Starting phenix.real_space_refine on Sun Jul 5 04:44:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kda_37129/07_2026/8kda_37129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kda_37129/07_2026/8kda_37129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kda_37129/07_2026/8kda_37129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kda_37129/07_2026/8kda_37129.map" model { file = "/net/cci-nas-00/data/ceres_data/8kda_37129/07_2026/8kda_37129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kda_37129/07_2026/8kda_37129.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 360 5.49 5 Mg 5 5.21 5 S 55 5.16 5 C 15292 2.51 5 N 4543 2.21 5 O 5967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26222 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "T" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'rna2p': 11, 'rna3p': 61} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 62} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 10, 'rna3p': 62} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "G" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "H" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "C" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "D" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "I" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "J" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "A" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "B" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1519 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "L" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.78, per 1000 atoms: 0.22 Number of scatterers: 26222 At special positions: 0 Unit cell: (140.07, 162.69, 229.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 360 15.00 Mg 5 11.99 O 5967 8.00 N 4543 7.00 C 15292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 808.9 milliseconds 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4282 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 19 sheets defined 67.2% alpha, 6.5% beta 121 base pairs and 157 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 23 through 36 removed outlier: 3.511A pdb=" N SER E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.555A pdb=" N GLU E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.783A pdb=" N VAL E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 78 removed outlier: 3.706A pdb=" N GLY E 78 " --> pdb=" O ARG E 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 78' Processing helix chain 'E' and resid 83 through 112 Processing helix chain 'E' and resid 118 through 135 removed outlier: 3.788A pdb=" N VAL E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.617A pdb=" N VAL E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.646A pdb=" N ARG E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 181 through 187 Processing helix chain 'F' and resid 8 through 12 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 23 through 36 removed outlier: 3.863A pdb=" N ILE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 83 through 115 removed outlier: 3.645A pdb=" N PHE F 89 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 135 removed outlier: 3.659A pdb=" N VAL F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.925A pdb=" N VAL F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 removed outlier: 3.998A pdb=" N TRP F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 181 through 189 Processing helix chain 'G' and resid 8 through 11 Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.653A pdb=" N TYR G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS G 18 " --> pdb=" O PRO G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.699A pdb=" N GLU G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.509A pdb=" N LYS G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 118 through 135 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.513A pdb=" N VAL G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 173 removed outlier: 3.514A pdb=" N LYS G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 181 through 189 removed outlier: 3.890A pdb=" N GLU G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 13 removed outlier: 4.406A pdb=" N PHE H 11 " --> pdb=" O ASP H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 23 through 36 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 83 through 112 Processing helix chain 'H' and resid 118 through 136 removed outlier: 3.823A pdb=" N VAL H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.886A pdb=" N VAL H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 170 Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 181 through 187 Processing helix chain 'C' and resid 7 through 13 removed outlier: 4.098A pdb=" N PHE C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.940A pdb=" N GLU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 83 through 112 removed outlier: 3.922A pdb=" N TYR C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.828A pdb=" N VAL C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.929A pdb=" N TRP C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 189 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.323A pdb=" N PHE D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.566A pdb=" N HIS D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 19' Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.604A pdb=" N SER D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.675A pdb=" N LYS D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.510A pdb=" N GLU D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 141 through 155 removed outlier: 3.947A pdb=" N VAL D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.563A pdb=" N TRP D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 181 through 189 Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 13 through 18 Processing helix chain 'I' and resid 23 through 37 removed outlier: 3.889A pdb=" N ILE I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS I 37 " --> pdb=" O SER I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 61 through 68 removed outlier: 3.797A pdb=" N LEU I 67 " --> pdb=" O PRO I 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL I 68 " --> pdb=" O LYS I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 83 through 113 Processing helix chain 'I' and resid 118 through 136 removed outlier: 3.781A pdb=" N VAL I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 155 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.648A pdb=" N TRP I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'J' and resid 7 through 13 removed outlier: 4.545A pdb=" N PHE J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 23 through 37 Processing helix chain 'J' and resid 45 through 53 Processing helix chain 'J' and resid 60 through 69 removed outlier: 4.559A pdb=" N LYS J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 114 Processing helix chain 'J' and resid 119 through 135 Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'J' and resid 163 through 171 Processing helix chain 'J' and resid 182 through 188 Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.695A pdb=" N HIS A 18 " --> pdb=" O PRO A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.857A pdb=" N GLU A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.674A pdb=" N TYR A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 removed outlier: 4.057A pdb=" N LEU A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 110 removed outlier: 3.612A pdb=" N TYR A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.777A pdb=" N VAL A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.361A pdb=" N VAL A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 189 removed outlier: 3.592A pdb=" N LEU A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.746A pdb=" N TYR B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 18 " --> pdb=" O PRO B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.511A pdb=" N GLU B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.558A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.555A pdb=" N GLU B 91 " --> pdb=" O TYR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.831A pdb=" N LYS B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 135 removed outlier: 3.966A pdb=" N GLU B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.717A pdb=" N VAL B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'K' and resid 7 through 11 removed outlier: 3.548A pdb=" N VAL K 10 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 11 " --> pdb=" O THR K 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 7 through 11' Processing helix chain 'K' and resid 23 through 36 removed outlier: 5.213A pdb=" N GLU K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.593A pdb=" N LYS K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 68 removed outlier: 3.781A pdb=" N VAL K 68 " --> pdb=" O LYS K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 4.184A pdb=" N GLU K 91 " --> pdb=" O TYR K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 114 No H-bonds generated for 'chain 'K' and resid 112 through 114' Processing helix chain 'K' and resid 118 through 135 removed outlier: 3.576A pdb=" N VAL K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 155 removed outlier: 3.542A pdb=" N LEU K 148 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 173 removed outlier: 3.773A pdb=" N ARG K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TRP K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 180 No H-bonds generated for 'chain 'K' and resid 178 through 180' Processing helix chain 'K' and resid 181 through 186 Processing helix chain 'L' and resid 13 through 18 Processing helix chain 'L' and resid 23 through 38 Processing helix chain 'L' and resid 45 through 56 removed outlier: 3.724A pdb=" N VAL L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 83 through 114 removed outlier: 3.983A pdb=" N TYR L 87 " --> pdb=" O ALA L 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY L 100 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 106 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS L 107 " --> pdb=" O ILE L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 135 removed outlier: 3.673A pdb=" N ARG L 125 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 155 removed outlier: 4.372A pdb=" N VAL L 145 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 173 removed outlier: 3.755A pdb=" N ASP L 170 " --> pdb=" O ARG L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 180 No H-bonds generated for 'chain 'L' and resid 178 through 180' Processing helix chain 'L' and resid 181 through 188 removed outlier: 3.663A pdb=" N ILE L 185 " --> pdb=" O ASN L 181 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 69 through 71 removed outlier: 8.674A pdb=" N ARG E 70 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE E 42 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR E 3 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL E 159 " --> pdb=" O THR E 3 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL E 5 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'F' and resid 70 through 72 removed outlier: 6.545A pdb=" N THR F 3 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL F 159 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL F 5 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 70 through 71 removed outlier: 8.885A pdb=" N ARG G 70 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE G 42 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP G 2 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE G 43 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE G 4 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR G 3 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL G 159 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL G 5 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 82 Processing sheet with id=AA6, first strand: chain 'H' and resid 70 through 72 removed outlier: 8.576A pdb=" N ARG H 70 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE H 42 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ARG H 72 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N MET H 44 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP H 2 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE H 43 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE H 4 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR H 3 " --> pdb=" O ILE H 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 71 removed outlier: 6.347A pdb=" N PHE C 42 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 3 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'D' and resid 70 through 72 removed outlier: 6.764A pdb=" N PHE D 42 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG D 72 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET D 44 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR D 3 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 69 through 71 removed outlier: 8.722A pdb=" N ARG I 70 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE I 42 " --> pdb=" O ARG I 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR I 3 " --> pdb=" O ILE I 157 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL I 159 " --> pdb=" O THR I 3 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL I 5 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'J' and resid 70 through 71 removed outlier: 6.522A pdb=" N PHE J 42 " --> pdb=" O ARG J 70 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE J 4 " --> pdb=" O PHE J 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.713A pdb=" N PHE A 42 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ARG A 72 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N MET A 44 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AB6, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.776A pdb=" N LEU B 6 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 69 through 71 removed outlier: 6.619A pdb=" N PHE K 42 " --> pdb=" O ARG K 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 80 through 82 Processing sheet with id=AC1, first strand: chain 'L' and resid 70 through 71 removed outlier: 6.406A pdb=" N PHE L 4 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR L 3 " --> pdb=" O ILE L 157 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 157 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 2.90 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: 7166 1.34 - 1.46: 7117 1.46 - 1.58: 12373 1.58 - 1.70: 720 1.70 - 1.82: 110 Bond restraints: 27486 Sorted by residual: bond pdb=" N ILE K 32 " pdb=" CA ILE K 32 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.14e-02 7.69e+03 6.59e+00 bond pdb=" N SER K 33 " pdb=" CA SER K 33 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.97e+00 bond pdb=" N PHE K 31 " pdb=" CA PHE K 31 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.76e+00 bond pdb=" N9 G P 30 " pdb=" C4 G P 30 " ideal model delta sigma weight residual 1.375 1.389 -0.014 8.00e-03 1.56e+04 3.27e+00 bond pdb=" N9 G N 20 " pdb=" C4 G N 20 " ideal model delta sigma weight residual 1.375 1.388 -0.013 8.00e-03 1.56e+04 2.78e+00 ... (remaining 27481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 38424 1.98 - 3.96: 426 3.96 - 5.94: 65 5.94 - 7.93: 8 7.93 - 9.91: 2 Bond angle restraints: 38925 Sorted by residual: angle pdb=" C ALA K 115 " pdb=" CA ALA K 115 " pdb=" CB ALA K 115 " ideal model delta sigma weight residual 117.23 110.28 6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" C1' C P 65 " pdb=" N1 C P 65 " pdb=" C2 C P 65 " ideal model delta sigma weight residual 118.80 124.33 -5.53 1.10e+00 8.26e-01 2.53e+01 angle pdb=" CA GLU L 118 " pdb=" CB GLU L 118 " pdb=" CG GLU L 118 " ideal model delta sigma weight residual 114.10 123.77 -9.67 2.00e+00 2.50e-01 2.34e+01 angle pdb=" C1' C P 27 " pdb=" N1 C P 27 " pdb=" C2 C P 27 " ideal model delta sigma weight residual 118.80 123.88 -5.08 1.10e+00 8.26e-01 2.13e+01 angle pdb=" O2 C O 71 " pdb=" C2 C O 71 " pdb=" N3 C O 71 " ideal model delta sigma weight residual 121.90 118.81 3.09 7.00e-01 2.04e+00 1.94e+01 ... (remaining 38920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 15336 33.77 - 67.54: 1662 67.54 - 101.32: 207 101.32 - 135.09: 5 135.09 - 168.86: 5 Dihedral angle restraints: 17215 sinusoidal: 10589 harmonic: 6626 Sorted by residual: dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual -128.00 40.86 -168.86 1 1.70e+01 3.46e-03 6.58e+01 dihedral pdb=" O4' U O 16 " pdb=" C1' U O 16 " pdb=" N1 U O 16 " pdb=" C2 U O 16 " ideal model delta sinusoidal sigma weight residual -160.00 -79.39 -80.61 1 1.50e+01 4.44e-03 3.57e+01 dihedral pdb=" O4' U M 16 " pdb=" C1' U M 16 " pdb=" N1 U M 16 " pdb=" C2 U M 16 " ideal model delta sinusoidal sigma weight residual -160.00 -81.87 -78.13 1 1.50e+01 4.44e-03 3.39e+01 ... (remaining 17212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4391 0.084 - 0.167: 220 0.167 - 0.251: 1 0.251 - 0.335: 0 0.335 - 0.418: 1 Chirality restraints: 4613 Sorted by residual: chirality pdb=" C1' G P 30 " pdb=" O4' G P 30 " pdb=" C2' G P 30 " pdb=" N9 G P 30 " both_signs ideal model delta sigma weight residual False 2.46 2.04 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" P U N 72 " pdb=" OP1 U N 72 " pdb=" OP2 U N 72 " pdb=" O5' U N 72 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3' A M 35 " pdb=" C4' A M 35 " pdb=" O3' A M 35 " pdb=" C2' A M 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 4610 not shown) Planarity restraints: 3638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 13 " 0.065 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO B 14 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G P 30 " -0.038 2.00e-02 2.50e+03 1.74e-02 9.10e+00 pdb=" N9 G P 30 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G P 30 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G P 30 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G P 30 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G P 30 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G P 30 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G P 30 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G P 30 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G P 30 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G P 30 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G P 30 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 60 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" CG ASP K 60 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP K 60 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 60 " -0.015 2.00e-02 2.50e+03 ... (remaining 3635 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 492 2.63 - 3.20: 21830 3.20 - 3.77: 45024 3.77 - 4.33: 59854 4.33 - 4.90: 91014 Nonbonded interactions: 218214 Sorted by model distance: nonbonded pdb=" OD1 ASP F 144 " pdb="MG MG F1001 " model vdw 2.066 2.170 nonbonded pdb=" O3' A T 0 " pdb="MG MG E1002 " model vdw 2.117 2.170 nonbonded pdb=" NH1 ARG L 96 " pdb=" O ALA L 136 " model vdw 2.203 3.120 nonbonded pdb=" O2' G P 2 " pdb=" OP1 G P 3 " model vdw 2.204 3.040 nonbonded pdb=" OG SER E 47 " pdb=" OD2 ASP E 146 " model vdw 2.207 3.040 ... (remaining 218209 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' and (resid 2 through 20 or resid 23 through 189)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'D' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'E' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'F' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'G' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'H' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'I' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'J' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'K' and (resid 2 through 20 or resid 23 through 189)) selection = (chain 'L' and (resid 2 through 20 or resid 23 through 189)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.980 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 0.066 27486 Z= 0.141 Angle : 0.535 9.907 38925 Z= 0.408 Chirality : 0.036 0.418 4613 Planarity : 0.004 0.097 3638 Dihedral : 23.277 168.860 12933 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.50 % Allowed : 32.40 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 2235 helix: 0.20 (0.15), residues: 1298 sheet: -0.93 (0.36), residues: 181 loop : -0.96 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 121 TYR 0.019 0.001 TYR G 50 PHE 0.023 0.001 PHE A 65 TRP 0.015 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (27486) covalent geometry : angle 0.53481 / 0.41 (38925) hydrogen bonds : bond 0.16994 / 11.33 ( 1271) hydrogen bonds : angle 6.03421 / 5.80 ( 3352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 0.561 Fit side-chains REVERT: H 21 GLU cc_start: 0.6416 (tp30) cc_final: 0.5768 (mt-10) REVERT: H 117 GLU cc_start: 0.6092 (pm20) cc_final: 0.5108 (pt0) REVERT: C 132 GLU cc_start: 0.6661 (mp0) cc_final: 0.6388 (mm-30) REVERT: A 25 LEU cc_start: 0.6798 (mm) cc_final: 0.6453 (mm) REVERT: A 55 MET cc_start: 0.5813 (ptt) cc_final: 0.5471 (mtt) REVERT: B 50 TYR cc_start: 0.5214 (m-80) cc_final: 0.4797 (m-80) REVERT: L 94 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7029 (ttt180) outliers start: 10 outliers final: 3 residues processed: 233 average time/residue: 0.1455 time to fit residues: 55.9872 Evaluate side-chains 209 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS B 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.203699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157661 restraints weight = 35642.154| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.40 r_work: 0.3830 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27486 Z= 0.117 Angle : 0.491 9.177 38925 Z= 0.281 Chirality : 0.038 0.458 4613 Planarity : 0.004 0.062 3638 Dihedral : 22.961 170.242 8333 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.55 % Allowed : 30.65 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2235 helix: 0.34 (0.15), residues: 1382 sheet: -0.71 (0.37), residues: 181 loop : -1.32 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 121 TYR 0.029 0.002 TYR G 50 PHE 0.013 0.001 PHE A 31 TRP 0.017 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (27486) covalent geometry : angle 0.49127 / 0.28 (38925) hydrogen bonds : bond 0.05844 / 3.90 ( 1271) hydrogen bonds : angle 4.28911 / 3.86 ( 3352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 0.714 Fit side-chains REVERT: G 125 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6039 (ttp-110) REVERT: G 162 ASP cc_start: 0.7544 (m-30) cc_final: 0.7287 (m-30) REVERT: H 21 GLU cc_start: 0.6683 (tp30) cc_final: 0.5775 (mt-10) REVERT: H 117 GLU cc_start: 0.6173 (pm20) cc_final: 0.5183 (pt0) REVERT: J 163 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7073 (tt0) REVERT: J 183 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7897 (ttt90) REVERT: A 25 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6539 (mm) REVERT: A 55 MET cc_start: 0.6507 (ptt) cc_final: 0.5691 (mtt) REVERT: A 152 TYR cc_start: 0.7481 (t80) cc_final: 0.7186 (t80) REVERT: A 162 ASP cc_start: 0.7088 (t0) cc_final: 0.6799 (t0) REVERT: B 85 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.7083 (m-80) outliers start: 51 outliers final: 29 residues processed: 263 average time/residue: 0.1563 time to fit residues: 66.3780 Evaluate side-chains 238 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 138 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 241 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 40.0000 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 18 HIS K 30 ASN L 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.202203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156915 restraints weight = 35799.778| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.40 r_work: 0.3812 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 27486 Z= 0.112 Angle : 0.476 9.353 38925 Z= 0.269 Chirality : 0.037 0.454 4613 Planarity : 0.004 0.046 3638 Dihedral : 22.838 170.821 8324 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.51 % Allowed : 30.10 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2235 helix: 0.47 (0.15), residues: 1387 sheet: -0.69 (0.37), residues: 181 loop : -1.29 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 131 TYR 0.028 0.002 TYR G 50 PHE 0.015 0.001 PHE A 31 TRP 0.011 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (27486) covalent geometry : angle 0.47642 / 0.27 (38925) hydrogen bonds : bond 0.05150 / 3.41 ( 1271) hydrogen bonds : angle 3.91590 / 3.47 ( 3352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 0.528 Fit side-chains REVERT: E 107 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6412 (m90) REVERT: H 21 GLU cc_start: 0.6571 (tp30) cc_final: 0.5830 (mt-10) REVERT: C 3 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7348 (t) REVERT: C 60 ASP cc_start: 0.6661 (t0) cc_final: 0.6403 (t0) REVERT: C 94 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6759 (tpp80) REVERT: C 131 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6169 (mmt90) REVERT: D 114 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4882 (tt) REVERT: I 170 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7465 (t0) REVERT: J 70 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7241 (mpt180) REVERT: J 163 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7165 (tt0) REVERT: J 183 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8049 (ttt90) REVERT: A 25 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6595 (mm) REVERT: A 55 MET cc_start: 0.6592 (ptt) cc_final: 0.5775 (mtt) REVERT: B 85 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7160 (m-80) outliers start: 70 outliers final: 33 residues processed: 279 average time/residue: 0.1573 time to fit residues: 70.8391 Evaluate side-chains 245 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 217 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.202363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156709 restraints weight = 35539.750| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.39 r_work: 0.3809 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27486 Z= 0.104 Angle : 0.458 9.325 38925 Z= 0.260 Chirality : 0.037 0.454 4613 Planarity : 0.004 0.038 3638 Dihedral : 22.770 171.352 8324 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.10 % Allowed : 30.35 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2235 helix: 0.59 (0.15), residues: 1387 sheet: -0.63 (0.37), residues: 181 loop : -1.26 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 131 TYR 0.025 0.002 TYR G 50 PHE 0.015 0.001 PHE A 31 TRP 0.010 0.001 TRP J 168 HIS 0.005 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (27486) covalent geometry : angle 0.45810 / 0.26 (38925) hydrogen bonds : bond 0.04842 / 3.20 ( 1271) hydrogen bonds : angle 3.76732 / 3.32 ( 3352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 0.689 Fit side-chains REVERT: E 80 MET cc_start: 0.7605 (mmp) cc_final: 0.7386 (mmp) REVERT: E 107 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.6488 (m90) REVERT: G 125 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6310 (ttp-110) REVERT: H 1 MET cc_start: 0.6952 (mmt) cc_final: 0.6519 (mmt) REVERT: H 21 GLU cc_start: 0.6529 (tp30) cc_final: 0.5870 (mt-10) REVERT: C 3 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7436 (t) REVERT: C 60 ASP cc_start: 0.6600 (t0) cc_final: 0.6385 (t0) REVERT: C 70 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6961 (mpp-170) REVERT: I 170 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (t0) REVERT: J 70 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7204 (mpt180) REVERT: J 163 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7322 (tt0) REVERT: A 25 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6632 (mm) REVERT: B 55 MET cc_start: 0.6205 (ptm) cc_final: 0.5873 (ptt) REVERT: B 85 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: L 88 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.5968 (mp0) outliers start: 62 outliers final: 40 residues processed: 269 average time/residue: 0.1688 time to fit residues: 73.5325 Evaluate side-chains 251 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 175 optimal weight: 0.0470 chunk 40 optimal weight: 50.0000 chunk 130 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 220 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS A 41 ASN B 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.199336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153194 restraints weight = 35467.093| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.39 r_work: 0.3761 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27486 Z= 0.145 Angle : 0.511 9.428 38925 Z= 0.285 Chirality : 0.039 0.442 4613 Planarity : 0.004 0.058 3638 Dihedral : 22.748 171.074 8324 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.61 % Allowed : 30.35 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2235 helix: 0.44 (0.15), residues: 1382 sheet: -0.71 (0.37), residues: 181 loop : -1.43 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 121 TYR 0.024 0.002 TYR G 50 PHE 0.016 0.002 PHE A 31 TRP 0.011 0.002 TRP J 168 HIS 0.008 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (27486) covalent geometry : angle 0.51124 / 0.29 (38925) hydrogen bonds : bond 0.05449 / 3.59 ( 1271) hydrogen bonds : angle 3.82340 / 3.38 ( 3352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 210 time to evaluate : 0.711 Fit side-chains REVERT: E 107 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6357 (m90) REVERT: G 125 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6253 (ttp-110) REVERT: H 1 MET cc_start: 0.6902 (mmt) cc_final: 0.6495 (mmt) REVERT: H 21 GLU cc_start: 0.6624 (tp30) cc_final: 0.5851 (mt-10) REVERT: C 3 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7625 (t) REVERT: C 70 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6971 (mpp-170) REVERT: C 131 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5486 (mtp-110) REVERT: C 152 TYR cc_start: 0.8214 (t80) cc_final: 0.7998 (t80) REVERT: I 170 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7463 (t0) REVERT: J 70 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7472 (mpt180) REVERT: J 166 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7309 (mtt90) REVERT: A 25 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6563 (mm) REVERT: A 55 MET cc_start: 0.6760 (ptm) cc_final: 0.5761 (mtt) REVERT: B 55 MET cc_start: 0.6251 (ptm) cc_final: 0.6015 (ptt) REVERT: B 85 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: B 89 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5747 (m-80) REVERT: L 51 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: L 88 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: L 152 TYR cc_start: 0.6927 (t80) cc_final: 0.6602 (t80) outliers start: 92 outliers final: 56 residues processed: 283 average time/residue: 0.1701 time to fit residues: 77.4881 Evaluate side-chains 271 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 43 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 49 optimal weight: 50.0000 chunk 156 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN A 41 ASN B 18 HIS ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.200238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154135 restraints weight = 35185.205| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.37 r_work: 0.3776 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27486 Z= 0.117 Angle : 0.482 9.415 38925 Z= 0.270 Chirality : 0.038 0.438 4613 Planarity : 0.004 0.039 3638 Dihedral : 22.711 171.360 8324 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.76 % Allowed : 30.95 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2235 helix: 0.54 (0.15), residues: 1382 sheet: -0.76 (0.37), residues: 181 loop : -1.38 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 121 TYR 0.023 0.002 TYR G 50 PHE 0.011 0.001 PHE C 85 TRP 0.011 0.001 TRP J 168 HIS 0.004 0.001 HIS J 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (27486) covalent geometry : angle 0.48189 / 0.27 (38925) hydrogen bonds : bond 0.05048 / 3.32 ( 1271) hydrogen bonds : angle 3.74811 / 3.30 ( 3352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 207 time to evaluate : 0.846 Fit side-chains REVERT: E 80 MET cc_start: 0.7655 (mmp) cc_final: 0.7408 (mmp) REVERT: E 107 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6329 (m90) REVERT: G 125 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6215 (ttp-110) REVERT: H 21 GLU cc_start: 0.6504 (tp30) cc_final: 0.5774 (mt-10) REVERT: C 3 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7617 (t) REVERT: C 70 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6935 (mpp-170) REVERT: C 131 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.5424 (mtp-110) REVERT: C 152 TYR cc_start: 0.8223 (t80) cc_final: 0.7970 (t80) REVERT: I 170 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7435 (t0) REVERT: J 166 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7312 (mtt90) REVERT: A 25 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6543 (mm) REVERT: A 55 MET cc_start: 0.6708 (ptm) cc_final: 0.5735 (mtt) REVERT: B 85 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: B 89 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: L 51 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: L 88 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.5800 (mp0) REVERT: L 131 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7489 (ttm110) REVERT: L 152 TYR cc_start: 0.6911 (t80) cc_final: 0.6608 (t80) outliers start: 75 outliers final: 52 residues processed: 268 average time/residue: 0.1608 time to fit residues: 69.6132 Evaluate side-chains 267 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 153 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 166 optimal weight: 0.0370 chunk 222 optimal weight: 0.9990 chunk 120 optimal weight: 0.0570 chunk 75 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.202634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156819 restraints weight = 35261.611| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.38 r_work: 0.3816 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27486 Z= 0.096 Angle : 0.452 9.466 38925 Z= 0.256 Chirality : 0.037 0.434 4613 Planarity : 0.004 0.039 3638 Dihedral : 22.636 172.236 8324 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.41 % Allowed : 31.10 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 2235 helix: 0.77 (0.15), residues: 1382 sheet: -0.72 (0.36), residues: 181 loop : -1.26 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 127 TYR 0.025 0.001 TYR G 50 PHE 0.018 0.001 PHE A 31 TRP 0.013 0.001 TRP H 168 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 (27486) covalent geometry : angle 0.45163 / 0.26 (38925) hydrogen bonds : bond 0.04475 / 2.95 ( 1271) hydrogen bonds : angle 3.62261 / 3.16 ( 3352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.844 Fit side-chains REVERT: E 80 MET cc_start: 0.7631 (mmp) cc_final: 0.7385 (mmp) REVERT: E 107 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6421 (m90) REVERT: G 80 MET cc_start: 0.6341 (mmt) cc_final: 0.5753 (mmt) REVERT: G 125 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6279 (ttp-110) REVERT: H 1 MET cc_start: 0.6834 (mmt) cc_final: 0.6427 (mmt) REVERT: H 21 GLU cc_start: 0.6356 (tp30) cc_final: 0.5715 (mt-10) REVERT: H 117 GLU cc_start: 0.6286 (pm20) cc_final: 0.5032 (pt0) REVERT: C 3 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7530 (t) REVERT: C 70 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6951 (mpp-170) REVERT: C 131 ARG cc_start: 0.6353 (OUTLIER) cc_final: 0.5314 (mtp-110) REVERT: C 152 TYR cc_start: 0.8181 (t80) cc_final: 0.7942 (t80) REVERT: I 170 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7436 (t0) REVERT: J 70 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7035 (mpt180) REVERT: A 25 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6507 (mm) REVERT: A 55 MET cc_start: 0.6535 (ptm) cc_final: 0.5610 (mtt) REVERT: B 85 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: B 89 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5568 (m-80) REVERT: L 51 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: L 88 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: L 152 TYR cc_start: 0.6888 (t80) cc_final: 0.6608 (t80) outliers start: 68 outliers final: 44 residues processed: 266 average time/residue: 0.1628 time to fit residues: 70.6346 Evaluate side-chains 257 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 204 optimal weight: 0.0050 chunk 93 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 172 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN B 18 HIS ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.203131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157438 restraints weight = 35521.837| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.37 r_work: 0.3824 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27486 Z= 0.096 Angle : 0.452 9.477 38925 Z= 0.255 Chirality : 0.037 0.430 4613 Planarity : 0.004 0.079 3638 Dihedral : 22.572 172.589 8324 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.46 % Allowed : 30.95 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 2235 helix: 0.87 (0.15), residues: 1381 sheet: -0.69 (0.36), residues: 181 loop : -1.24 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 131 TYR 0.026 0.001 TYR G 50 PHE 0.008 0.001 PHE C 85 TRP 0.011 0.001 TRP J 168 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (27486) covalent geometry : angle 0.45225 / 0.26 (38925) hydrogen bonds : bond 0.04372 / 2.88 ( 1271) hydrogen bonds : angle 3.55690 / 3.11 ( 3352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 0.812 Fit side-chains REVERT: E 107 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6484 (m90) REVERT: E 114 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6991 (tp) REVERT: G 80 MET cc_start: 0.6272 (mmt) cc_final: 0.5644 (mmt) REVERT: G 125 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6217 (ttp-110) REVERT: H 1 MET cc_start: 0.6814 (mmt) cc_final: 0.6401 (mmt) REVERT: H 51 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: C 3 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7526 (t) REVERT: C 70 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6953 (mpp-170) REVERT: C 131 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6096 (mmt90) REVERT: C 152 TYR cc_start: 0.8155 (t80) cc_final: 0.7909 (t80) REVERT: I 170 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7420 (t0) REVERT: A 25 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6327 (mm) REVERT: A 55 MET cc_start: 0.6489 (ptm) cc_final: 0.5640 (mtt) REVERT: B 85 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: B 89 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: L 51 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: L 88 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: L 152 TYR cc_start: 0.6907 (t80) cc_final: 0.6654 (t80) outliers start: 69 outliers final: 49 residues processed: 259 average time/residue: 0.1594 time to fit residues: 67.5506 Evaluate side-chains 257 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 174 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 47 optimal weight: 50.0000 chunk 234 optimal weight: 0.1980 chunk 19 optimal weight: 40.0000 chunk 20 optimal weight: 40.0000 chunk 199 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS A 41 ASN ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.202360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156438 restraints weight = 35470.315| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.38 r_work: 0.3811 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27486 Z= 0.104 Angle : 0.461 9.492 38925 Z= 0.259 Chirality : 0.037 0.422 4613 Planarity : 0.004 0.041 3638 Dihedral : 22.541 172.494 8324 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.76 % Allowed : 30.80 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 2235 helix: 0.88 (0.15), residues: 1382 sheet: -0.66 (0.36), residues: 181 loop : -1.26 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 131 TYR 0.024 0.001 TYR G 50 PHE 0.019 0.001 PHE A 31 TRP 0.010 0.001 TRP J 168 HIS 0.006 0.001 HIS J 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (27486) covalent geometry : angle 0.46073 / 0.26 (38925) hydrogen bonds : bond 0.04494 / 2.96 ( 1271) hydrogen bonds : angle 3.54623 / 3.10 ( 3352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 195 time to evaluate : 0.847 Fit side-chains REVERT: E 107 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6426 (m90) REVERT: G 125 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6242 (ttp-110) REVERT: H 1 MET cc_start: 0.6801 (mmt) cc_final: 0.6391 (mmt) REVERT: H 21 GLU cc_start: 0.6620 (tp30) cc_final: 0.5726 (mt-10) REVERT: H 51 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: H 117 GLU cc_start: 0.6265 (pm20) cc_final: 0.4882 (pt0) REVERT: C 3 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7544 (t) REVERT: C 70 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6979 (mpp-170) REVERT: C 131 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.6120 (mmt90) REVERT: C 152 TYR cc_start: 0.8158 (t80) cc_final: 0.7946 (t80) REVERT: I 170 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7436 (t0) REVERT: A 25 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6381 (mm) REVERT: A 55 MET cc_start: 0.6492 (ptm) cc_final: 0.5619 (mtt) REVERT: B 85 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: B 89 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5647 (m-80) REVERT: L 51 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: L 88 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.5811 (mp0) REVERT: L 152 TYR cc_start: 0.6901 (t80) cc_final: 0.6672 (t80) outliers start: 75 outliers final: 53 residues processed: 256 average time/residue: 0.1537 time to fit residues: 64.6396 Evaluate side-chains 260 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 84 optimal weight: 0.0970 chunk 71 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 0.0000 chunk 229 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.204109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160385 restraints weight = 35356.458| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.33 r_work: 0.3838 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27486 Z= 0.093 Angle : 0.449 9.496 38925 Z= 0.252 Chirality : 0.036 0.414 4613 Planarity : 0.003 0.039 3638 Dihedral : 22.483 172.823 8324 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.20 % Allowed : 31.00 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 2235 helix: 1.00 (0.15), residues: 1381 sheet: -0.60 (0.36), residues: 181 loop : -1.21 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 127 TYR 0.025 0.001 TYR G 50 PHE 0.009 0.001 PHE D 85 TRP 0.011 0.001 TRP H 168 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (27486) covalent geometry : angle 0.44863 / 0.25 (38925) hydrogen bonds : bond 0.04221 / 2.78 ( 1271) hydrogen bonds : angle 3.49527 / 3.05 ( 3352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.732 Fit side-chains REVERT: E 107 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6567 (m90) REVERT: G 125 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6229 (ttp-110) REVERT: H 1 MET cc_start: 0.6781 (mmt) cc_final: 0.6374 (mmt) REVERT: H 21 GLU cc_start: 0.6562 (tp30) cc_final: 0.5774 (mt-10) REVERT: H 117 GLU cc_start: 0.6308 (pm20) cc_final: 0.4949 (pt0) REVERT: C 3 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7471 (t) REVERT: C 70 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7015 (mpp-170) REVERT: C 131 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5210 (mtp-110) REVERT: C 152 TYR cc_start: 0.8115 (t80) cc_final: 0.7903 (t80) REVERT: A 25 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6412 (mm) REVERT: B 85 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: B 89 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: L 51 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: L 88 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.5738 (mp0) REVERT: L 118 GLU cc_start: 0.5260 (tp30) cc_final: 0.4978 (tp30) REVERT: L 152 TYR cc_start: 0.6965 (t80) cc_final: 0.6713 (t80) outliers start: 64 outliers final: 48 residues processed: 255 average time/residue: 0.1606 time to fit residues: 68.0565 Evaluate side-chains 258 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 40.0000 chunk 116 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 50.0000 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.202495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.157381 restraints weight = 35250.408| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.38 r_work: 0.3816 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27486 Z= 0.107 Angle : 0.463 9.522 38925 Z= 0.259 Chirality : 0.037 0.407 4613 Planarity : 0.004 0.040 3638 Dihedral : 22.452 172.462 8322 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.25 % Allowed : 31.05 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.19), residues: 2235 helix: 0.95 (0.15), residues: 1381 sheet: -0.61 (0.37), residues: 181 loop : -1.27 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 127 TYR 0.024 0.002 TYR G 50 PHE 0.016 0.001 PHE A 31 TRP 0.009 0.001 TRP J 168 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (27486) covalent geometry : angle 0.46279 / 0.26 (38925) hydrogen bonds : bond 0.04503 / 2.97 ( 1271) hydrogen bonds : angle 3.51887 / 3.08 ( 3352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7330.33 seconds wall clock time: 125 minutes 46.77 seconds (7546.77 seconds total)