Starting phenix.real_space_refine on Mon Aug 25 05:42:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kda_37129/08_2025/8kda_37129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kda_37129/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kda_37129/08_2025/8kda_37129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kda_37129/08_2025/8kda_37129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kda_37129/08_2025/8kda_37129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kda_37129/08_2025/8kda_37129.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 360 5.49 5 Mg 5 5.21 5 S 55 5.16 5 C 15292 2.51 5 N 4543 2.21 5 O 5967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26222 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "T" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'rna2p': 11, 'rna3p': 61} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 62} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 10, 'rna3p': 62} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "G" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "H" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "C" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "D" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "I" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "J" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "A" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "B" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1519 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1537 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "L" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1545 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.15, per 1000 atoms: 0.23 Number of scatterers: 26222 At special positions: 0 Unit cell: (140.07, 162.69, 229.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 360 15.00 Mg 5 11.99 O 5967 8.00 N 4543 7.00 C 15292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 921.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.70 Creating SS restraints... Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 23 through 36 removed outlier: 3.511A pdb=" N SER E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.555A pdb=" N GLU E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.783A pdb=" N VAL E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 78 removed outlier: 3.706A pdb=" N GLY E 78 " --> pdb=" O ARG E 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 78' Processing helix chain 'E' and resid 83 through 112 Processing helix chain 'E' and resid 118 through 135 removed outlier: 3.788A pdb=" N VAL E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.617A pdb=" N VAL E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.646A pdb=" N ARG E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 181 through 187 Processing helix chain 'F' and resid 8 through 12 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 23 through 36 removed outlier: 3.863A pdb=" N ILE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 83 through 115 removed outlier: 3.645A pdb=" N PHE F 89 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 135 removed outlier: 3.659A pdb=" N VAL F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.925A pdb=" N VAL F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 removed outlier: 3.998A pdb=" N TRP F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 181 through 189 Processing helix chain 'G' and resid 8 through 11 Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.653A pdb=" N TYR G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS G 18 " --> pdb=" O PRO G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.699A pdb=" N GLU G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.509A pdb=" N LYS G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 118 through 135 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.513A pdb=" N VAL G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 173 removed outlier: 3.514A pdb=" N LYS G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 181 through 189 removed outlier: 3.890A pdb=" N GLU G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 13 removed outlier: 4.406A pdb=" N PHE H 11 " --> pdb=" O ASP H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 23 through 36 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 83 through 112 Processing helix chain 'H' and resid 118 through 136 removed outlier: 3.823A pdb=" N VAL H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.886A pdb=" N VAL H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 170 Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 181 through 187 Processing helix chain 'C' and resid 7 through 13 removed outlier: 4.098A pdb=" N PHE C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.940A pdb=" N GLU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 83 through 112 removed outlier: 3.922A pdb=" N TYR C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.828A pdb=" N VAL C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.929A pdb=" N TRP C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 189 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.323A pdb=" N PHE D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.566A pdb=" N HIS D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 19' Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.604A pdb=" N SER D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.675A pdb=" N LYS D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.510A pdb=" N GLU D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 141 through 155 removed outlier: 3.947A pdb=" N VAL D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.563A pdb=" N TRP D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 181 through 189 Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 13 through 18 Processing helix chain 'I' and resid 23 through 37 removed outlier: 3.889A pdb=" N ILE I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS I 37 " --> pdb=" O SER I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 61 through 68 removed outlier: 3.797A pdb=" N LEU I 67 " --> pdb=" O PRO I 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL I 68 " --> pdb=" O LYS I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 83 through 113 Processing helix chain 'I' and resid 118 through 136 removed outlier: 3.781A pdb=" N VAL I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 155 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.648A pdb=" N TRP I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'J' and resid 7 through 13 removed outlier: 4.545A pdb=" N PHE J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 23 through 37 Processing helix chain 'J' and resid 45 through 53 Processing helix chain 'J' and resid 60 through 69 removed outlier: 4.559A pdb=" N LYS J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 114 Processing helix chain 'J' and resid 119 through 135 Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'J' and resid 163 through 171 Processing helix chain 'J' and resid 182 through 188 Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.695A pdb=" N HIS A 18 " --> pdb=" O PRO A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.857A pdb=" N GLU A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.674A pdb=" N TYR A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 removed outlier: 4.057A pdb=" N LEU A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 110 removed outlier: 3.612A pdb=" N TYR A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.777A pdb=" N VAL A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.361A pdb=" N VAL A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 189 removed outlier: 3.592A pdb=" N LEU A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.746A pdb=" N TYR B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 18 " --> pdb=" O PRO B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.511A pdb=" N GLU B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.558A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.555A pdb=" N GLU B 91 " --> pdb=" O TYR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.831A pdb=" N LYS B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 135 removed outlier: 3.966A pdb=" N GLU B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.717A pdb=" N VAL B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'K' and resid 7 through 11 removed outlier: 3.548A pdb=" N VAL K 10 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 11 " --> pdb=" O THR K 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 7 through 11' Processing helix chain 'K' and resid 23 through 36 removed outlier: 5.213A pdb=" N GLU K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.593A pdb=" N LYS K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 68 removed outlier: 3.781A pdb=" N VAL K 68 " --> pdb=" O LYS K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 4.184A pdb=" N GLU K 91 " --> pdb=" O TYR K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 114 No H-bonds generated for 'chain 'K' and resid 112 through 114' Processing helix chain 'K' and resid 118 through 135 removed outlier: 3.576A pdb=" N VAL K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 155 removed outlier: 3.542A pdb=" N LEU K 148 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 173 removed outlier: 3.773A pdb=" N ARG K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TRP K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 180 No H-bonds generated for 'chain 'K' and resid 178 through 180' Processing helix chain 'K' and resid 181 through 186 Processing helix chain 'L' and resid 13 through 18 Processing helix chain 'L' and resid 23 through 38 Processing helix chain 'L' and resid 45 through 56 removed outlier: 3.724A pdb=" N VAL L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 83 through 114 removed outlier: 3.983A pdb=" N TYR L 87 " --> pdb=" O ALA L 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY L 100 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 106 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS L 107 " --> pdb=" O ILE L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 135 removed outlier: 3.673A pdb=" N ARG L 125 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 155 removed outlier: 4.372A pdb=" N VAL L 145 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 173 removed outlier: 3.755A pdb=" N ASP L 170 " --> pdb=" O ARG L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 180 No H-bonds generated for 'chain 'L' and resid 178 through 180' Processing helix chain 'L' and resid 181 through 188 removed outlier: 3.663A pdb=" N ILE L 185 " --> pdb=" O ASN L 181 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 69 through 71 removed outlier: 8.674A pdb=" N ARG E 70 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE E 42 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR E 3 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL E 159 " --> pdb=" O THR E 3 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL E 5 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'F' and resid 70 through 72 removed outlier: 6.545A pdb=" N THR F 3 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL F 159 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL F 5 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 70 through 71 removed outlier: 8.885A pdb=" N ARG G 70 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE G 42 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP G 2 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE G 43 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE G 4 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR G 3 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL G 159 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL G 5 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 82 Processing sheet with id=AA6, first strand: chain 'H' and resid 70 through 72 removed outlier: 8.576A pdb=" N ARG H 70 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE H 42 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ARG H 72 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N MET H 44 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP H 2 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE H 43 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE H 4 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR H 3 " --> pdb=" O ILE H 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 71 removed outlier: 6.347A pdb=" N PHE C 42 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 3 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'D' and resid 70 through 72 removed outlier: 6.764A pdb=" N PHE D 42 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG D 72 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET D 44 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR D 3 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 69 through 71 removed outlier: 8.722A pdb=" N ARG I 70 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE I 42 " --> pdb=" O ARG I 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR I 3 " --> pdb=" O ILE I 157 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL I 159 " --> pdb=" O THR I 3 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL I 5 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'J' and resid 70 through 71 removed outlier: 6.522A pdb=" N PHE J 42 " --> pdb=" O ARG J 70 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE J 4 " --> pdb=" O PHE J 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.713A pdb=" N PHE A 42 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ARG A 72 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N MET A 44 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AB6, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.776A pdb=" N LEU B 6 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 69 through 71 removed outlier: 6.619A pdb=" N PHE K 42 " --> pdb=" O ARG K 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 80 through 82 Processing sheet with id=AC1, first strand: chain 'L' and resid 70 through 71 removed outlier: 6.406A pdb=" N PHE L 4 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR L 3 " --> pdb=" O ILE L 157 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 157 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.96 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: 3.970 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.440 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.19), residues: 2235 helix: 0.20 (0.15), residues: 1298 sheet: -0.93 (0.36), residues: 181 loop : -0.96 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 121 TYR 0.019 0.001 TYR G 50 PHE 0.023 0.001 PHE A 65 TRP 0.015 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00214 (27486) covalent geometry : angle 0.53461 (38925) hydrogen bonds : bond 0.16994 ( 1271) hydrogen bonds : angle 6.03421 ( 3352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 0.685 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: 0.1561 time to fit residues: 59.4299 Evaluate side-chains 209 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain L residue 37 HIS Chi-restraints excluded: chain L residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4560 r_free = 0.4560 target = 0.203548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157913 restraints weight = 35702.102| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.40 r_work: 0.3819 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1081 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= 0.111 Angle : 0.526 9.411 38925 Z= 0.272 Chirality : 0.037 0.413 4613 Planarity : 0.004 0.064 3638 Dihedral : 22.758 168.447 8333 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.90 % Allowed : 29.84 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 2235 helix: 0.48 (0.15), residues: 1347 sheet: -0.82 (0.37), residues: 181 loop : -0.98 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 127 TYR 0.030 0.002 TYR G 50 PHE 0.015 0.001 PHE A 31 TRP 0.015 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00232 (27486) covalent geometry : angle 0.52634 (38925) hydrogen bonds : bond 0.04655 ( 1271) hydrogen bonds : angle 3.98840 ( 3352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 0.759 Fit side-chains REVERT: G 125 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6198 (ttp-110) REVERT: H 21 GLU cc_start: 0.6613 (tp30) cc_final: 0.5903 (mt-10) REVERT: C 94 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6813 (tpp80) REVERT: C 118 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5519 (mm-30) REVERT: I 170 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7439 (t0) REVERT: J 70 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7091 (mpt180) REVERT: J 163 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7158 (tt0) REVERT: A 25 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6607 (mm) REVERT: A 55 MET cc_start: 0.6568 (ptt) cc_final: 0.5703 (mtt) REVERT: A 116 GLU cc_start: 0.5166 (pm20) cc_final: 0.4957 (tp30) REVERT: A 162 ASP cc_start: 0.7110 (t0) cc_final: 0.6798 (t0) REVERT: B 85 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7158 (m-80) outliers start: 58 outliers final: 29 residues processed: 277 average time/residue: 0.1571 time to fit residues: 69.6294 Evaluate side-chains 245 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 55 MET Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 85 PHE 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 138 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 241 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 chunk 143 optimal weight: 0.4980 chunk 123 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.4576 r_free = 0.4576 target = 0.205134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159519 restraints weight = 35907.547| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.45 r_work: 0.3844 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27486 Z= 0.097 Angle : 0.496 9.547 38925 Z= 0.254 Chirality : 0.036 0.404 4613 Planarity : 0.004 0.050 3638 Dihedral : 22.544 168.720 8324 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.46 % Allowed : 29.29 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.19), residues: 2235 helix: 0.69 (0.15), residues: 1381 sheet: -0.74 (0.36), residues: 181 loop : -1.25 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 131 TYR 0.028 0.001 TYR G 50 PHE 0.016 0.001 PHE A 31 TRP 0.012 0.001 TRP K 77 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00196 (27486) covalent geometry : angle 0.49615 (38925) hydrogen bonds : bond 0.04119 ( 1271) hydrogen bonds : angle 3.67720 ( 3352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 225 time to evaluate : 0.839 Fit side-chains REVERT: E 107 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6509 (m90) REVERT: G 125 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6381 (ttp-110) REVERT: H 117 GLU cc_start: 0.6346 (pm20) cc_final: 0.5265 (pt0) REVERT: C 3 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7394 (t) REVERT: C 70 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6908 (mpp-170) REVERT: C 118 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.5240 (mm-30) REVERT: C 152 TYR cc_start: 0.8068 (t80) cc_final: 0.7787 (t80) REVERT: J 163 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7235 (tt0) REVERT: A 25 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6397 (mm) REVERT: A 106 GLU cc_start: 0.6646 (mm-30) cc_final: 0.5986 (tm-30) REVERT: A 116 GLU cc_start: 0.5319 (pm20) cc_final: 0.5069 (tp30) REVERT: B 85 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: B 89 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.4682 (t80) REVERT: L 51 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: L 152 TYR cc_start: 0.6948 (t80) cc_final: 0.6679 (t80) REVERT: L 184 TYR cc_start: 0.7296 (t80) cc_final: 0.6701 (t80) outliers start: 69 outliers final: 31 residues processed: 282 average time/residue: 0.1504 time to fit residues: 68.9032 Evaluate side-chains 244 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 140 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 118 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 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 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 217 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 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 = 0.4529 r_free = 0.4529 target = 0.200149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154043 restraints weight = 35489.528| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.40 r_work: 0.3772 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1814 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= 0.129 Angle : 0.541 9.501 38925 Z= 0.277 Chirality : 0.038 0.387 4613 Planarity : 0.004 0.045 3638 Dihedral : 22.495 167.594 8324 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.36 % Allowed : 29.04 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2235 helix: 0.55 (0.15), residues: 1381 sheet: -0.80 (0.36), residues: 181 loop : -1.37 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 127 TYR 0.022 0.002 TYR G 50 PHE 0.016 0.001 PHE A 31 TRP 0.010 0.001 TRP K 168 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00287 (27486) covalent geometry : angle 0.54134 (38925) hydrogen bonds : bond 0.04932 ( 1271) hydrogen bonds : angle 3.73035 ( 3352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 216 time to evaluate : 0.761 Fit side-chains REVERT: E 107 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6450 (m90) REVERT: G 125 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6288 (ttp-110) REVERT: H 21 GLU cc_start: 0.6660 (tp30) cc_final: 0.5896 (mt-10) REVERT: C 3 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7581 (t) REVERT: C 70 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7009 (mpp-170) REVERT: C 131 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5468 (mtp-110) REVERT: C 152 TYR cc_start: 0.8138 (t80) cc_final: 0.7896 (t80) REVERT: J 166 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7286 (mpp80) REVERT: A 25 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6444 (mm) REVERT: A 116 GLU cc_start: 0.5268 (pm20) cc_final: 0.4947 (tp30) REVERT: B 55 MET cc_start: 0.6213 (ptm) cc_final: 0.6006 (ptt) REVERT: B 85 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: B 89 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5861 (m-80) REVERT: L 88 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.5883 (mp0) REVERT: L 152 TYR cc_start: 0.6969 (t80) cc_final: 0.6733 (t80) REVERT: L 184 TYR cc_start: 0.7324 (t80) cc_final: 0.6874 (t80) outliers start: 87 outliers final: 47 residues processed: 285 average time/residue: 0.1670 time to fit residues: 76.8165 Evaluate side-chains 259 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain D residue 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 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 119 VAL Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 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 58 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 175 optimal weight: 0.9990 chunk 40 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS C 107 HIS B 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.198459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152427 restraints weight = 35557.975| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.39 r_work: 0.3747 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27486 Z= 0.150 Angle : 0.574 11.268 38925 Z= 0.292 Chirality : 0.039 0.362 4613 Planarity : 0.004 0.042 3638 Dihedral : 22.497 166.520 8324 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.56 % Allowed : 29.79 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.18), residues: 2235 helix: 0.40 (0.15), residues: 1382 sheet: -0.90 (0.37), residues: 181 loop : -1.50 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 131 TYR 0.024 0.002 TYR G 50 PHE 0.014 0.001 PHE C 85 TRP 0.011 0.002 TRP L 168 HIS 0.004 0.001 HIS H 107 Details of bonding type rmsd covalent geometry : bond 0.00343 (27486) covalent geometry : angle 0.57425 (38925) hydrogen bonds : bond 0.05308 ( 1271) hydrogen bonds : angle 3.79960 ( 3352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 209 time to evaluate : 0.821 Fit side-chains REVERT: E 107 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.6127 (m90) REVERT: G 125 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6185 (ttp-110) REVERT: H 51 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: H 86 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7475 (mt) REVERT: C 3 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7832 (t) REVERT: C 70 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7030 (mpp-170) REVERT: C 131 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5519 (mtp-110) REVERT: J 70 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7527 (mpt180) REVERT: A 25 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6443 (mm) REVERT: A 116 GLU cc_start: 0.5424 (pm20) cc_final: 0.5028 (tp30) REVERT: B 85 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: B 89 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5911 (m-80) REVERT: L 51 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: L 88 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: L 152 TYR cc_start: 0.6990 (t80) cc_final: 0.6721 (t80) REVERT: L 184 TYR cc_start: 0.7371 (t80) cc_final: 0.6956 (t80) outliers start: 91 outliers final: 59 residues processed: 283 average time/residue: 0.1523 time to fit residues: 69.7675 Evaluate side-chains 267 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 34 LEU 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 44 MET Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 51 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 128 GLU 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 128 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 51 GLU 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 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 25 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 81 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 147 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 Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 43 optimal weight: 30.0000 chunk 112 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 185 optimal weight: 0.0870 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 156 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS C 188 ASN B 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.201806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156032 restraints weight = 35267.546| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.40 r_work: 0.3802 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27486 Z= 0.102 Angle : 0.511 9.512 38925 Z= 0.260 Chirality : 0.036 0.352 4613 Planarity : 0.004 0.040 3638 Dihedral : 22.350 167.338 8324 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.06 % Allowed : 30.25 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.18), residues: 2235 helix: 0.70 (0.15), residues: 1383 sheet: -0.79 (0.36), residues: 181 loop : -1.37 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 127 TYR 0.027 0.001 TYR G 50 PHE 0.017 0.001 PHE A 31 TRP 0.011 0.001 TRP J 168 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00212 (27486) covalent geometry : angle 0.51140 (38925) hydrogen bonds : bond 0.04273 ( 1271) hydrogen bonds : angle 3.59838 ( 3352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 215 time to evaluate : 0.750 Fit side-chains REVERT: E 107 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6322 (m90) REVERT: H 21 GLU cc_start: 0.6637 (tp30) cc_final: 0.5834 (mt-10) REVERT: H 51 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: H 86 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7105 (mt) REVERT: C 3 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7683 (t) REVERT: C 70 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6988 (mpp-170) REVERT: C 131 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5338 (mtp-110) REVERT: A 25 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6361 (mm) REVERT: A 116 GLU cc_start: 0.5418 (pm20) cc_final: 0.5072 (tp30) REVERT: B 85 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: B 89 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5696 (m-80) REVERT: L 51 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: L 88 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.5807 (mp0) REVERT: L 152 TYR cc_start: 0.6999 (t80) cc_final: 0.6795 (t80) REVERT: L 184 TYR cc_start: 0.7284 (t80) cc_final: 0.6869 (t80) outliers start: 81 outliers final: 50 residues processed: 277 average time/residue: 0.1658 time to fit residues: 75.0906 Evaluate side-chains 261 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 51 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 128 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 I residue 51 GLU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 119 VAL 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 105 GLU 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 182 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 153 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.198200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152107 restraints weight = 35336.898| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.39 r_work: 0.3744 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27486 Z= 0.156 Angle : 0.575 9.536 38925 Z= 0.293 Chirality : 0.039 0.343 4613 Planarity : 0.004 0.042 3638 Dihedral : 22.404 165.920 8324 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.26 % Allowed : 29.69 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2235 helix: 0.42 (0.15), residues: 1390 sheet: -0.86 (0.37), residues: 181 loop : -1.50 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 127 TYR 0.022 0.002 TYR J 17 PHE 0.014 0.002 PHE C 85 TRP 0.011 0.002 TRP L 168 HIS 0.004 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00363 (27486) covalent geometry : angle 0.57516 (38925) hydrogen bonds : bond 0.05357 ( 1271) hydrogen bonds : angle 3.77246 ( 3352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 200 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: E 107 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6327 (m90) REVERT: H 1 MET cc_start: 0.7019 (mmt) cc_final: 0.6600 (mmt) REVERT: H 21 GLU cc_start: 0.6855 (tp30) cc_final: 0.6016 (mt-10) REVERT: H 86 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7540 (mt) REVERT: C 3 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7811 (t) REVERT: C 70 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7056 (mpp-170) REVERT: C 131 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.5411 (mtp-110) REVERT: J 70 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7131 (mpt180) REVERT: A 25 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6429 (mm) REVERT: A 110 GLU cc_start: 0.6666 (tm-30) cc_final: 0.5792 (tt0) REVERT: A 116 GLU cc_start: 0.5459 (pm20) cc_final: 0.5061 (tp30) REVERT: B 85 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: B 89 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: L 80 MET cc_start: 0.7758 (mmp) cc_final: 0.7466 (mmt) REVERT: L 184 TYR cc_start: 0.7380 (t80) cc_final: 0.6988 (t80) outliers start: 85 outliers final: 59 residues processed: 268 average time/residue: 0.1722 time to fit residues: 74.8764 Evaluate side-chains 267 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 199 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 GLU 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 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 93 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 D residue 25 LEU 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 37 HIS Chi-restraints excluded: chain I residue 51 GLU 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 76 LYS Chi-restraints excluded: chain J residue 119 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 93 VAL Chi-restraints excluded: chain A residue 105 GLU 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 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 60 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 HIS Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 144 optimal weight: 0.0270 chunk 204 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.200076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154456 restraints weight = 35529.287| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.34 r_work: 0.3789 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27486 Z= 0.122 Angle : 0.534 9.506 38925 Z= 0.271 Chirality : 0.037 0.321 4613 Planarity : 0.004 0.041 3638 Dihedral : 22.336 166.240 8324 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.16 % Allowed : 29.89 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.18), residues: 2235 helix: 0.59 (0.15), residues: 1383 sheet: -0.80 (0.37), residues: 181 loop : -1.46 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 127 TYR 0.024 0.002 TYR G 50 PHE 0.017 0.001 PHE A 31 TRP 0.010 0.001 TRP H 168 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00271 (27486) covalent geometry : angle 0.53372 (38925) hydrogen bonds : bond 0.04720 ( 1271) hydrogen bonds : angle 3.65922 ( 3352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 203 time to evaluate : 0.898 Fit side-chains REVERT: E 107 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6201 (m90) REVERT: G 125 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6153 (ttp-110) REVERT: H 1 MET cc_start: 0.6961 (mmt) cc_final: 0.6527 (mmt) REVERT: H 21 GLU cc_start: 0.6809 (tp30) cc_final: 0.6040 (mt-10) REVERT: H 51 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: H 86 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7266 (mt) REVERT: C 3 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7768 (t) REVERT: C 70 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6997 (mpp-170) REVERT: C 131 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5427 (mtp-110) REVERT: D 121 ARG cc_start: 0.7153 (mtt-85) cc_final: 0.6722 (mmt180) REVERT: J 70 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6732 (mpt180) REVERT: A 25 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6430 (mm) REVERT: A 110 GLU cc_start: 0.6584 (tm-30) cc_final: 0.5588 (tt0) REVERT: A 116 GLU cc_start: 0.5491 (pm20) cc_final: 0.5094 (tp30) REVERT: B 85 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: B 89 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.5859 (m-80) REVERT: L 51 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: L 80 MET cc_start: 0.7708 (mmp) cc_final: 0.7413 (mmt) REVERT: L 88 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.5728 (mp0) REVERT: L 184 TYR cc_start: 0.7347 (t80) cc_final: 0.6965 (t80) outliers start: 83 outliers final: 63 residues processed: 268 average time/residue: 0.1772 time to fit residues: 76.8509 Evaluate side-chains 275 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 199 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 44 MET Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 51 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 68 VAL Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 LEU 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 D residue 25 LEU 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 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 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 105 GLU 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 182 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain K residue 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 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 177 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 174 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 234 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 107 HIS G 188 ASN B 18 HIS B 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.194021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.148697 restraints weight = 35691.687| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.46 r_work: 0.3687 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 27486 Z= 0.294 Angle : 0.745 10.133 38925 Z= 0.380 Chirality : 0.046 0.306 4613 Planarity : 0.005 0.055 3638 Dihedral : 22.655 163.288 8324 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.81 % Allowed : 29.59 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.18), residues: 2235 helix: -0.30 (0.14), residues: 1403 sheet: -1.00 (0.38), residues: 181 loop : -1.89 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 131 TYR 0.027 0.003 TYR K 87 PHE 0.021 0.003 PHE C 85 TRP 0.015 0.003 TRP G 77 HIS 0.009 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00705 (27486) covalent geometry : angle 0.74512 (38925) hydrogen bonds : bond 0.07244 ( 1271) hydrogen bonds : angle 4.22635 ( 3352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 207 time to evaluate : 0.878 Fit side-chains REVERT: E 107 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6033 (m90) REVERT: G 125 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6033 (ttp-110) REVERT: H 86 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7747 (mt) REVERT: C 70 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6897 (mpp-170) REVERT: J 70 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7273 (mpt180) REVERT: A 25 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6514 (mm) REVERT: A 110 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6210 (tt0) REVERT: A 116 GLU cc_start: 0.5478 (pm20) cc_final: 0.5080 (tp30) REVERT: B 89 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: L 88 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.5808 (mp0) outliers start: 96 outliers final: 71 residues processed: 291 average time/residue: 0.1881 time to fit residues: 87.1368 Evaluate side-chains 272 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 125 ARG 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 44 MET Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 86 LEU 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 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 93 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 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 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 37 HIS 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 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 25 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 107 HIS 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 177 ILE 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 84 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.199391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153718 restraints weight = 35208.595| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.39 r_work: 0.3768 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2609 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= 0.119 Angle : 0.554 9.812 38925 Z= 0.283 Chirality : 0.038 0.293 4613 Planarity : 0.004 0.043 3638 Dihedral : 22.402 166.798 8324 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.36 % Allowed : 31.30 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.18), residues: 2235 helix: 0.33 (0.15), residues: 1390 sheet: -1.00 (0.37), residues: 181 loop : -1.62 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 131 TYR 0.025 0.002 TYR G 50 PHE 0.019 0.001 PHE A 31 TRP 0.014 0.002 TRP H 168 HIS 0.026 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00254 (27486) covalent geometry : angle 0.55443 (38925) hydrogen bonds : bond 0.04793 ( 1271) hydrogen bonds : angle 3.77878 ( 3352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: G 125 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6282 (ttp-110) REVERT: H 1 MET cc_start: 0.7112 (mmt) cc_final: 0.6682 (mmt) REVERT: H 21 GLU cc_start: 0.6806 (tp30) cc_final: 0.6024 (mt-10) REVERT: H 86 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7271 (mt) REVERT: C 3 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7850 (t) REVERT: C 131 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5447 (mtp-110) REVERT: C 189 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.5818 (mp) REVERT: D 121 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.6832 (mmt180) REVERT: A 25 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6620 (mm) REVERT: A 31 PHE cc_start: 0.7707 (t80) cc_final: 0.7417 (t80) REVERT: A 55 MET cc_start: 0.6325 (ptt) cc_final: 0.5738 (mtt) REVERT: A 110 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5612 (tt0) REVERT: A 116 GLU cc_start: 0.5534 (pm20) cc_final: 0.5116 (tp30) REVERT: B 85 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: B 89 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5797 (m-80) REVERT: L 152 TYR cc_start: 0.7053 (t80) cc_final: 0.6770 (t80) outliers start: 67 outliers final: 53 residues processed: 249 average time/residue: 0.1688 time to fit residues: 68.6339 Evaluate side-chains 253 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 44 MET 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 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 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 58 LEU 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 I residue 19 GLN Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 51 GLU 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 76 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain B residue 25 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 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 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 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.196129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149602 restraints weight = 35242.153| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.30 r_work: 0.3731 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27486 Z= 0.195 Angle : 0.635 10.048 38925 Z= 0.324 Chirality : 0.041 0.284 4613 Planarity : 0.004 0.048 3638 Dihedral : 22.494 165.227 8324 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.76 % Allowed : 30.55 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.18), residues: 2235 helix: 0.07 (0.14), residues: 1403 sheet: -1.05 (0.38), residues: 181 loop : -1.76 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 127 TYR 0.024 0.002 TYR J 17 PHE 0.017 0.002 PHE A 31 TRP 0.013 0.002 TRP L 168 HIS 0.005 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00458 (27486) covalent geometry : angle 0.63534 (38925) hydrogen bonds : bond 0.05938 ( 1271) hydrogen bonds : angle 3.95867 ( 3352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7501.32 seconds wall clock time: 128 minutes 51.65 seconds (7731.65 seconds total)