Starting phenix.real_space_refine on Fri Jun 20 04:19:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6he7_0211/06_2025/6he7_0211.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he7_0211/06_2025/6he7_0211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6he7_0211/06_2025/6he7_0211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he7_0211/06_2025/6he7_0211.map" model { file = "/net/cci-nas-00/data/ceres_data/6he7_0211/06_2025/6he7_0211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he7_0211/06_2025/6he7_0211.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 15113 2.51 5 N 3990 2.21 5 O 4634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 369 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23821 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "C" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "D" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "E" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "F" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "G" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "1" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 15.49, per 1000 atoms: 0.65 Number of scatterers: 23821 At special positions: 0 Unit cell: (134, 134, 104.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 4634 8.00 N 3990 7.00 C 15113 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: 5.68 Conformation dependent library (CDL) restraints added in 3.0 seconds 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 30 sheets defined 43.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.745A pdb=" N PHE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 4.041A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 Processing helix chain 'A' and resid 225 through 244 Proline residue: A 231 - end of helix removed outlier: 3.775A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.535A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.585A pdb=" N ILE B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 225 through 245 removed outlier: 3.963A pdb=" N LYS B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.514A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 81 through 104 removed outlier: 3.678A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.568A pdb=" N TYR C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.976A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 225 through 244 Proline residue: C 231 - end of helix removed outlier: 3.537A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.627A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 244 removed outlier: 4.004A pdb=" N LYS D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) Proline residue: D 231 - end of helix removed outlier: 3.659A pdb=" N ARG D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.691A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.761A pdb=" N ALA E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.563A pdb=" N SER E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 244 Proline residue: E 231 - end of helix removed outlier: 3.668A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 81 through 104 removed outlier: 3.727A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.544A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.688A pdb=" N LYS F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 225 through 243 Proline residue: F 231 - end of helix removed outlier: 3.802A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.623A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.659A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 201 removed outlier: 3.545A pdb=" N ILE G 200 " --> pdb=" O MET G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 244 Proline residue: G 231 - end of helix removed outlier: 3.621A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) Processing helix chain '1' and resid 60 through 82 Processing helix chain '1' and resid 86 through 101 Processing helix chain '1' and resid 143 through 155 removed outlier: 4.175A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL 1 150 " --> pdb=" O THR 1 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP 1 153 " --> pdb=" O GLY 1 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG 1 154 " --> pdb=" O VAL 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 177 removed outlier: 4.247A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 1 167 " --> pdb=" O GLU 1 163 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA 1 175 " --> pdb=" O ALA 1 171 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 1 176 " --> pdb=" O ILE 1 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS 1 177 " --> pdb=" O TYR 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 206 removed outlier: 4.485A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 1 204 " --> pdb=" O SER 1 200 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.775A pdb=" N ALA 2 63 " --> pdb=" O SER 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 Processing helix chain '2' and resid 143 through 155 removed outlier: 4.215A pdb=" N GLY 2 149 " --> pdb=" O LEU 2 145 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG 2 154 " --> pdb=" O VAL 2 150 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 179 removed outlier: 4.194A pdb=" N ARG 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP 2 179 " --> pdb=" O ALA 2 175 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 208 removed outlier: 4.511A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE 2 207 " --> pdb=" O GLU 2 203 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 Processing helix chain '3' and resid 86 through 101 removed outlier: 3.564A pdb=" N ASN 3 99 " --> pdb=" O SER 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 143 through 155 removed outlier: 3.798A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG 3 154 " --> pdb=" O VAL 3 150 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 177 Processing helix chain '3' and resid 200 through 212 removed outlier: 3.501A pdb=" N GLN 3 206 " --> pdb=" O GLU 3 202 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE 3 207 " --> pdb=" O GLU 3 203 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS 3 210 " --> pdb=" O GLN 3 206 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE 3 211 " --> pdb=" O ILE 3 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG 3 212 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) Processing helix chain '4' and resid 59 through 82 removed outlier: 4.239A pdb=" N ALA 4 63 " --> pdb=" O SER 4 59 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN 4 64 " --> pdb=" O VAL 4 60 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE 4 65 " --> pdb=" O GLY 4 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU 4 66 " --> pdb=" O ASP 4 62 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 4 68 " --> pdb=" O GLN 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 removed outlier: 3.566A pdb=" N ILE 4 90 " --> pdb=" O THR 4 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) Processing helix chain '4' and resid 143 through 152 Processing helix chain '4' and resid 160 through 179 removed outlier: 3.549A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 4 179 " --> pdb=" O ALA 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 205 removed outlier: 3.826A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) Processing helix chain '4' and resid 206 through 208 No H-bonds generated for 'chain '4' and resid 206 through 208' Processing helix chain '5' and resid 59 through 82 Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 155 removed outlier: 3.981A pdb=" N ARG 5 154 " --> pdb=" O VAL 5 150 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.776A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) Processing helix chain '5' and resid 200 through 206 removed outlier: 3.830A pdb=" N GLN 5 206 " --> pdb=" O GLU 5 202 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.537A pdb=" N ALA 6 63 " --> pdb=" O SER 6 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG 6 68 " --> pdb=" O GLN 6 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.532A pdb=" N ALA 6 91 " --> pdb=" O VAL 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 104 No H-bonds generated for 'chain '6' and resid 102 through 104' Processing helix chain '6' and resid 143 through 155 removed outlier: 4.120A pdb=" N ASP 6 153 " --> pdb=" O GLY 6 149 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.537A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.090A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 82 removed outlier: 3.588A pdb=" N ALA 7 63 " --> pdb=" O SER 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 155 removed outlier: 3.595A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 160 through 176 removed outlier: 3.514A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 208 removed outlier: 4.415A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 7 207 " --> pdb=" O GLU 7 203 " (cutoff:3.500A) Processing helix chain '7' and resid 209 through 211 No H-bonds generated for 'chain '7' and resid 209 through 211' Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 3.885A pdb=" N GLY A 45 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.878A pdb=" N ILE A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.720A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.674A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.767A pdb=" N GLY C 45 " --> pdb=" O CYS C 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.984A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.567A pdb=" N GLY D 45 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 220 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 7.343A pdb=" N ILE D 67 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS D 69 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA D 76 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP D 151 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 4.205A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 220 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.465A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.599A pdb=" N ALA F 37 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 222 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.995A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 161 through 162 removed outlier: 4.175A pdb=" N VAL G 211 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.539A pdb=" N ILE G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU G 147 " --> pdb=" O TYR G 159 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 157 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 137 through 141 removed outlier: 3.669A pdb=" N GLY 1 22 " --> pdb=" O CYS 1 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1' and resid 45 through 49 removed outlier: 6.525A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY 1 113 " --> pdb=" O ALA 1 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 1 110 " --> pdb=" O ILE 1 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 14 through 18 Processing sheet with id=AB9, first strand: chain '2' and resid 31 through 32 removed outlier: 3.945A pdb=" N ALA 2 31 " --> pdb=" O SER 2 39 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER 2 39 " --> pdb=" O ALA 2 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '2' and resid 45 through 49 removed outlier: 6.948A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 14 through 18 Processing sheet with id=AC3, first strand: chain '3' and resid 45 through 49 removed outlier: 6.531A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER 3 121 " --> pdb=" O GLY 3 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 3 122 " --> pdb=" O GLU 3 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 137 through 138 removed outlier: 3.525A pdb=" N ALA 4 26 " --> pdb=" O VAL 4 15 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 45 through 49 removed outlier: 6.625A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER 4 121 " --> pdb=" O GLY 4 114 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE 4 122 " --> pdb=" O GLU 4 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 137 through 141 removed outlier: 6.543A pdb=" N THR 5 13 " --> pdb=" O GLU 5 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU 5 28 " --> pdb=" O THR 5 13 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET 5 25 " --> pdb=" O VAL 5 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 45 through 49 removed outlier: 6.794A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 137 through 138 Processing sheet with id=AC9, first strand: chain '6' and resid 45 through 49 removed outlier: 6.454A pdb=" N MET 6 52 " --> pdb=" O ILE 6 48 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '7' and resid 137 through 138 Processing sheet with id=AD2, first strand: chain '7' and resid 32 through 33 removed outlier: 3.507A pdb=" N PHE 7 36 " --> pdb=" O MET 7 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 45 through 49 removed outlier: 6.836A pdb=" N MET 7 52 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.72 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 17623 1.52 - 1.88: 6505 1.88 - 2.24: 13 2.24 - 2.61: 1 2.61 - 2.97: 1 Bond restraints: 24143 Sorted by residual: bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.968 -1.584 2.10e-02 2.27e+03 5.69e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.182 -0.798 2.10e-02 2.27e+03 1.44e+03 bond pdb=" CE1 PHE 5 211 " pdb=" CZ PHE 5 211 " ideal model delta sigma weight residual 1.382 2.264 -0.882 3.00e-02 1.11e+03 8.64e+02 bond pdb=" CD2 PHE 5 211 " pdb=" CE2 PHE 5 211 " ideal model delta sigma weight residual 1.382 2.225 -0.843 3.00e-02 1.11e+03 7.89e+02 bond pdb=" CE2 PHE 5 211 " pdb=" CZ PHE 5 211 " ideal model delta sigma weight residual 1.382 2.200 -0.818 3.00e-02 1.11e+03 7.44e+02 ... (remaining 24138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.77: 31969 8.77 - 17.53: 595 17.53 - 26.30: 4 26.30 - 35.06: 1 35.06 - 43.83: 2 Bond angle restraints: 32571 Sorted by residual: angle pdb=" O ASP C 181 " pdb=" C ASP C 181 " pdb=" N ASP C 182 " ideal model delta sigma weight residual 122.59 166.42 -43.83 1.33e+00 5.65e-01 1.09e+03 angle pdb=" CA ASP C 181 " pdb=" C ASP C 181 " pdb=" O ASP C 181 " ideal model delta sigma weight residual 120.51 84.84 35.67 1.43e+00 4.89e-01 6.22e+02 angle pdb=" CA ASP C 181 " pdb=" C ASP C 181 " pdb=" N ASP C 182 " ideal model delta sigma weight residual 116.84 84.96 31.88 1.71e+00 3.42e-01 3.48e+02 angle pdb=" N ASP C 182 " pdb=" CA ASP C 182 " pdb=" CB ASP C 182 " ideal model delta sigma weight residual 110.56 133.77 -23.21 1.86e+00 2.89e-01 1.56e+02 angle pdb=" N LYS A 66 " pdb=" CA LYS A 66 " pdb=" C LYS A 66 " ideal model delta sigma weight residual 114.62 100.61 14.01 1.14e+00 7.69e-01 1.51e+02 ... (remaining 32566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.74: 13908 24.74 - 49.48: 657 49.48 - 74.21: 203 74.21 - 98.95: 78 98.95 - 123.69: 1 Dihedral angle restraints: 14847 sinusoidal: 5992 harmonic: 8855 Sorted by residual: dihedral pdb=" CA VAL G 54 " pdb=" C VAL G 54 " pdb=" N GLY G 55 " pdb=" CA GLY G 55 " ideal model delta harmonic sigma weight residual 180.00 56.31 123.69 0 5.00e+00 4.00e-02 6.12e+02 dihedral pdb=" CA ARG G 53 " pdb=" C ARG G 53 " pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta harmonic sigma weight residual 180.00 112.64 67.36 0 5.00e+00 4.00e-02 1.81e+02 dihedral pdb=" CA LYS G 52 " pdb=" C LYS G 52 " pdb=" N ARG G 53 " pdb=" CA ARG G 53 " ideal model delta harmonic sigma weight residual 180.00 -117.93 -62.07 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 14844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2343 0.180 - 0.360: 1110 0.360 - 0.539: 289 0.539 - 0.719: 27 0.719 - 0.899: 4 Chirality restraints: 3773 Sorted by residual: chirality pdb=" CA THR 6 140 " pdb=" N THR 6 140 " pdb=" C THR 6 140 " pdb=" CB THR 6 140 " both_signs ideal model delta sigma weight residual False 2.53 1.63 0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" CA LEU 2 208 " pdb=" N LEU 2 208 " pdb=" C LEU 2 208 " pdb=" CB LEU 2 208 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA ARG D 219 " pdb=" N ARG D 219 " pdb=" C ARG D 219 " pdb=" CB ARG D 219 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 3770 not shown) Planarity restraints: 4193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 103 " -0.240 2.00e-02 2.50e+03 1.63e-01 5.32e+02 pdb=" CG TYR 4 103 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 103 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 103 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 103 " 0.195 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 103 " 0.147 2.00e-02 2.50e+03 pdb=" CZ TYR 4 103 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR 4 103 " -0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 197 " 0.315 2.00e-02 2.50e+03 1.62e-01 5.25e+02 pdb=" CG TYR 1 197 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 197 " -0.190 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 197 " -0.129 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 197 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 197 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR 1 197 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR 1 197 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 211 " 0.115 2.00e-02 2.50e+03 1.71e-01 5.10e+02 pdb=" CG PHE 5 211 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 211 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 211 " -0.228 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 211 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 211 " 0.320 2.00e-02 2.50e+03 pdb=" CZ PHE 5 211 " -0.114 2.00e-02 2.50e+03 ... (remaining 4190 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 961 2.64 - 3.21: 19098 3.21 - 3.77: 36443 3.77 - 4.34: 52672 4.34 - 4.90: 85789 Nonbonded interactions: 194963 Sorted by model distance: nonbonded pdb=" NH1 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.081 3.420 nonbonded pdb=" NE ARG 5 170 " pdb=" CD1 PHE 5 211 " model vdw 2.159 3.420 nonbonded pdb=" OE1 GLU 5 166 " pdb=" CE2 PHE 5 211 " model vdw 2.184 3.340 nonbonded pdb=" CZ ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.192 3.570 nonbonded pdb=" NH1 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.206 3.340 ... (remaining 194958 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: 0.02 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 55.680 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 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 : 0.039 1.584 24143 Z= 2.402 Angle : 3.601 43.828 32571 Z= 2.410 Chirality : 0.206 0.899 3773 Planarity : 0.030 0.298 4193 Dihedral : 17.647 123.688 9177 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 1.55 % Allowed : 5.58 % Favored : 92.87 % Rotamer: Outliers : 4.93 % Allowed : 10.89 % Favored : 84.18 % Cbeta Deviations : 7.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.13), residues: 3031 helix: -0.35 (0.13), residues: 1211 sheet: -1.06 (0.18), residues: 620 loop : -3.29 (0.12), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.035 0.011 HIS C 73 PHE 0.320 0.039 PHE 5 211 TYR 0.315 0.050 TYR 1 197 ARG 0.084 0.012 ARG 3 51 Details of bonding type rmsd hydrogen bonds : bond 0.26365 ( 1337) hydrogen bonds : angle 9.18254 ( 3924) covalent geometry : bond 0.03865 (24143) covalent geometry : angle 3.60083 (32571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 669 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 VAL cc_start: 0.9124 (t) cc_final: 0.8870 (m) REVERT: C 104 ASP cc_start: 0.8250 (t70) cc_final: 0.7989 (t0) REVERT: C 141 VAL cc_start: 0.9226 (t) cc_final: 0.8984 (m) REVERT: D 111 GLU cc_start: 0.7408 (tp30) cc_final: 0.6757 (tp30) REVERT: D 129 VAL cc_start: 0.8767 (p) cc_final: 0.8474 (m) REVERT: D 203 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6856 (mt-10) REVERT: G 71 ASP cc_start: 0.7580 (t0) cc_final: 0.6916 (t0) REVERT: G 159 TYR cc_start: 0.8344 (m-80) cc_final: 0.8034 (m-80) REVERT: G 196 MET cc_start: 0.7652 (ttm) cc_final: 0.7358 (ttm) REVERT: 1 128 ILE cc_start: 0.3763 (OUTLIER) cc_final: 0.3506 (tt) REVERT: 2 72 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.7783 (mp) REVERT: 3 39 SER cc_start: 0.3347 (OUTLIER) cc_final: 0.2804 (t) REVERT: 3 40 LYS cc_start: 0.3887 (OUTLIER) cc_final: 0.2321 (tppt) REVERT: 3 137 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5916 (mm) REVERT: 4 71 LYS cc_start: 0.8276 (tttt) cc_final: 0.8000 (tttm) REVERT: 4 88 ARG cc_start: 0.7170 (ttp-110) cc_final: 0.6890 (ttm-80) REVERT: 4 134 GLU cc_start: 0.7099 (mp0) cc_final: 0.6898 (mp0) REVERT: 5 33 MET cc_start: -0.0386 (mtp) cc_final: -0.2142 (ppp) REVERT: 6 123 TYR cc_start: 0.8062 (m-80) cc_final: 0.7561 (m-80) REVERT: 7 84 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8688 (mmmm) REVERT: 7 205 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.4948 (mp0) outliers start: 125 outliers final: 29 residues processed: 762 average time/residue: 0.4253 time to fit residues: 470.5000 Evaluate side-chains 560 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 525 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain 1 residue 72 ILE Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 3 residue 39 SER Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 125 ILE Chi-restraints excluded: chain 3 residue 137 ILE Chi-restraints excluded: chain 4 residue 72 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 105 PRO Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 103 TYR Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 175 optimal weight: 0.2980 chunk 273 optimal weight: 0.0050 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 169 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN D 23 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN E 23 GLN E 237 ASN G 73 HIS G 237 ASN 1 96 ASN 3 96 ASN 6 47 GLN 6 64 GLN 6 96 ASN 7 75 ASN 7 96 ASN 7 198 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.184983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149425 restraints weight = 25486.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.152658 restraints weight = 18716.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.154810 restraints weight = 15255.148| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.852 24143 Z= 0.465 Angle : 0.803 30.148 32571 Z= 0.440 Chirality : 0.049 0.269 3773 Planarity : 0.006 0.092 4193 Dihedral : 7.708 84.133 3457 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 3.24 % Allowed : 15.79 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3031 helix: 0.88 (0.14), residues: 1253 sheet: -0.57 (0.18), residues: 652 loop : -2.40 (0.15), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.032 0.002 PHE 5 211 TYR 0.020 0.002 TYR E 213 ARG 0.034 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1337) hydrogen bonds : angle 5.73695 ( 3924) covalent geometry : bond 0.01222 (24143) covalent geometry : angle 0.80311 (32571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 544 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8626 (mmmt) cc_final: 0.7955 (mmtp) REVERT: A 234 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 201 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 239 ARG cc_start: 0.7780 (tpt170) cc_final: 0.7375 (tpt170) REVERT: C 95 GLU cc_start: 0.8557 (tp30) cc_final: 0.8055 (tp30) REVERT: C 104 ASP cc_start: 0.8234 (t70) cc_final: 0.8016 (t70) REVERT: D 33 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7806 (ttm110) REVERT: D 56 SER cc_start: 0.8480 (p) cc_final: 0.8028 (p) REVERT: E 159 TYR cc_start: 0.9021 (m-80) cc_final: 0.8776 (m-80) REVERT: E 239 ARG cc_start: 0.7584 (ttt90) cc_final: 0.7145 (tpt-90) REVERT: E 242 GLU cc_start: 0.7740 (tt0) cc_final: 0.7494 (mt-10) REVERT: G 203 GLU cc_start: 0.8281 (mp0) cc_final: 0.7996 (mp0) REVERT: 1 52 MET cc_start: 0.8094 (mtp) cc_final: 0.7873 (mtp) REVERT: 1 84 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8531 (mtpp) REVERT: 1 128 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4514 (tt) REVERT: 2 17 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7488 (pt) REVERT: 2 155 PHE cc_start: 0.7783 (t80) cc_final: 0.7458 (t80) REVERT: 3 52 MET cc_start: 0.8159 (mtm) cc_final: 0.7934 (mtm) REVERT: 3 84 LYS cc_start: 0.8880 (mttm) cc_final: 0.8571 (mtmt) REVERT: 3 106 TYR cc_start: 0.3180 (OUTLIER) cc_final: 0.1671 (t80) REVERT: 3 206 GLN cc_start: 0.7428 (mp10) cc_final: 0.7145 (mp10) REVERT: 4 25 MET cc_start: 0.7232 (mtp) cc_final: 0.6868 (ttp) REVERT: 4 33 MET cc_start: -0.0915 (OUTLIER) cc_final: -0.1561 (mtm) REVERT: 4 71 LYS cc_start: 0.8051 (tttt) cc_final: 0.7828 (tttm) REVERT: 4 134 GLU cc_start: 0.7703 (mp0) cc_final: 0.6634 (mp0) REVERT: 4 191 ILE cc_start: 0.8498 (mp) cc_final: 0.8296 (mt) REVERT: 5 159 ILE cc_start: 0.8557 (tt) cc_final: 0.8270 (mm) REVERT: 6 82 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7093 (mm-30) REVERT: 7 84 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8829 (mmmm) REVERT: 7 205 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.4290 (mp0) outliers start: 82 outliers final: 40 residues processed: 595 average time/residue: 0.3895 time to fit residues: 348.7627 Evaluate side-chains 484 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 439 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 194 ASP Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 52 MET Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 287 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 99 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS G 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.183106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.140980 restraints weight = 26112.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146068 restraints weight = 16480.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149418 restraints weight = 12184.306| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.845 24143 Z= 0.476 Angle : 0.752 30.136 32571 Z= 0.408 Chirality : 0.049 0.219 3773 Planarity : 0.005 0.065 4193 Dihedral : 6.487 86.892 3412 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.40 % Favored : 96.44 % Rotamer: Outliers : 4.54 % Allowed : 17.36 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3031 helix: 0.85 (0.14), residues: 1252 sheet: -0.44 (0.19), residues: 644 loop : -2.06 (0.15), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 73 PHE 0.035 0.002 PHE 5 211 TYR 0.024 0.002 TYR G 213 ARG 0.016 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 1337) hydrogen bonds : angle 5.35538 ( 3924) covalent geometry : bond 0.01252 (24143) covalent geometry : angle 0.75155 (32571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 473 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8093 (mmtp) REVERT: A 183 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 234 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 219 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7634 (tpp80) REVERT: B 239 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7591 (tpt170) REVERT: C 95 GLU cc_start: 0.8533 (tp30) cc_final: 0.8082 (tp30) REVERT: C 196 MET cc_start: 0.9075 (tpp) cc_final: 0.8805 (tpp) REVERT: C 217 ASP cc_start: 0.8457 (p0) cc_final: 0.8134 (p0) REVERT: D 33 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7933 (ttm110) REVERT: D 129 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8910 (m) REVERT: D 178 GLU cc_start: 0.7465 (tp30) cc_final: 0.7185 (tm-30) REVERT: E 38 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8353 (mt) REVERT: E 222 LYS cc_start: 0.8542 (tttt) cc_final: 0.7940 (tttt) REVERT: F 121 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8086 (tm-30) REVERT: G 60 GLU cc_start: 0.7661 (tt0) cc_final: 0.7379 (tt0) REVERT: G 104 ASP cc_start: 0.8116 (t0) cc_final: 0.7868 (t0) REVERT: 1 83 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8312 (ttp-110) REVERT: 1 84 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8544 (mtpp) REVERT: 2 88 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7363 (ttm-80) REVERT: 3 52 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7986 (mtm) REVERT: 3 106 TYR cc_start: 0.3639 (OUTLIER) cc_final: 0.2056 (t80) REVERT: 3 206 GLN cc_start: 0.7448 (mp10) cc_final: 0.6901 (mp10) REVERT: 4 25 MET cc_start: 0.7508 (mtp) cc_final: 0.7250 (ttm) REVERT: 4 33 MET cc_start: 0.0595 (OUTLIER) cc_final: -0.0134 (mtm) REVERT: 4 88 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7472 (ttm-80) REVERT: 5 51 ARG cc_start: 0.7829 (mmp80) cc_final: 0.7363 (mmt180) REVERT: 5 116 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7648 (p0) REVERT: 6 25 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6990 (ttm) REVERT: 7 44 LYS cc_start: 0.7811 (tppt) cc_final: 0.7239 (tptp) REVERT: 7 205 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.4673 (mp0) outliers start: 115 outliers final: 76 residues processed: 546 average time/residue: 0.3781 time to fit residues: 314.2045 Evaluate side-chains 507 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 422 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 87 VAL Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 176 MET Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 52 MET Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 25 MET Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 163 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 258 optimal weight: 0.0070 chunk 283 optimal weight: 0.0870 chunk 240 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN 1 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.148523 restraints weight = 26042.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.153676 restraints weight = 16383.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.157076 restraints weight = 12045.784| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.843 24143 Z= 0.438 Angle : 0.642 30.098 32571 Z= 0.352 Chirality : 0.045 0.222 3773 Planarity : 0.004 0.049 4193 Dihedral : 5.959 88.252 3407 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.33 % Rotamer: Outliers : 3.35 % Allowed : 19.34 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3031 helix: 1.15 (0.15), residues: 1257 sheet: -0.24 (0.19), residues: 655 loop : -1.78 (0.16), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 73 PHE 0.034 0.001 PHE 5 211 TYR 0.018 0.001 TYR 5 173 ARG 0.007 0.001 ARG 3 170 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 1337) hydrogen bonds : angle 5.03036 ( 3924) covalent geometry : bond 0.01174 (24143) covalent geometry : angle 0.64212 (32571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 437 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8024 (mmtp) REVERT: B 104 ASP cc_start: 0.8053 (m-30) cc_final: 0.7798 (t0) REVERT: B 239 ARG cc_start: 0.7723 (tpt170) cc_final: 0.7419 (tpt170) REVERT: C 95 GLU cc_start: 0.8279 (tp30) cc_final: 0.7855 (tp30) REVERT: C 196 MET cc_start: 0.9005 (tpp) cc_final: 0.8696 (tpp) REVERT: C 217 ASP cc_start: 0.8307 (p0) cc_final: 0.8082 (p0) REVERT: D 153 SER cc_start: 0.8739 (t) cc_final: 0.8486 (p) REVERT: E 239 ARG cc_start: 0.7337 (ttt90) cc_final: 0.6931 (tpt-90) REVERT: F 121 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7801 (tm-30) REVERT: F 194 VAL cc_start: 0.8674 (t) cc_final: 0.8437 (m) REVERT: G 60 GLU cc_start: 0.7451 (tt0) cc_final: 0.7063 (tt0) REVERT: 1 84 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8526 (mtpp) REVERT: 2 163 GLU cc_start: 0.7197 (pm20) cc_final: 0.6949 (pm20) REVERT: 3 106 TYR cc_start: 0.3436 (OUTLIER) cc_final: 0.1656 (t80) REVERT: 3 118 GLU cc_start: 0.8183 (pp20) cc_final: 0.7795 (pp20) REVERT: 3 134 GLU cc_start: 0.7410 (mp0) cc_final: 0.6816 (mt-10) REVERT: 4 25 MET cc_start: 0.7317 (mtp) cc_final: 0.7065 (ttp) REVERT: 4 33 MET cc_start: -0.0173 (mtm) cc_final: -0.1090 (mtm) REVERT: 4 88 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7390 (ttm-80) REVERT: 4 163 GLU cc_start: 0.8413 (tp30) cc_final: 0.7915 (mp0) REVERT: 5 51 ARG cc_start: 0.7800 (mmp80) cc_final: 0.7293 (mmt180) REVERT: 5 110 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8638 (mt) REVERT: 5 116 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7502 (p0) REVERT: 5 154 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7225 (ptp-170) REVERT: 6 88 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7669 (ttp-110) REVERT: 7 25 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6616 (ttm) REVERT: 7 44 LYS cc_start: 0.7895 (tppt) cc_final: 0.7142 (tptp) REVERT: 7 83 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.8040 (ttp-170) REVERT: 7 84 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8837 (mmmm) REVERT: 7 133 GLU cc_start: 0.8100 (tp30) cc_final: 0.7382 (tp30) REVERT: 7 158 GLU cc_start: 0.7798 (tp30) cc_final: 0.6890 (tp30) REVERT: 7 205 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.4790 (mp0) outliers start: 85 outliers final: 47 residues processed: 490 average time/residue: 0.3845 time to fit residues: 290.6610 Evaluate side-chains 460 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 407 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 82 GLU Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 25 MET Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 253 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN 4 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.187294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.145129 restraints weight = 25998.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.150349 restraints weight = 16147.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.153745 restraints weight = 11855.243| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.848 24143 Z= 0.447 Angle : 0.649 29.992 32571 Z= 0.354 Chirality : 0.046 0.198 3773 Planarity : 0.004 0.047 4193 Dihedral : 5.757 86.696 3404 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.96 % Rotamer: Outliers : 3.79 % Allowed : 19.89 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3031 helix: 1.16 (0.15), residues: 1253 sheet: -0.19 (0.19), residues: 653 loop : -1.68 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.035 0.001 PHE 5 211 TYR 0.018 0.001 TYR D 213 ARG 0.008 0.001 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 1337) hydrogen bonds : angle 4.99675 ( 3924) covalent geometry : bond 0.01195 (24143) covalent geometry : angle 0.64905 (32571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 418 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8073 (mmtp) REVERT: B 104 ASP cc_start: 0.8261 (m-30) cc_final: 0.8021 (t0) REVERT: C 95 GLU cc_start: 0.8338 (tp30) cc_final: 0.7860 (tp30) REVERT: C 217 ASP cc_start: 0.8364 (p0) cc_final: 0.8115 (p0) REVERT: D 153 SER cc_start: 0.8866 (t) cc_final: 0.8556 (p) REVERT: E 71 ASP cc_start: 0.8207 (t0) cc_final: 0.7939 (t0) REVERT: E 222 LYS cc_start: 0.8445 (tttt) cc_final: 0.7857 (tttt) REVERT: E 239 ARG cc_start: 0.7319 (ttt90) cc_final: 0.6961 (tpt-90) REVERT: F 121 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7832 (tm-30) REVERT: 1 83 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8381 (ttp80) REVERT: 1 84 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8509 (mtpp) REVERT: 1 134 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: 2 84 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8728 (mmmm) REVERT: 3 51 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7658 (mmp80) REVERT: 3 106 TYR cc_start: 0.3115 (OUTLIER) cc_final: 0.1047 (t80) REVERT: 3 118 GLU cc_start: 0.8148 (pp20) cc_final: 0.7709 (pp20) REVERT: 4 29 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7753 (ttmm) REVERT: 4 33 MET cc_start: -0.0229 (OUTLIER) cc_final: -0.1315 (mtm) REVERT: 4 88 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7507 (ttm-80) REVERT: 5 51 ARG cc_start: 0.7844 (mmp80) cc_final: 0.7381 (mmt180) REVERT: 5 110 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8635 (mt) REVERT: 5 156 THR cc_start: 0.8721 (t) cc_final: 0.8411 (m) REVERT: 6 88 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7725 (ttp-110) REVERT: 7 25 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6528 (ttp) REVERT: 7 44 LYS cc_start: 0.7863 (tppt) cc_final: 0.7447 (tptp) REVERT: 7 83 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.8074 (ttp-170) REVERT: 7 84 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8835 (mmmm) REVERT: 7 133 GLU cc_start: 0.8180 (tp30) cc_final: 0.7569 (tp30) REVERT: 7 158 GLU cc_start: 0.7726 (tp30) cc_final: 0.7323 (mm-30) REVERT: 7 205 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.4853 (mp0) outliers start: 96 outliers final: 66 residues processed: 477 average time/residue: 0.3710 time to fit residues: 274.9374 Evaluate side-chains 477 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 405 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 87 VAL Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 25 MET Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 185 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 138 optimal weight: 0.0570 chunk 193 optimal weight: 0.2980 chunk 242 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 chunk 151 optimal weight: 0.0070 chunk 104 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 222 optimal weight: 0.5980 chunk 210 optimal weight: 3.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN 3 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.188880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.146594 restraints weight = 25676.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.151523 restraints weight = 16399.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.154939 restraints weight = 12217.387| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.851 24143 Z= 0.437 Angle : 0.620 29.926 32571 Z= 0.339 Chirality : 0.045 0.179 3773 Planarity : 0.004 0.046 4193 Dihedral : 5.544 85.423 3404 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.33 % Rotamer: Outliers : 3.67 % Allowed : 21.03 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3031 helix: 1.31 (0.15), residues: 1253 sheet: -0.15 (0.19), residues: 649 loop : -1.57 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 73 PHE 0.036 0.001 PHE 5 211 TYR 0.014 0.001 TYR E 213 ARG 0.009 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 1337) hydrogen bonds : angle 4.89422 ( 3924) covalent geometry : bond 0.01176 (24143) covalent geometry : angle 0.62033 (32571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 426 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8025 (mmtp) REVERT: A 159 TYR cc_start: 0.8958 (m-80) cc_final: 0.8558 (m-80) REVERT: C 95 GLU cc_start: 0.8293 (tp30) cc_final: 0.7864 (tp30) REVERT: C 217 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8122 (p0) REVERT: D 153 SER cc_start: 0.8780 (t) cc_final: 0.8505 (p) REVERT: E 38 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (mt) REVERT: E 71 ASP cc_start: 0.8274 (t0) cc_final: 0.7934 (t0) REVERT: E 239 ARG cc_start: 0.7362 (ttt90) cc_final: 0.7053 (tpt-90) REVERT: F 121 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7758 (tm-30) REVERT: F 223 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: 1 83 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8396 (ttp80) REVERT: 1 84 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8487 (mtpp) REVERT: 1 134 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: 2 44 LYS cc_start: 0.7557 (mtpt) cc_final: 0.7317 (tttt) REVERT: 2 84 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8688 (mmmm) REVERT: 3 51 ARG cc_start: 0.8146 (mmp80) cc_final: 0.7741 (mmp80) REVERT: 3 106 TYR cc_start: 0.3037 (OUTLIER) cc_final: 0.0882 (t80) REVERT: 3 118 GLU cc_start: 0.8187 (pp20) cc_final: 0.7729 (pp20) REVERT: 4 33 MET cc_start: -0.0253 (OUTLIER) cc_final: -0.0996 (mtm) REVERT: 4 88 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7407 (ttm-80) REVERT: 4 158 GLU cc_start: 0.7398 (tp30) cc_final: 0.7184 (tp30) REVERT: 4 163 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7651 (mp0) REVERT: 5 51 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7301 (mmt180) REVERT: 5 110 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8670 (mt) REVERT: 5 156 THR cc_start: 0.8750 (t) cc_final: 0.8491 (m) REVERT: 6 88 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7777 (ttp-110) REVERT: 7 25 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6587 (ttp) REVERT: 7 44 LYS cc_start: 0.8038 (tppt) cc_final: 0.7490 (tptp) REVERT: 7 84 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8837 (mmmm) REVERT: 7 133 GLU cc_start: 0.8176 (tp30) cc_final: 0.7624 (tp30) REVERT: 7 205 GLU cc_start: 0.6118 (OUTLIER) cc_final: 0.4813 (mp0) outliers start: 93 outliers final: 62 residues processed: 486 average time/residue: 0.3687 time to fit residues: 274.5785 Evaluate side-chains 484 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 413 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 25 MET Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 218 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 253 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 293 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 198 GLN 4 96 ASN 4 109 GLN 5 198 GLN 6 96 ASN 7 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.180801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137468 restraints weight = 26003.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142512 restraints weight = 16106.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.145924 restraints weight = 11868.891| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.858 24143 Z= 0.456 Angle : 0.654 29.831 32571 Z= 0.354 Chirality : 0.046 0.227 3773 Planarity : 0.004 0.064 4193 Dihedral : 5.550 84.409 3404 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 4.26 % Allowed : 20.72 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3031 helix: 1.25 (0.15), residues: 1244 sheet: -0.20 (0.19), residues: 648 loop : -1.53 (0.16), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.036 0.001 PHE 5 211 TYR 0.017 0.001 TYR D 213 ARG 0.018 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 1337) hydrogen bonds : angle 5.00779 ( 3924) covalent geometry : bond 0.01216 (24143) covalent geometry : angle 0.65405 (32571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 437 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8158 (mmtp) REVERT: A 159 TYR cc_start: 0.9006 (m-80) cc_final: 0.8574 (m-80) REVERT: B 104 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7620 (t0) REVERT: C 43 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (mtmm) REVERT: C 95 GLU cc_start: 0.8346 (tp30) cc_final: 0.7844 (tp30) REVERT: E 71 ASP cc_start: 0.8398 (t0) cc_final: 0.8057 (t0) REVERT: E 239 ARG cc_start: 0.7443 (ttt90) cc_final: 0.7191 (tpt-90) REVERT: F 121 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7807 (tm-30) REVERT: F 194 VAL cc_start: 0.8805 (t) cc_final: 0.8564 (m) REVERT: F 223 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: G 60 GLU cc_start: 0.7694 (tt0) cc_final: 0.7376 (tp30) REVERT: G 208 ASN cc_start: 0.7940 (p0) cc_final: 0.7397 (p0) REVERT: 1 83 ARG cc_start: 0.8619 (ttp80) cc_final: 0.8370 (ttp80) REVERT: 1 134 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: 2 44 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7341 (ttmm) REVERT: 2 84 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8675 (mmmm) REVERT: 2 163 GLU cc_start: 0.7303 (pm20) cc_final: 0.7009 (pm20) REVERT: 3 51 ARG cc_start: 0.8166 (mmp80) cc_final: 0.7694 (mmp80) REVERT: 3 106 TYR cc_start: 0.2920 (OUTLIER) cc_final: 0.0720 (t80) REVERT: 4 33 MET cc_start: -0.0313 (OUTLIER) cc_final: -0.1095 (mtm) REVERT: 4 88 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7497 (ttm-80) REVERT: 5 45 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5967 (mm) REVERT: 5 51 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7374 (mmt180) REVERT: 5 55 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7469 (p) REVERT: 5 110 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8681 (mt) REVERT: 6 154 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6537 (mtt-85) REVERT: 7 25 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6595 (ttm) REVERT: 7 44 LYS cc_start: 0.8082 (tppt) cc_final: 0.7551 (tptp) REVERT: 7 51 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7864 (mmt-90) REVERT: 7 205 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.4919 (mp0) outliers start: 108 outliers final: 83 residues processed: 497 average time/residue: 0.3606 time to fit residues: 276.1851 Evaluate side-chains 520 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 425 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 189 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 154 ARG Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 25 MET Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 234 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 145 optimal weight: 0.2980 chunk 292 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.181447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.139319 restraints weight = 26095.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144420 restraints weight = 16322.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147744 restraints weight = 11955.781| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.870 24143 Z= 0.465 Angle : 0.674 29.632 32571 Z= 0.365 Chirality : 0.047 0.257 3773 Planarity : 0.004 0.096 4193 Dihedral : 5.609 83.325 3402 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.42 % Allowed : 20.96 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3031 helix: 1.14 (0.14), residues: 1250 sheet: -0.27 (0.19), residues: 645 loop : -1.50 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.034 0.002 PHE 5 211 TYR 0.018 0.002 TYR D 213 ARG 0.026 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 1337) hydrogen bonds : angle 5.10475 ( 3924) covalent geometry : bond 0.01239 (24143) covalent geometry : angle 0.67439 (32571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 424 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8090 (mmtp) REVERT: A 159 TYR cc_start: 0.9030 (m-80) cc_final: 0.8590 (m-80) REVERT: B 104 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7976 (t70) REVERT: C 95 GLU cc_start: 0.8341 (tp30) cc_final: 0.7847 (tp30) REVERT: E 71 ASP cc_start: 0.8386 (t0) cc_final: 0.8039 (t0) REVERT: F 121 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7830 (tm-30) REVERT: F 223 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: G 60 GLU cc_start: 0.7783 (tt0) cc_final: 0.7431 (tp30) REVERT: G 208 ASN cc_start: 0.7933 (p0) cc_final: 0.7458 (p0) REVERT: 1 29 LYS cc_start: 0.8037 (tttt) cc_final: 0.7716 (ttmm) REVERT: 1 83 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8345 (mtm-85) REVERT: 1 134 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: 2 44 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7308 (ttmm) REVERT: 3 51 ARG cc_start: 0.8148 (mmp80) cc_final: 0.7715 (mmp80) REVERT: 3 106 TYR cc_start: 0.3219 (OUTLIER) cc_final: 0.0927 (t80) REVERT: 3 116 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8012 (p0) REVERT: 4 33 MET cc_start: -0.0702 (OUTLIER) cc_final: -0.1356 (mtm) REVERT: 4 88 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7533 (ttm-80) REVERT: 4 135 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6832 (mmtm) REVERT: 4 158 GLU cc_start: 0.7241 (tp30) cc_final: 0.6603 (tp30) REVERT: 5 51 ARG cc_start: 0.7928 (mmp80) cc_final: 0.7366 (mmt180) REVERT: 5 55 THR cc_start: 0.7487 (OUTLIER) cc_final: 0.7225 (p) REVERT: 5 110 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8750 (mt) REVERT: 6 83 ARG cc_start: 0.8427 (ttp80) cc_final: 0.7928 (ptt90) REVERT: 6 154 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6464 (mtt-85) REVERT: 7 25 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6791 (ttm) REVERT: 7 44 LYS cc_start: 0.8145 (tppt) cc_final: 0.7622 (tptp) REVERT: 7 51 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7854 (mmt-90) REVERT: 7 205 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.4978 (mp0) outliers start: 112 outliers final: 87 residues processed: 497 average time/residue: 0.3634 time to fit residues: 276.5132 Evaluate side-chains 511 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 413 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 193 GLU Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 14 THR Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 116 ASP Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 154 ARG Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 25 MET Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 277 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 232 optimal weight: 0.0030 chunk 272 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 255 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.183071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.140659 restraints weight = 25892.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.145531 restraints weight = 16478.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.148615 restraints weight = 12345.268| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.881 24143 Z= 0.442 Angle : 0.638 29.388 32571 Z= 0.346 Chirality : 0.045 0.199 3773 Planarity : 0.005 0.123 4193 Dihedral : 5.492 81.772 3402 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 3.55 % Allowed : 22.34 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3031 helix: 1.29 (0.15), residues: 1254 sheet: -0.16 (0.19), residues: 630 loop : -1.48 (0.16), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 73 PHE 0.029 0.001 PHE 5 211 TYR 0.021 0.001 TYR 7 77 ARG 0.033 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 1337) hydrogen bonds : angle 4.99429 ( 3924) covalent geometry : bond 0.01191 (24143) covalent geometry : angle 0.63827 (32571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 414 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8091 (mmtp) REVERT: A 159 TYR cc_start: 0.8993 (m-80) cc_final: 0.8588 (m-80) REVERT: B 104 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7733 (t0) REVERT: C 95 GLU cc_start: 0.8287 (tp30) cc_final: 0.7820 (tp30) REVERT: D 153 SER cc_start: 0.8800 (t) cc_final: 0.8494 (p) REVERT: E 71 ASP cc_start: 0.8332 (t0) cc_final: 0.7972 (t0) REVERT: E 222 LYS cc_start: 0.8582 (tttt) cc_final: 0.8022 (tttt) REVERT: F 121 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7755 (tm-30) REVERT: F 223 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: G 60 GLU cc_start: 0.7656 (tt0) cc_final: 0.7347 (tp30) REVERT: G 168 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7898 (ttt-90) REVERT: G 208 ASN cc_start: 0.7842 (p0) cc_final: 0.7574 (p0) REVERT: 1 29 LYS cc_start: 0.7944 (tttt) cc_final: 0.7616 (ttmm) REVERT: 1 83 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8375 (mtm-85) REVERT: 1 134 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: 2 163 GLU cc_start: 0.7289 (pm20) cc_final: 0.7014 (pm20) REVERT: 3 25 MET cc_start: 0.7916 (ptm) cc_final: 0.7694 (ptp) REVERT: 3 51 ARG cc_start: 0.8129 (mmp80) cc_final: 0.7724 (mmp80) REVERT: 3 106 TYR cc_start: 0.3428 (OUTLIER) cc_final: 0.1183 (t80) REVERT: 4 33 MET cc_start: -0.0793 (OUTLIER) cc_final: -0.1391 (mtm) REVERT: 4 88 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7762 (ttm-80) REVERT: 4 135 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6835 (mmtm) REVERT: 4 158 GLU cc_start: 0.7245 (tp30) cc_final: 0.6545 (tp30) REVERT: 5 51 ARG cc_start: 0.7951 (mmp80) cc_final: 0.7333 (mmt180) REVERT: 5 55 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7243 (p) REVERT: 5 110 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8744 (mt) REVERT: 6 83 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7939 (ptt90) REVERT: 7 44 LYS cc_start: 0.8199 (tppt) cc_final: 0.7715 (tptp) REVERT: 7 51 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7853 (mmt-90) REVERT: 7 205 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.4918 (mp0) outliers start: 90 outliers final: 72 residues processed: 471 average time/residue: 0.3691 time to fit residues: 267.0293 Evaluate side-chains 481 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 400 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 117 CYS Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 168 ARG Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 50 optimal weight: 0.7980 chunk 195 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.180995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138624 restraints weight = 26131.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.143629 restraints weight = 16294.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146792 restraints weight = 12005.231| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.883 24143 Z= 0.454 Angle : 0.663 29.312 32571 Z= 0.357 Chirality : 0.046 0.192 3773 Planarity : 0.005 0.130 4193 Dihedral : 5.479 80.212 3400 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 3.59 % Allowed : 22.22 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3031 helix: 1.21 (0.14), residues: 1256 sheet: -0.18 (0.19), residues: 628 loop : -1.46 (0.16), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.028 0.001 PHE 5 211 TYR 0.016 0.001 TYR E 213 ARG 0.034 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1337) hydrogen bonds : angle 5.05920 ( 3924) covalent geometry : bond 0.01218 (24143) covalent geometry : angle 0.66299 (32571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 422 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.9017 (m-80) cc_final: 0.8614 (m-80) REVERT: A 177 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8255 (ttpt) REVERT: B 104 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7803 (t0) REVERT: C 95 GLU cc_start: 0.8307 (tp30) cc_final: 0.7834 (tp30) REVERT: D 91 ARG cc_start: 0.8476 (tpt-90) cc_final: 0.8267 (tpt-90) REVERT: E 71 ASP cc_start: 0.8347 (t0) cc_final: 0.8020 (t0) REVERT: F 121 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7802 (tm-30) REVERT: G 60 GLU cc_start: 0.7725 (tt0) cc_final: 0.7411 (tp30) REVERT: G 168 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7993 (ttt-90) REVERT: G 208 ASN cc_start: 0.7873 (p0) cc_final: 0.7651 (p0) REVERT: 1 29 LYS cc_start: 0.8006 (tttt) cc_final: 0.7668 (ttmm) REVERT: 1 83 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8368 (mtm-85) REVERT: 1 134 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: 3 51 ARG cc_start: 0.8161 (mmp80) cc_final: 0.7769 (mmp80) REVERT: 3 106 TYR cc_start: 0.3435 (OUTLIER) cc_final: 0.1075 (t80) REVERT: 3 116 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7908 (p0) REVERT: 3 206 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7681 (tm-30) REVERT: 4 33 MET cc_start: -0.0885 (OUTLIER) cc_final: -0.1328 (mtm) REVERT: 4 88 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7773 (ttm-80) REVERT: 4 158 GLU cc_start: 0.7185 (tp30) cc_final: 0.6488 (tp30) REVERT: 5 51 ARG cc_start: 0.8003 (mmp80) cc_final: 0.7400 (mmt180) REVERT: 5 55 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7352 (p) REVERT: 5 110 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8752 (mt) REVERT: 6 25 MET cc_start: 0.7808 (ttm) cc_final: 0.7539 (ttp) REVERT: 6 83 ARG cc_start: 0.8416 (ttp80) cc_final: 0.7986 (ptt90) REVERT: 6 133 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7811 (tm-30) REVERT: 6 154 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6558 (mtt-85) REVERT: 7 44 LYS cc_start: 0.8135 (tppt) cc_final: 0.7575 (tptp) REVERT: 7 51 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7873 (mmt-90) REVERT: 7 205 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.4987 (mp0) outliers start: 91 outliers final: 76 residues processed: 483 average time/residue: 0.3705 time to fit residues: 274.3739 Evaluate side-chains 504 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 418 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 168 ARG Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 116 ASP Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 120 LYS Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 154 ARG Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 296 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 156 optimal weight: 0.8980 chunk 288 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.182049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.140674 restraints weight = 25859.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.145407 restraints weight = 16572.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.148185 restraints weight = 12406.335| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.883 24143 Z= 0.461 Angle : 0.676 29.307 32571 Z= 0.364 Chirality : 0.047 0.180 3773 Planarity : 0.005 0.128 4193 Dihedral : 5.503 81.003 3400 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.67 % Allowed : 22.26 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3031 helix: 1.12 (0.14), residues: 1259 sheet: -0.20 (0.20), residues: 629 loop : -1.45 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.028 0.001 PHE 5 211 TYR 0.017 0.001 TYR E 213 ARG 0.034 0.001 ARG 5 170 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 1337) hydrogen bonds : angle 5.12046 ( 3924) covalent geometry : bond 0.01234 (24143) covalent geometry : angle 0.67600 (32571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8117.94 seconds wall clock time: 142 minutes 3.47 seconds (8523.47 seconds total)