Starting phenix.real_space_refine on Sun Apr 5 07:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e93_47752/04_2026/9e93_47752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e93_47752/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e93_47752/04_2026/9e93_47752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e93_47752/04_2026/9e93_47752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e93_47752/04_2026/9e93_47752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e93_47752/04_2026/9e93_47752.map" } 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-2.1rc1-6017/lib/python3.9/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: 2.00, per 1000 atoms: 0.23 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: 0.60 Conformation dependent library (CDL) restraints added in 290.2 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: 0.87 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: 1.33 Time building geometry restraints manager: 0.82 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=" 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=" CB PRO o 100 " pdb=" CG PRO o 100 " ideal model delta sigma weight residual 1.492 1.520 -0.028 5.00e-02 4.00e+02 3.11e-01 bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.36e-02 5.41e+03 2.90e-01 bond pdb=" C SER p 130 " pdb=" N PRO p 131 " ideal model delta sigma weight residual 1.330 1.337 -0.007 1.22e-02 6.72e+03 2.85e-01 ... (remaining 9044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 12106 1.10 - 2.20: 199 2.20 - 3.30: 48 3.30 - 4.40: 6 4.40 - 5.50: 9 Bond angle restraints: 12368 Sorted by residual: angle pdb=" C2' U H 2 " pdb=" C1' U H 2 " pdb=" N1 U H 2 " ideal model delta sigma weight residual 112.00 114.81 -2.81 1.50e+00 4.44e-01 3.52e+00 angle pdb=" CG1 ILE t 159 " pdb=" CB ILE t 159 " pdb=" CG2 ILE t 159 " ideal model delta sigma weight residual 110.70 105.53 5.17 3.00e+00 1.11e-01 2.97e+00 angle pdb=" CA LEU t 72 " pdb=" CB LEU t 72 " pdb=" CG LEU t 72 " ideal model delta sigma weight residual 116.30 121.80 -5.50 3.50e+00 8.16e-02 2.47e+00 angle pdb=" N SER t 130 " pdb=" CA SER t 130 " pdb=" C SER t 130 " ideal model delta sigma weight residual 109.81 113.19 -3.38 2.21e+00 2.05e-01 2.34e+00 angle pdb=" CA LEU s 64 " pdb=" CB LEU s 64 " pdb=" CG LEU s 64 " ideal model delta sigma weight residual 116.30 121.65 -5.35 3.50e+00 8.16e-02 2.33e+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: 1021 0.034 - 0.068: 198 0.068 - 0.102: 67 0.102 - 0.135: 32 0.135 - 0.169: 1 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=" CA ILE p 66 " pdb=" N ILE p 66 " pdb=" C ILE p 66 " pdb=" CB ILE p 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE t 66 " pdb=" N ILE t 66 " pdb=" C ILE t 66 " pdb=" CB ILE t 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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= 0.074 Angle : 0.398 5.503 12368 Z= 0.201 Chirality : 0.035 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 covalent geometry : bond 0.00156 ( 9049) covalent geometry : angle 0.39759 (12368) hydrogen bonds : bond 0.17560 ( 407) hydrogen bonds : angle 7.68717 ( 1225) metal coordination : bond 0.00274 ( 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 : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.7586 (t) cc_final: 0.7159 (p) REVERT: E 136 MET cc_start: 0.7744 (mtp) cc_final: 0.7123 (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: 0.7384 (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: 0.7626 (ttp80) REVERT: s 141 GLN cc_start: 0.8090 (mt0) cc_final: 0.7842 (mt0) REVERT: t 16 MET cc_start: 0.7777 (mtm) cc_final: 0.7485 (mtm) REVERT: t 83 GLN cc_start: 0.7905 (mt0) cc_final: 0.7547 (mt0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1620 time to fit residues: 72.2466 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 : 0.351 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 37 GLN A 38 ASN A 97 GLN E 49 ASN E 101 HIS E 119 GLN ** o 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.078391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068180 restraints weight = 28782.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070051 restraints weight = 15427.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071270 restraints weight = 9958.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.072041 restraints weight = 7316.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072642 restraints weight = 5893.694| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4360 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= 0.188 Angle : 0.641 8.202 12368 Z= 0.329 Chirality : 0.042 0.198 1319 Planarity : 0.006 0.045 1466 Dihedral : 13.698 73.433 1623 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.36 % Allowed : 14.60 % Favored : 82.04 % 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: 0.28 (0.27), residues: 945 helix: 1.12 (0.26), residues: 382 sheet: -0.34 (0.40), residues: 169 loop : -0.37 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 124 TYR 0.026 0.002 TYR t 94 PHE 0.017 0.002 PHE E 148 TRP 0.019 0.002 TRP s 113 HIS 0.005 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9049) covalent geometry : angle 0.64127 (12368) hydrogen bonds : bond 0.03867 ( 407) hydrogen bonds : angle 5.05272 ( 1225) metal coordination : bond 0.00412 ( 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 301 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.348 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 51 LYS cc_start: 0.7647 (tppt) cc_final: 0.7061 (tppt) REVERT: E 69 ASP cc_start: 0.7845 (p0) cc_final: 0.7324 (p0) REVERT: E 136 MET cc_start: 0.8594 (mtp) cc_final: 0.8065 (mtm) REVERT: E 146 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7817 (tm-30) REVERT: o 109 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8085 (mt) REVERT: o 118 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7435 (ptm160) REVERT: o 140 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7702 (tp-100) REVERT: p 146 GLN cc_start: 0.6590 (pm20) cc_final: 0.6252 (pt0) REVERT: s 27 ILE cc_start: 0.8185 (mt) cc_final: 0.7929 (mt) REVERT: s 120 ASP cc_start: 0.8076 (t0) cc_final: 0.7206 (t0) REVERT: t 45 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7249 (tt0) REVERT: t 147 TYR cc_start: 0.7593 (t80) cc_final: 0.7293 (t80) outliers start: 29 outliers final: 19 residues processed: 286 average time/residue: 0.1574 time to fit residues: 54.9775 Evaluate side-chains 266 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain o residue 66 LEU 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 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 67 THR Chi-restraints excluded: chain t residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 77 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.0040 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067990 restraints weight = 28400.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069805 restraints weight = 15221.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.071015 restraints weight = 9899.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071822 restraints weight = 7247.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072358 restraints weight = 5801.516| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9061 Z= 0.136 Angle : 0.594 6.607 12368 Z= 0.302 Chirality : 0.040 0.202 1319 Planarity : 0.005 0.078 1466 Dihedral : 13.742 73.437 1623 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.82 % Allowed : 17.03 % Favored : 79.14 % 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: 1.18 (0.27), residues: 372 sheet: -0.47 (0.39), residues: 180 loop : -0.37 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG s 9 TYR 0.024 0.001 TYR A 32 PHE 0.022 0.001 PHE E 148 TRP 0.018 0.001 TRP s 113 HIS 0.004 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9049) covalent geometry : angle 0.59384 (12368) hydrogen bonds : bond 0.03422 ( 407) hydrogen bonds : angle 4.75285 ( 1225) metal coordination : bond 0.00223 ( 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 287 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.241 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: E 51 LYS cc_start: 0.7928 (tppt) cc_final: 0.7376 (tppt) REVERT: E 136 MET cc_start: 0.8596 (mtp) cc_final: 0.8196 (mtt) REVERT: o 45 GLN cc_start: 0.7427 (tp40) cc_final: 0.6168 (tp40) REVERT: o 109 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8034 (mt) REVERT: o 118 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7527 (ptm160) REVERT: p 90 ARG cc_start: 0.8545 (ptp90) cc_final: 0.8339 (ptm160) REVERT: s 20 LYS cc_start: 0.7877 (tttt) cc_final: 0.7640 (tmtt) REVERT: s 118 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7697 (ttp80) REVERT: s 120 ASP cc_start: 0.7921 (t0) cc_final: 0.7084 (t0) REVERT: t 16 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7905 (mtm) REVERT: t 45 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7145 (tt0) outliers start: 33 outliers final: 21 residues processed: 266 average time/residue: 0.1520 time to fit residues: 49.5477 Evaluate side-chains 263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 106 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 75 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 95 VAL Chi-restraints excluded: chain o residue 109 ILE Chi-restraints excluded: chain p residue 18 ILE 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 16 MET 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: 0.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 139 HIS ** p 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063376 restraints weight = 28901.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.065153 restraints weight = 15448.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066312 restraints weight = 10019.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.067078 restraints weight = 7369.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067626 restraints weight = 5957.336| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5681 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= 0.186 Angle : 0.653 8.531 12368 Z= 0.331 Chirality : 0.042 0.211 1319 Planarity : 0.005 0.050 1466 Dihedral : 13.735 73.458 1623 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.94 % Allowed : 18.77 % Favored : 77.29 % 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: 0.08 (0.27), residues: 945 helix: 0.71 (0.27), residues: 382 sheet: -0.18 (0.41), residues: 164 loop : -0.35 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 10 TYR 0.020 0.002 TYR t 94 PHE 0.016 0.002 PHE E 107 TRP 0.024 0.002 TRP s 113 HIS 0.004 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9049) covalent geometry : angle 0.65319 (12368) hydrogen bonds : bond 0.03919 ( 407) hydrogen bonds : angle 4.79297 ( 1225) metal coordination : bond 0.00348 ( 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 297 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7599 (ttp80) REVERT: E 136 MET cc_start: 0.8935 (mtp) cc_final: 0.8693 (mtt) REVERT: p 90 ARG cc_start: 0.8628 (ptp90) cc_final: 0.8330 (ptp90) REVERT: p 140 ASN cc_start: 0.7626 (t0) cc_final: 0.7249 (t0) REVERT: p 146 GLN cc_start: 0.7163 (pm20) cc_final: 0.6761 (pt0) REVERT: s 118 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7918 (ttp80) REVERT: s 120 ASP cc_start: 0.8057 (t0) cc_final: 0.7382 (t0) REVERT: t 127 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6831 (ttp-110) REVERT: t 167 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7614 (mpp80) outliers start: 34 outliers final: 23 residues processed: 278 average time/residue: 0.1556 time to fit residues: 52.8344 Evaluate side-chains 263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 106 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 180 ILE 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 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 16 MET 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 127 ARG Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 49 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 HIS o 45 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 122 ASN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063673 restraints weight = 28505.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065442 restraints weight = 15279.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066608 restraints weight = 9944.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067393 restraints weight = 7345.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067893 restraints weight = 5903.219| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9061 Z= 0.153 Angle : 0.648 9.853 12368 Z= 0.325 Chirality : 0.040 0.230 1319 Planarity : 0.004 0.056 1466 Dihedral : 13.766 73.453 1623 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.06 % Allowed : 21.09 % Favored : 74.86 % 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: 0.03 (0.27), residues: 945 helix: 0.66 (0.26), residues: 382 sheet: -0.22 (0.40), residues: 176 loop : -0.35 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 167 TYR 0.021 0.002 TYR A 32 PHE 0.021 0.001 PHE o 18 TRP 0.024 0.002 TRP s 113 HIS 0.006 0.001 HIS o 37 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9049) covalent geometry : angle 0.64826 (12368) hydrogen bonds : bond 0.03571 ( 407) hydrogen bonds : angle 4.62036 ( 1225) metal coordination : bond 0.00225 ( 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 293 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.287 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: 0.8775 (mtp) cc_final: 0.8394 (mtt) REVERT: o 118 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7685 (ptm160) REVERT: p 83 GLN cc_start: 0.8178 (mm110) cc_final: 0.7966 (mm110) REVERT: p 90 ARG cc_start: 0.8664 (ptp90) cc_final: 0.8256 (ptm160) REVERT: p 146 GLN cc_start: 0.6968 (pm20) cc_final: 0.6658 (pt0) REVERT: t 111 TYR cc_start: 0.8314 (m-80) cc_final: 0.8064 (m-80) REVERT: t 127 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6876 (ttp-110) REVERT: t 167 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7530 (mpp80) outliers start: 35 outliers final: 25 residues processed: 274 average time/residue: 0.1503 time to fit residues: 50.9577 Evaluate side-chains 263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 106 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 180 ILE 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 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 127 ARG 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 72 LEU Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Chi-restraints excluded: chain t residue 159 ILE Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 49 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061472 restraints weight = 28793.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063221 restraints weight = 15401.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064390 restraints weight = 10002.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.065163 restraints weight = 7349.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065692 restraints weight = 5910.090| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9061 Z= 0.194 Angle : 0.702 14.319 12368 Z= 0.351 Chirality : 0.042 0.248 1319 Planarity : 0.005 0.041 1466 Dihedral : 13.770 73.483 1623 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.75 % Allowed : 22.71 % Favored : 72.54 % 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: -0.15 (0.27), residues: 945 helix: 0.47 (0.26), residues: 380 sheet: -0.30 (0.39), residues: 183 loop : -0.42 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG o 49 TYR 0.018 0.002 TYR A 32 PHE 0.017 0.002 PHE E 148 TRP 0.028 0.002 TRP s 113 HIS 0.007 0.001 HIS p 139 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9049) covalent geometry : angle 0.70168 (12368) hydrogen bonds : bond 0.03981 ( 407) hydrogen bonds : angle 4.69802 ( 1225) metal coordination : bond 0.00342 ( 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 290 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.376 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 141 PHE cc_start: 0.8305 (m-80) cc_final: 0.8067 (m-80) REVERT: E 44 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8241 (ptt180) REVERT: E 51 LYS cc_start: 0.8381 (tppt) cc_final: 0.7227 (tppt) REVERT: E 143 ASP cc_start: 0.8211 (t0) cc_final: 0.7796 (t0) REVERT: o 45 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7078 (tp40) REVERT: o 145 GLU cc_start: 0.8058 (tp30) cc_final: 0.7433 (tp30) REVERT: p 14 ASP cc_start: 0.7285 (t0) cc_final: 0.6738 (t0) REVERT: p 90 ARG cc_start: 0.8723 (ptp90) cc_final: 0.8029 (ptm160) REVERT: t 111 TYR cc_start: 0.8377 (m-80) cc_final: 0.8137 (m-80) REVERT: t 127 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6896 (ttp-110) REVERT: t 167 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7679 (mpp80) outliers start: 41 outliers final: 32 residues processed: 268 average time/residue: 0.1473 time to fit residues: 48.9779 Evaluate side-chains 272 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN 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 106 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain E residue 44 ARG 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 E residue 160 CYS Chi-restraints excluded: chain E residue 180 ILE 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 o residue 125 LEU Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 127 ARG 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 140 GLN Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 19 ASN Chi-restraints excluded: chain t residue 47 THR Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 127 ARG Chi-restraints excluded: chain t residue 159 ILE Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 15 ASN A 49 ASN ** 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 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061072 restraints weight = 28475.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062762 restraints weight = 15407.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063911 restraints weight = 10017.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.064652 restraints weight = 7342.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065180 restraints weight = 5915.576| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9061 Z= 0.190 Angle : 0.712 12.793 12368 Z= 0.359 Chirality : 0.042 0.274 1319 Planarity : 0.005 0.070 1466 Dihedral : 13.726 73.526 1623 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.75 % Allowed : 23.29 % Favored : 71.96 % 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: 0.32 (0.26), residues: 381 sheet: -0.36 (0.39), residues: 173 loop : -0.46 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG s 49 TYR 0.027 0.002 TYR p 147 PHE 0.034 0.002 PHE E 148 TRP 0.030 0.002 TRP s 113 HIS 0.005 0.001 HIS t 108 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9049) covalent geometry : angle 0.71152 (12368) hydrogen bonds : bond 0.03878 ( 407) hydrogen bonds : angle 4.71853 ( 1225) metal coordination : bond 0.00351 ( 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 292 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.334 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: A 12 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8207 (mm-40) REVERT: E 44 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8322 (ptt180) REVERT: E 50 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6932 (pttp) REVERT: E 143 ASP cc_start: 0.8241 (t0) cc_final: 0.7923 (t0) REVERT: o 120 ASP cc_start: 0.7990 (t0) cc_final: 0.7763 (t0) REVERT: o 145 GLU cc_start: 0.8088 (tp30) cc_final: 0.7436 (tp30) REVERT: p 90 ARG cc_start: 0.8746 (ptp90) cc_final: 0.8051 (ptm160) REVERT: s 9 ARG cc_start: 0.6934 (mmm160) cc_final: 0.6730 (tpp-160) REVERT: s 118 ARG cc_start: 0.8533 (mtp180) cc_final: 0.8046 (ttp80) REVERT: t 111 TYR cc_start: 0.8392 (m-80) cc_final: 0.8189 (m-80) REVERT: t 167 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7640 (mpp80) outliers start: 41 outliers final: 31 residues processed: 271 average time/residue: 0.1524 time to fit residues: 50.8892 Evaluate side-chains 275 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN 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 106 ILE Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 50 LYS 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 E residue 160 CYS 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 o residue 125 LEU Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 127 ARG 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 165 SER Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 109 ILE Chi-restraints excluded: chain s residue 140 GLN Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 47 THR Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 159 ILE Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 45 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 49 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** t 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062247 restraints weight = 28409.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063941 restraints weight = 15152.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065078 restraints weight = 9850.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065865 restraints weight = 7262.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066375 restraints weight = 5810.214| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9061 Z= 0.152 Angle : 0.710 12.336 12368 Z= 0.356 Chirality : 0.040 0.255 1319 Planarity : 0.005 0.049 1466 Dihedral : 13.735 73.551 1623 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.87 % Allowed : 23.87 % Favored : 71.26 % 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: -0.25 (0.27), residues: 945 helix: 0.35 (0.26), residues: 381 sheet: -0.35 (0.39), residues: 181 loop : -0.42 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 10 TYR 0.031 0.002 TYR s 29 PHE 0.030 0.002 PHE E 148 TRP 0.029 0.002 TRP o 113 HIS 0.004 0.001 HIS t 108 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9049) covalent geometry : angle 0.71018 (12368) hydrogen bonds : bond 0.03448 ( 407) hydrogen bonds : angle 4.58020 ( 1225) metal coordination : bond 0.00255 ( 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 299 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.351 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: A 12 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: E 44 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8277 (ptt180) REVERT: E 143 ASP cc_start: 0.8230 (t0) cc_final: 0.7862 (t0) REVERT: o 120 ASP cc_start: 0.7950 (t0) cc_final: 0.7667 (t0) REVERT: o 145 GLU cc_start: 0.8099 (tp30) cc_final: 0.7491 (tp30) REVERT: p 90 ARG cc_start: 0.8752 (ptp90) cc_final: 0.8290 (ptm160) REVERT: s 118 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8047 (ttp80) REVERT: t 111 TYR cc_start: 0.8352 (m-80) cc_final: 0.8102 (m-80) REVERT: t 167 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7464 (mpp80) outliers start: 42 outliers final: 29 residues processed: 281 average time/residue: 0.1482 time to fit residues: 51.4835 Evaluate side-chains 288 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 27 LYS 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 93 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain E residue 44 ARG 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 109 ILE Chi-restraints excluded: chain o residue 125 LEU Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 127 ARG 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 7 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 19 ASN Chi-restraints excluded: chain t residue 47 THR Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 159 ILE Chi-restraints excluded: chain t residue 165 SER Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 15 ASN A 49 ASN ** o 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 140 GLN ** p 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063532 restraints weight = 28149.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065308 restraints weight = 14997.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066480 restraints weight = 9664.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067278 restraints weight = 7028.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067825 restraints weight = 5586.436| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9061 Z= 0.142 Angle : 0.711 11.040 12368 Z= 0.358 Chirality : 0.040 0.260 1319 Planarity : 0.004 0.036 1466 Dihedral : 13.728 73.573 1623 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.94 % Allowed : 24.80 % Favored : 71.26 % 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 (0.28), residues: 945 helix: 0.48 (0.27), residues: 378 sheet: -0.24 (0.39), residues: 181 loop : -0.43 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 10 TYR 0.025 0.002 TYR p 147 PHE 0.024 0.001 PHE E 148 TRP 0.033 0.002 TRP s 113 HIS 0.004 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9049) covalent geometry : angle 0.71112 (12368) hydrogen bonds : bond 0.03233 ( 407) hydrogen bonds : angle 4.53983 ( 1225) metal coordination : bond 0.00262 ( 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 298 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.331 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 46 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.6823 (p90) REVERT: E 10 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7652 (ttp80) REVERT: E 44 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8228 (ptt180) REVERT: o 145 GLU cc_start: 0.8068 (tp30) cc_final: 0.7504 (tp30) REVERT: p 16 MET cc_start: 0.8086 (mtp) cc_final: 0.7829 (mtm) REVERT: p 90 ARG cc_start: 0.8747 (ptp90) cc_final: 0.8280 (ptm160) REVERT: s 118 ARG cc_start: 0.8438 (mtp180) cc_final: 0.8178 (ttp80) REVERT: s 140 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7709 (tp40) REVERT: t 111 TYR cc_start: 0.8335 (m-80) cc_final: 0.8100 (m-80) REVERT: t 167 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7497 (mpp80) outliers start: 34 outliers final: 26 residues processed: 285 average time/residue: 0.1520 time to fit residues: 53.7189 Evaluate side-chains 279 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS 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 93 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain E residue 44 ARG 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 109 ILE Chi-restraints excluded: chain o residue 125 LEU Chi-restraints excluded: chain p residue 120 ILE Chi-restraints excluded: chain p residue 127 ARG 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 7 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 47 THR Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 120 ILE Chi-restraints excluded: chain t residue 159 ILE Chi-restraints excluded: chain t residue 165 SER Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061705 restraints weight = 28416.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063423 restraints weight = 15150.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064566 restraints weight = 9804.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065346 restraints weight = 7178.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065820 restraints weight = 5750.115| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9061 Z= 0.178 Angle : 0.755 10.780 12368 Z= 0.382 Chirality : 0.042 0.268 1319 Planarity : 0.006 0.101 1466 Dihedral : 13.677 73.575 1623 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.59 % Allowed : 26.65 % Favored : 69.76 % 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: 0.32 (0.26), residues: 379 sheet: -0.27 (0.40), residues: 171 loop : -0.51 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG s 49 TYR 0.027 0.002 TYR A 32 PHE 0.026 0.002 PHE E 148 TRP 0.034 0.002 TRP s 113 HIS 0.005 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9049) covalent geometry : angle 0.75515 (12368) hydrogen bonds : bond 0.03651 ( 407) hydrogen bonds : angle 4.65984 ( 1225) metal coordination : bond 0.00334 ( 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 288 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.305 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: o 118 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7418 (ptm-80) REVERT: o 144 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7997 (mm-30) REVERT: o 145 GLU cc_start: 0.8033 (tp30) cc_final: 0.7522 (tp30) REVERT: p 90 ARG cc_start: 0.8760 (ptp90) cc_final: 0.8060 (ptm160) REVERT: s 118 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8210 (ttp80) REVERT: t 69 TYR cc_start: 0.8513 (m-10) cc_final: 0.8280 (m-10) REVERT: t 91 LYS cc_start: 0.8237 (tppt) cc_final: 0.7905 (tppt) REVERT: t 167 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7448 (mpp80) outliers start: 31 outliers final: 26 residues processed: 275 average time/residue: 0.1496 time to fit residues: 51.0211 Evaluate side-chains 274 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 64 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 ILE 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 109 ILE Chi-restraints excluded: chain o residue 125 LEU Chi-restraints excluded: chain p residue 99 ASP Chi-restraints excluded: chain p residue 127 ARG 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 7 VAL Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 47 THR Chi-restraints excluded: chain t residue 67 THR Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 95 SER Chi-restraints excluded: chain t residue 159 ILE Chi-restraints excluded: chain t residue 165 SER Chi-restraints excluded: chain t residue 167 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062460 restraints weight = 28325.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064213 restraints weight = 15123.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065368 restraints weight = 9734.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066161 restraints weight = 7129.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066678 restraints weight = 5691.873| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9061 Z= 0.165 Angle : 0.773 12.750 12368 Z= 0.389 Chirality : 0.041 0.272 1319 Planarity : 0.005 0.059 1466 Dihedral : 13.699 73.604 1623 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.48 % Allowed : 27.11 % Favored : 69.41 % 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: -0.38 (0.27), residues: 945 helix: 0.30 (0.27), residues: 377 sheet: -0.40 (0.40), residues: 171 loop : -0.57 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG s 49 TYR 0.026 0.002 TYR p 147 PHE 0.022 0.002 PHE E 148 TRP 0.030 0.002 TRP o 113 HIS 0.005 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9049) covalent geometry : angle 0.77317 (12368) hydrogen bonds : bond 0.03497 ( 407) hydrogen bonds : angle 4.66225 ( 1225) metal coordination : bond 0.00297 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.95 seconds wall clock time: 34 minutes 12.88 seconds (2052.88 seconds total)