Starting phenix.real_space_refine on Sat May 24 15:17:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kda_37129/05_2025/8kda_37129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kda_37129/05_2025/8kda_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_37129/05_2025/8kda_37129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kda_37129/05_2025/8kda_37129.map" model { file = "/net/cci-nas-00/data/ceres_data/8kda_37129/05_2025/8kda_37129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kda_37129/05_2025/8kda_37129.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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:plan2': 1, ' A%5*END:plan': 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:plan2': 1, ' A%5*END:plan': 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:plan2': 1, ' A%5*END:plan': 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:plan2': 1, ' A%5*END:plan': 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:plan2': 1, ' A%5*END:plan': 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: 15.30, per 1000 atoms: 0.58 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: 6.29 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 9.96 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: 8.12 Time building geometry restraints manager: 7.37 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=" CA SER K 33 " pdb=" CB SER K 33 " ideal model delta sigma weight residual 1.530 1.507 0.023 1.57e-02 4.06e+03 2.17e+00 bond pdb=" CB GLU L 118 " pdb=" CG GLU L 118 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+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=" 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=" N GLU F 163 " pdb=" CA GLU F 163 " pdb=" C GLU F 163 " ideal model delta sigma weight residual 114.04 108.99 5.05 1.24e+00 6.50e-01 1.66e+01 angle pdb=" C3' C N 71 " pdb=" O3' C N 71 " pdb=" P U N 72 " ideal model delta sigma weight residual 120.20 126.18 -5.98 1.50e+00 4.44e-01 1.59e+01 angle pdb=" N LEU A 134 " pdb=" CA LEU A 134 " pdb=" C LEU A 134 " ideal model delta sigma weight residual 114.31 109.51 4.80 1.29e+00 6.01e-01 1.39e+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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 60.150 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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= 0.112 Angle : 0.535 9.907 38925 Z= 0.286 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 PHE 0.023 0.001 PHE A 65 TYR 0.019 0.001 TYR G 50 ARG 0.007 0.000 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.16994 ( 1271) hydrogen bonds : angle 6.03421 ( 3352) covalent geometry : bond 0.00214 (27486) covalent geometry : angle 0.53461 (38925) *********************** 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 : 2.373 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: 0.3411 time to fit residues: 129.9982 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 : 2.469 ------------------------------------------------------------------------------- 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 211 optimal weight: 3.9990 chunk 190 optimal weight: 0.0030 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 227 optimal weight: 0.9980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4542 r_free = 0.4542 target = 0.201468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156092 restraints weight = 35381.845| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.36 r_work: 0.3798 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1169 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= 0.124 Angle : 0.543 9.336 38925 Z= 0.281 Chirality : 0.038 0.410 4613 Planarity : 0.004 0.064 3638 Dihedral : 22.775 168.231 8333 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 30.30 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 2235 helix: 0.38 (0.15), residues: 1351 sheet: -0.85 (0.37), residues: 181 loop : -1.00 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 PHE 0.015 0.001 PHE A 31 TYR 0.030 0.002 TYR G 50 ARG 0.006 0.000 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 1271) hydrogen bonds : angle 4.00061 ( 3352) covalent geometry : bond 0.00264 (27486) covalent geometry : angle 0.54320 (38925) *********************** 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 288 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 2.145 Fit side-chains REVERT: G 125 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6194 (ttp-110) REVERT: H 21 GLU cc_start: 0.6637 (tp30) cc_final: 0.5927 (mt-10) REVERT: C 94 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6811 (tpp80) REVERT: C 118 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5519 (mm-30) REVERT: I 170 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7429 (t0) REVERT: J 70 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7362 (mpt180) REVERT: A 25 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6579 (mm) REVERT: A 116 GLU cc_start: 0.5320 (pm20) cc_final: 0.5025 (tp30) outliers start: 60 outliers final: 32 residues processed: 274 average time/residue: 0.3450 time to fit residues: 150.8630 Evaluate side-chains 244 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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 F residue 9 SER 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 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 C residue 94 ARG Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 148 LEU 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 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain K residue 87 TYR 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 107 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 233 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 190 optimal weight: 0.0270 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN 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 = 0.4517 r_free = 0.4517 target = 0.198994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153602 restraints weight = 35412.905| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.32 r_work: 0.3774 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27486 Z= 0.142 Angle : 0.559 9.514 38925 Z= 0.288 Chirality : 0.039 0.393 4613 Planarity : 0.004 0.063 3638 Dihedral : 22.690 167.409 8324 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.51 % Allowed : 29.24 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2235 helix: 0.32 (0.15), residues: 1382 sheet: -0.85 (0.37), residues: 181 loop : -1.43 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 168 HIS 0.005 0.001 HIS H 107 PHE 0.015 0.001 PHE A 31 TYR 0.025 0.002 TYR G 50 ARG 0.008 0.000 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.05287 ( 1271) hydrogen bonds : angle 3.90982 ( 3352) covalent geometry : bond 0.00320 (27486) covalent geometry : angle 0.55919 (38925) *********************** 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 307 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 2.230 Fit side-chains REVERT: E 25 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7893 (mm) REVERT: E 107 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.6257 (m90) REVERT: F 134 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7737 (mp) REVERT: G 125 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6213 (ttp-110) REVERT: C 3 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7619 (t) REVERT: C 60 ASP cc_start: 0.6906 (t0) cc_final: 0.6678 (t0) REVERT: C 70 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6910 (mpp-170) REVERT: C 131 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5511 (mtp-110) REVERT: C 152 TYR cc_start: 0.8159 (t80) cc_final: 0.7918 (t80) REVERT: J 44 MET cc_start: 0.7111 (tpp) cc_final: 0.6541 (ttp) REVERT: A 25 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6499 (mm) REVERT: A 55 MET cc_start: 0.6583 (ptm) cc_final: 0.5753 (mtt) REVERT: A 116 GLU cc_start: 0.5456 (pm20) cc_final: 0.5068 (tp30) REVERT: A 162 ASP cc_start: 0.6976 (t0) cc_final: 0.6774 (t0) REVERT: B 85 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: B 89 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5728 (m-80) REVERT: L 88 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.5792 (mp0) REVERT: L 152 TYR cc_start: 0.6883 (t80) cc_final: 0.6581 (t80) outliers start: 90 outliers final: 49 residues processed: 290 average time/residue: 0.3496 time to fit residues: 162.6141 Evaluate side-chains 263 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 LEU 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 134 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 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 47 SER Chi-restraints excluded: chain H residue 86 LEU 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 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 25 LEU Chi-restraints excluded: chain D residue 58 LEU 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 J residue 34 LEU Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 148 LEU 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 103 ILE Chi-restraints excluded: chain A residue 154 LEU 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 184 TYR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 37 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 15 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 201 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 HIS 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 = 0.4534 r_free = 0.4534 target = 0.200778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.155438 restraints weight = 35698.963| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.29 r_work: 0.3802 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1786 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= 0.115 Angle : 0.522 9.500 38925 Z= 0.267 Chirality : 0.037 0.384 4613 Planarity : 0.004 0.045 3638 Dihedral : 22.564 167.599 8324 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.41 % Allowed : 29.29 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2235 helix: 0.49 (0.15), residues: 1382 sheet: -0.87 (0.36), residues: 181 loop : -1.40 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 168 HIS 0.006 0.001 HIS H 107 PHE 0.011 0.001 PHE C 85 TYR 0.027 0.002 TYR G 50 ARG 0.007 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 1271) hydrogen bonds : angle 3.71557 ( 3352) covalent geometry : bond 0.00249 (27486) covalent geometry : angle 0.52238 (38925) *********************** 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 303 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 215 time to evaluate : 2.188 Fit side-chains REVERT: E 107 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6239 (m90) REVERT: G 80 MET cc_start: 0.6255 (mmt) cc_final: 0.5571 (mmt) REVERT: G 125 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6119 (ttp-110) REVERT: H 21 GLU cc_start: 0.6625 (tp30) cc_final: 0.5831 (mt-10) REVERT: C 3 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7614 (t) REVERT: C 60 ASP cc_start: 0.6672 (t0) cc_final: 0.6442 (t0) REVERT: C 70 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6969 (mpp-170) REVERT: C 118 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.5110 (mm-30) REVERT: C 131 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.5401 (mtp-110) REVERT: C 152 TYR cc_start: 0.8143 (t80) cc_final: 0.7897 (t80) REVERT: J 44 MET cc_start: 0.7074 (tpp) cc_final: 0.6738 (ttt) REVERT: A 25 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6500 (mm) REVERT: A 105 GLU cc_start: 0.6336 (tt0) cc_final: 0.6066 (mt-10) REVERT: A 116 GLU cc_start: 0.5482 (pm20) cc_final: 0.5103 (tp30) REVERT: B 85 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: B 89 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: L 51 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: L 88 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: L 152 TYR cc_start: 0.6891 (t80) cc_final: 0.6619 (t80) outliers start: 88 outliers final: 51 residues processed: 281 average time/residue: 0.3398 time to fit residues: 153.7212 Evaluate side-chains 264 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 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 155 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 118 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 25 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 J residue 36 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 148 LEU 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 103 ILE Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 124 ASN 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 155 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 30 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 188 ASN C 18 HIS I 37 HIS A 37 HIS A 41 ASN B 18 HIS ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.195345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149756 restraints weight = 35785.928| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.37 r_work: 0.3713 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27486 Z= 0.231 Angle : 0.671 9.693 38925 Z= 0.344 Chirality : 0.043 0.356 4613 Planarity : 0.005 0.055 3638 Dihedral : 22.744 165.120 8324 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.66 % Allowed : 29.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2235 helix: -0.11 (0.14), residues: 1397 sheet: -0.99 (0.37), residues: 181 loop : -1.71 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 168 HIS 0.006 0.001 HIS A 37 PHE 0.018 0.002 PHE C 85 TYR 0.024 0.003 TYR J 17 ARG 0.009 0.001 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.06619 ( 1271) hydrogen bonds : angle 4.12318 ( 3352) covalent geometry : bond 0.00547 (27486) covalent geometry : angle 0.67089 (38925) *********************** 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 318 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 205 time to evaluate : 2.260 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6005 (m90) REVERT: C 70 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6993 (mpp-170) REVERT: C 131 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5543 (mtp-110) REVERT: C 189 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6506 (mp) REVERT: J 44 MET cc_start: 0.7242 (tpp) cc_final: 0.6945 (ttt) REVERT: J 127 ARG cc_start: 0.6964 (mmt-90) cc_final: 0.6759 (mpt180) REVERT: A 25 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6540 (mm) REVERT: A 116 GLU cc_start: 0.5503 (pm20) cc_final: 0.5112 (tp30) REVERT: B 85 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: B 89 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6025 (m-80) outliers start: 113 outliers final: 72 residues processed: 298 average time/residue: 0.3472 time to fit residues: 165.2238 Evaluate side-chains 276 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 2.345 ------------------------------------------------------------------------------- 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 162 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 139 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 84 GLU Chi-restraints excluded: chain H residue 86 LEU 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 155 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 119 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 36 SER 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 147 VAL Chi-restraints excluded: chain J residue 148 LEU 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 107 HIS Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 154 LEU 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 140 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 189 LEU 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 57 SER 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 64 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.197990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152557 restraints weight = 35471.186| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.37 r_work: 0.3750 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27486 Z= 0.141 Angle : 0.568 9.504 38925 Z= 0.290 Chirality : 0.039 0.350 4613 Planarity : 0.004 0.043 3638 Dihedral : 22.605 166.943 8324 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.91 % Allowed : 30.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2235 helix: 0.17 (0.14), residues: 1389 sheet: -1.03 (0.37), residues: 181 loop : -1.66 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 168 HIS 0.006 0.001 HIS C 18 PHE 0.013 0.001 PHE C 85 TYR 0.025 0.002 TYR G 50 ARG 0.007 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 1271) hydrogen bonds : angle 3.85874 ( 3352) covalent geometry : bond 0.00317 (27486) covalent geometry : angle 0.56765 (38925) *********************** 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 301 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 203 time to evaluate : 2.254 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6002 (m90) REVERT: H 1 MET cc_start: 0.6962 (mmt) cc_final: 0.6559 (mmt) REVERT: H 21 GLU cc_start: 0.6779 (tp30) cc_final: 0.5859 (mt-10) REVERT: C 3 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7844 (t) REVERT: C 70 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6993 (mpp-170) REVERT: C 131 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5422 (mtp-110) REVERT: C 189 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6145 (mp) REVERT: J 44 MET cc_start: 0.7176 (tpp) cc_final: 0.6925 (ttt) REVERT: J 75 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8020 (mtm-85) REVERT: A 25 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6546 (mm) REVERT: A 31 PHE cc_start: 0.7568 (t80) cc_final: 0.7340 (t80) REVERT: A 116 GLU cc_start: 0.5548 (pm20) cc_final: 0.5128 (tp30) REVERT: B 85 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: B 89 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5883 (m-80) outliers start: 98 outliers final: 69 residues processed: 286 average time/residue: 0.3413 time to fit residues: 156.8833 Evaluate side-chains 277 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 199 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 93 VAL 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 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain H residue 47 SER 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 155 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 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 155 ASP 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 60 ASP 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 124 ASN 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 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 57 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 49 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 172 optimal weight: 0.0670 chunk 169 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4535 r_free = 0.4535 target = 0.201092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.155459 restraints weight = 35533.098| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.37 r_work: 0.3795 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2245 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= 0.106 Angle : 0.517 9.503 38925 Z= 0.265 Chirality : 0.037 0.345 4613 Planarity : 0.004 0.042 3638 Dihedral : 22.415 167.786 8324 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.16 % Allowed : 30.85 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2235 helix: 0.58 (0.15), residues: 1383 sheet: -0.91 (0.36), residues: 181 loop : -1.52 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 168 HIS 0.006 0.001 HIS F 107 PHE 0.010 0.001 PHE C 85 TYR 0.027 0.001 TYR G 50 ARG 0.011 0.000 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 1271) hydrogen bonds : angle 3.62508 ( 3352) covalent geometry : bond 0.00220 (27486) covalent geometry : angle 0.51747 (38925) *********************** 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 304 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 221 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6175 (m90) REVERT: G 125 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6292 (ttp-110) REVERT: H 1 MET cc_start: 0.6944 (mmt) cc_final: 0.6535 (mmt) REVERT: H 21 GLU cc_start: 0.6810 (tp30) cc_final: 0.5994 (mt-10) REVERT: H 51 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: C 3 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7683 (t) REVERT: C 60 ASP cc_start: 0.6816 (t0) cc_final: 0.6594 (t0) REVERT: C 70 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6955 (mpp-170) REVERT: C 131 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5354 (mtp-110) REVERT: J 70 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6917 (mpt180) REVERT: A 25 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6450 (mm) REVERT: A 116 GLU cc_start: 0.5397 (pm20) cc_final: 0.5004 (tp30) REVERT: B 85 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: B 89 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.5653 (m-80) REVERT: L 51 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7229 (tp30) outliers start: 83 outliers final: 59 residues processed: 290 average time/residue: 0.4221 time to fit residues: 197.7857 Evaluate side-chains 268 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 198 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain F residue 93 VAL 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 G residue 188 ASN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 51 GLU 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 155 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 128 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain J residue 36 SER 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 75 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 VAL 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 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 124 ASN 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 19 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 210 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.199306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154180 restraints weight = 35446.557| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.42 r_work: 0.3758 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27486 Z= 0.128 Angle : 0.547 9.525 38925 Z= 0.280 Chirality : 0.038 0.332 4613 Planarity : 0.004 0.042 3638 Dihedral : 22.403 167.029 8324 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.56 % Allowed : 30.60 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2235 helix: 0.53 (0.15), residues: 1385 sheet: -0.97 (0.36), residues: 181 loop : -1.57 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 168 HIS 0.004 0.001 HIS F 107 PHE 0.028 0.001 PHE A 31 TYR 0.024 0.002 TYR G 50 ARG 0.010 0.000 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 1271) hydrogen bonds : angle 3.68139 ( 3352) covalent geometry : bond 0.00287 (27486) covalent geometry : angle 0.54692 (38925) *********************** 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 288 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 197 time to evaluate : 2.231 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6343 (m90) REVERT: G 80 MET cc_start: 0.6892 (mmt) cc_final: 0.6362 (mmt) REVERT: H 1 MET cc_start: 0.6977 (mmt) cc_final: 0.6586 (mmt) REVERT: H 21 GLU cc_start: 0.6861 (tp30) cc_final: 0.6136 (mt-10) REVERT: C 3 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7658 (t) REVERT: C 70 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7046 (mpp-170) REVERT: C 131 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.5468 (mtp-110) REVERT: D 29 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: D 121 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.6935 (mmt180) REVERT: A 25 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6629 (mm) REVERT: A 116 GLU cc_start: 0.5341 (pm20) cc_final: 0.4942 (tp30) REVERT: B 85 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 89 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: L 152 TYR cc_start: 0.7155 (t80) cc_final: 0.6946 (t80) outliers start: 91 outliers final: 70 residues processed: 273 average time/residue: 0.3388 time to fit residues: 149.7187 Evaluate side-chains 273 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 2.145 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain F residue 93 VAL 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 58 LEU 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 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 155 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 108 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 GLU 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 12 THR Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 36 SER 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 75 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 148 LEU 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 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 124 ASN 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 19 GLN 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 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 47 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 212 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4508 r_free = 0.4508 target = 0.198387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152328 restraints weight = 35540.142| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.37 r_work: 0.3749 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27486 Z= 0.140 Angle : 0.563 9.532 38925 Z= 0.288 Chirality : 0.038 0.306 4613 Planarity : 0.004 0.042 3638 Dihedral : 22.399 166.252 8324 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.66 % Allowed : 30.60 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2235 helix: 0.44 (0.15), residues: 1391 sheet: -0.98 (0.37), residues: 181 loop : -1.59 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 168 HIS 0.004 0.001 HIS F 107 PHE 0.026 0.001 PHE A 31 TYR 0.024 0.002 TYR C 17 ARG 0.013 0.000 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 1271) hydrogen bonds : angle 3.74309 ( 3352) covalent geometry : bond 0.00317 (27486) covalent geometry : angle 0.56264 (38925) *********************** 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 294 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 201 time to evaluate : 2.446 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6244 (m90) REVERT: G 80 MET cc_start: 0.6775 (mmt) cc_final: 0.6127 (mmt) REVERT: G 125 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6138 (ttp-110) REVERT: H 1 MET cc_start: 0.6972 (mmt) cc_final: 0.6594 (mmt) REVERT: H 21 GLU cc_start: 0.6760 (tp30) cc_final: 0.6010 (mt-10) REVERT: C 3 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7811 (t) REVERT: C 70 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7045 (mpp-170) REVERT: C 131 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.5423 (mtp-110) REVERT: D 29 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: D 121 ARG cc_start: 0.7345 (mtt-85) cc_final: 0.6909 (mmt180) REVERT: A 25 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6600 (mm) REVERT: A 55 MET cc_start: 0.6530 (ptm) cc_final: 0.5683 (mtt) REVERT: A 116 GLU cc_start: 0.5368 (pm20) cc_final: 0.4965 (tp30) REVERT: B 85 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: B 89 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: L 41 ASN cc_start: 0.7389 (t0) cc_final: 0.6912 (m-40) REVERT: L 152 TYR cc_start: 0.6840 (t80) cc_final: 0.6459 (t80) outliers start: 93 outliers final: 77 residues processed: 280 average time/residue: 0.3604 time to fit residues: 163.2394 Evaluate side-chains 279 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 193 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 153 GLU 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 47 SER 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 155 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 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 93 VAL 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 51 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 148 LEU 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 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 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 19 GLN 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 57 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 43 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 143 optimal weight: 0.0070 chunk 173 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.200748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155890 restraints weight = 35382.679| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.43 r_work: 0.3789 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27486 Z= 0.111 Angle : 0.529 9.515 38925 Z= 0.270 Chirality : 0.037 0.288 4613 Planarity : 0.004 0.042 3638 Dihedral : 22.292 166.798 8324 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.41 % Allowed : 31.05 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2235 helix: 0.68 (0.15), residues: 1384 sheet: -0.93 (0.37), residues: 181 loop : -1.47 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 168 HIS 0.005 0.001 HIS F 107 PHE 0.025 0.001 PHE A 31 TYR 0.026 0.002 TYR G 50 ARG 0.009 0.000 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 1271) hydrogen bonds : angle 3.60681 ( 3352) covalent geometry : bond 0.00239 (27486) covalent geometry : angle 0.52871 (38925) ********************** 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 287 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 199 time to evaluate : 2.308 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6309 (m90) REVERT: H 1 MET cc_start: 0.6961 (mmt) cc_final: 0.6563 (mmt) REVERT: H 21 GLU cc_start: 0.6781 (tp30) cc_final: 0.6142 (mt-10) REVERT: C 3 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7686 (t) REVERT: C 70 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7023 (mpp-170) REVERT: C 131 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5402 (mtp-110) REVERT: D 29 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: D 121 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.6825 (mmt180) REVERT: A 25 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6471 (mm) REVERT: A 55 MET cc_start: 0.6635 (ptm) cc_final: 0.5717 (mtt) REVERT: A 116 GLU cc_start: 0.5361 (pm20) cc_final: 0.4971 (tp30) REVERT: B 85 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: B 89 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.5725 (m-80) REVERT: L 41 ASN cc_start: 0.7425 (t0) cc_final: 0.7048 (m-40) REVERT: L 125 ARG cc_start: 0.6032 (ttp-170) cc_final: 0.5241 (mtm110) REVERT: L 152 TYR cc_start: 0.6985 (t80) cc_final: 0.6610 (t80) outliers start: 88 outliers final: 73 residues processed: 275 average time/residue: 0.3406 time to fit residues: 151.0185 Evaluate side-chains 275 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 194 time to evaluate : 2.162 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 153 GLU 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 58 LEU 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 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 155 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 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 93 VAL 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 J residue 34 LEU Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 148 LEU 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 81 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 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 19 GLN 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 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 134 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 0.0670 chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 189 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.201022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155762 restraints weight = 35381.861| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.39 r_work: 0.3791 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27486 Z= 0.109 Angle : 0.525 9.507 38925 Z= 0.268 Chirality : 0.036 0.268 4613 Planarity : 0.004 0.041 3638 Dihedral : 22.261 166.342 8324 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.21 % Allowed : 31.20 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2235 helix: 0.76 (0.15), residues: 1385 sheet: -0.87 (0.36), residues: 181 loop : -1.42 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 168 HIS 0.004 0.001 HIS F 107 PHE 0.027 0.001 PHE A 31 TYR 0.024 0.002 TYR G 50 ARG 0.009 0.000 ARG L 131 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 1271) hydrogen bonds : angle 3.57812 ( 3352) covalent geometry : bond 0.00233 (27486) covalent geometry : angle 0.52549 (38925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15094.11 seconds wall clock time: 260 minutes 49.67 seconds (15649.67 seconds total)