints weight = 15418.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066743 restraints weight = 9955.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067520 restraints weight = 7324.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068048 restraints weight = 5871.653| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9061 Z= 0.204 Angle : 0.778 8.869 12368 Z= 0.400 Chirality : 0.043 0.234 1319 Planarity : 0.007 0.146 1466 Dihedral : 13.871 73.489 1623 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.29 % Allowed : 23.06 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.43 (0.27), residues: 945 helix: 0.17 (0.27), residues: 375 sheet: -0.29 (0.39), residues: 176 loop : -0.57 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG o 49 TYR 0.019 0.002 TYR A 32 PHE 0.032 0.002 PHE o 32 TRP 0.061 0.002 TRP E 115 HIS 0.008 0.001 HIS o 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 9049) covalent geometry : angle 0.77753 / 0.40 (12368) hydrogen bonds : bond 0.04105 / 4.29 ( 407) hydrogen bonds : angle 4.95812 / 4.96 ( 1225) metal coordination : bond 0.00394 / 0.30 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1756.75 seconds wall clock time: 31 minutes 0.91 seconds (1860.91 seconds total)