Starting phenix.real_space_refine on Fri Sep 19 04:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6he7_0211/09_2025/6he7_0211.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he7_0211/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6he7_0211/09_2025/6he7_0211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he7_0211/09_2025/6he7_0211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6he7_0211/09_2025/6he7_0211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he7_0211/09_2025/6he7_0211.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.87, per 1000 atoms: 0.25 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: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.78 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: 4.17 Time building geometry restraints manager: 2.42 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: 0.01 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.100 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 28.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.084 0.012 ARG 3 51 TYR 0.315 0.050 TYR 1 197 PHE 0.320 0.039 PHE 5 211 HIS 0.035 0.011 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.03865 (24143) covalent geometry : angle 3.60083 (32571) hydrogen bonds : bond 0.26365 ( 1337) hydrogen bonds : angle 9.18254 ( 3924) *********************** 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 : 0.965 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: 0.2161 time to fit residues: 239.2341 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 : 0.912 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 1 198 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.182595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146574 restraints weight = 25941.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.149709 restraints weight = 19095.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151661 restraints weight = 15578.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153391 restraints weight = 13635.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.154141 restraints weight = 12343.939| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.858 24143 Z= 0.480 Angle : 0.828 30.164 32571 Z= 0.454 Chirality : 0.050 0.293 3773 Planarity : 0.006 0.092 4193 Dihedral : 7.742 85.056 3457 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 3.51 % Allowed : 15.94 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3031 helix: 0.78 (0.14), residues: 1252 sheet: -0.64 (0.18), residues: 650 loop : -2.42 (0.15), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG 5 170 TYR 0.021 0.002 TYR E 213 PHE 0.034 0.002 PHE 5 211 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01255 (24143) covalent geometry : angle 0.82785 (32571) hydrogen bonds : bond 0.04892 ( 1337) hydrogen bonds : angle 5.77427 ( 3924) *********************** 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 632 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 543 time to evaluate : 0.915 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: 0.8602 (mmmt) cc_final: 0.7961 (mmtp) REVERT: A 228 GLU cc_start: 0.8619 (tt0) cc_final: 0.8390 (tt0) REVERT: A 234 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 190 VAL cc_start: 0.8873 (t) cc_final: 0.8673 (m) REVERT: B 239 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7559 (tpt170) REVERT: C 95 GLU cc_start: 0.8599 (tp30) cc_final: 0.8103 (tp30) REVERT: D 33 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7771 (ttm110) REVERT: D 56 SER cc_start: 0.8512 (p) cc_final: 0.8051 (p) REVERT: E 159 TYR cc_start: 0.9045 (m-80) cc_final: 0.8758 (m-80) REVERT: E 239 ARG cc_start: 0.7634 (ttt90) cc_final: 0.7241 (tpt-90) REVERT: 1 84 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8511 (mtpp) REVERT: 1 205 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6791 (mm-30) REVERT: 2 17 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7600 (pt) REVERT: 2 155 PHE cc_start: 0.7800 (t80) cc_final: 0.7491 (t80) REVERT: 3 52 MET cc_start: 0.8161 (mtm) cc_final: 0.7949 (mtm) REVERT: 3 84 LYS cc_start: 0.8820 (mttm) cc_final: 0.8547 (mtmt) REVERT: 3 106 TYR cc_start: 0.3251 (OUTLIER) cc_final: 0.1777 (t80) REVERT: 3 195 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7267 (tt0) REVERT: 3 206 GLN cc_start: 0.7412 (mp10) cc_final: 0.7141 (mp10) REVERT: 4 25 MET cc_start: 0.7247 (mtp) cc_final: 0.7029 (ttp) REVERT: 4 33 MET cc_start: -0.0935 (OUTLIER) cc_final: -0.1601 (mtm) REVERT: 5 159 ILE cc_start: 0.8381 (tt) cc_final: 0.8144 (mm) REVERT: 5 205 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: 7 44 LYS cc_start: 0.8153 (tppt) cc_final: 0.7602 (tptp) REVERT: 7 84 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8815 (mmmm) REVERT: 7 205 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.4340 (mp0) outliers start: 89 outliers final: 43 residues processed: 600 average time/residue: 0.1852 time to fit residues: 167.4238 Evaluate side-chains 492 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 444 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 98 ILE 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 36 THR Chi-restraints excluded: chain E residue 82 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 220 THR Chi-restraints excluded: chain F residue 233 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 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL 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 5 residue 205 GLU 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 17 LEU 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 47 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 174 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN 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 ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.183641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142610 restraints weight = 26361.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.147487 restraints weight = 16879.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.150677 restraints weight = 12616.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.152583 restraints weight = 10435.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.154046 restraints weight = 9262.010| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.842 24143 Z= 0.475 Angle : 0.744 30.145 32571 Z= 0.405 Chirality : 0.048 0.221 3773 Planarity : 0.005 0.065 4193 Dihedral : 6.695 87.267 3419 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.60 % Rotamer: Outliers : 4.38 % Allowed : 17.09 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3031 helix: 0.83 (0.14), residues: 1253 sheet: -0.53 (0.19), residues: 646 loop : -2.05 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG 5 170 TYR 0.023 0.002 TYR G 213 PHE 0.034 0.002 PHE 5 211 HIS 0.008 0.002 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01251 (24143) covalent geometry : angle 0.74424 (32571) hydrogen bonds : bond 0.04152 ( 1337) hydrogen bonds : angle 5.39054 ( 3924) *********************** 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 579 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 468 time to evaluate : 0.726 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: 0.8644 (mmmt) cc_final: 0.8057 (mmtp) REVERT: A 183 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8354 (mp) REVERT: A 234 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 121 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 190 VAL cc_start: 0.8888 (t) cc_final: 0.8655 (m) REVERT: B 239 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7580 (tpt170) REVERT: C 95 GLU cc_start: 0.8488 (tp30) cc_final: 0.7973 (tp30) REVERT: C 196 MET cc_start: 0.9080 (tpp) cc_final: 0.8804 (tpp) REVERT: C 217 ASP cc_start: 0.8444 (p0) cc_final: 0.8133 (p0) REVERT: D 33 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7967 (ttm110) REVERT: D 129 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8914 (m) REVERT: D 178 GLU cc_start: 0.7424 (tp30) cc_final: 0.7163 (tm-30) REVERT: E 22 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: E 222 LYS cc_start: 0.8559 (tttt) cc_final: 0.7961 (tttt) REVERT: F 121 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8083 (tm-30) REVERT: G 60 GLU cc_start: 0.7705 (tt0) cc_final: 0.7334 (tt0) REVERT: G 104 ASP cc_start: 0.8062 (t0) cc_final: 0.7815 (t0) REVERT: G 196 MET cc_start: 0.8825 (tpp) cc_final: 0.8445 (tpp) REVERT: 1 83 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8289 (ttp-110) REVERT: 1 84 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8510 (mtpp) REVERT: 2 88 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7339 (ttm-80) REVERT: 2 133 GLU cc_start: 0.8237 (tp30) cc_final: 0.7848 (tp30) REVERT: 3 52 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: 3 106 TYR cc_start: 0.3654 (OUTLIER) cc_final: 0.2031 (t80) REVERT: 4 25 MET cc_start: 0.7543 (mtp) cc_final: 0.7279 (ttm) REVERT: 4 33 MET cc_start: 0.0722 (OUTLIER) cc_final: -0.0036 (mtm) REVERT: 4 52 MET cc_start: 0.8279 (ttm) cc_final: 0.7989 (mtp) REVERT: 4 88 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7455 (ttm-80) REVERT: 5 51 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7333 (mmt180) REVERT: 5 110 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8659 (mt) REVERT: 5 120 LYS cc_start: 0.8041 (mptt) cc_final: 0.7838 (mttp) REVERT: 5 205 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6531 (tp30) REVERT: 6 25 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7061 (ttm) REVERT: 6 193 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7180 (tm-30) REVERT: 7 44 LYS cc_start: 0.7899 (tppt) cc_final: 0.7626 (tptp) REVERT: 7 51 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7596 (mmt-90) REVERT: 7 83 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.6884 (ttt90) REVERT: 7 84 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8899 (mmmm) REVERT: 7 133 GLU cc_start: 0.8296 (tp30) cc_final: 0.7853 (tp30) REVERT: 7 205 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.4815 (mp0) outliers start: 111 outliers final: 73 residues processed: 545 average time/residue: 0.1727 time to fit residues: 143.1521 Evaluate side-chains 511 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 428 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 89 ILE 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 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 78 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE 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 E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 36 THR 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 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 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 58 LEU 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 121 SER Chi-restraints excluded: chain 1 residue 132 ILE 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 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 5 residue 205 GLU 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 17 LEU 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 286 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 195 optimal weight: 0.0010 chunk 245 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 231 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 122 GLN 7 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.185255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.144529 restraints weight = 26032.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.149395 restraints weight = 16569.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.152374 restraints weight = 12340.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.154652 restraints weight = 10241.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.155846 restraints weight = 9011.408| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.841 24143 Z= 0.454 Angle : 0.675 30.154 32571 Z= 0.368 Chirality : 0.046 0.184 3773 Planarity : 0.004 0.049 4193 Dihedral : 6.323 89.742 3418 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.77 % Favored : 97.06 % Rotamer: Outliers : 4.10 % Allowed : 18.82 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3031 helix: 0.96 (0.14), residues: 1258 sheet: -0.35 (0.19), residues: 643 loop : -1.82 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 5 170 TYR 0.018 0.001 TYR 5 173 PHE 0.033 0.002 PHE 5 211 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01208 (24143) covalent geometry : angle 0.67469 (32571) hydrogen bonds : bond 0.03681 ( 1337) hydrogen bonds : angle 5.17045 ( 3924) *********************** 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 551 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 447 time to evaluate : 0.824 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: 0.8729 (mmmt) cc_final: 0.8052 (mmtp) REVERT: A 143 GLU cc_start: 0.6531 (pt0) cc_final: 0.6061 (pm20) REVERT: A 183 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8371 (mp) REVERT: B 104 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (t0) REVERT: B 121 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 239 ARG cc_start: 0.7828 (tpt170) cc_final: 0.7570 (tpt170) REVERT: C 95 GLU cc_start: 0.8375 (tp30) cc_final: 0.7912 (tp30) REVERT: C 217 ASP cc_start: 0.8333 (p0) cc_final: 0.8111 (p0) REVERT: D 129 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8945 (m) REVERT: D 178 GLU cc_start: 0.7414 (tp30) cc_final: 0.7179 (tm-30) REVERT: E 38 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8429 (mt) REVERT: E 71 ASP cc_start: 0.8230 (t0) cc_final: 0.7944 (t0) REVERT: E 239 ARG cc_start: 0.7342 (ttt90) cc_final: 0.7021 (tpt-90) REVERT: F 121 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7894 (tm-30) REVERT: G 104 ASP cc_start: 0.7963 (t0) cc_final: 0.7506 (t0) REVERT: G 196 MET cc_start: 0.8758 (tpp) cc_final: 0.8418 (tpp) REVERT: G 208 ASN cc_start: 0.7665 (p0) cc_final: 0.7450 (p0) REVERT: G 242 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7628 (mm-30) REVERT: 1 84 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8472 (mtpp) REVERT: 1 88 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.6846 (ttm-80) REVERT: 3 25 MET cc_start: 0.8031 (ptm) cc_final: 0.7812 (ptp) REVERT: 3 52 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8082 (mtm) REVERT: 3 106 TYR cc_start: 0.3496 (OUTLIER) cc_final: 0.1674 (t80) REVERT: 3 118 GLU cc_start: 0.8169 (pp20) cc_final: 0.7823 (pp20) REVERT: 4 25 MET cc_start: 0.7490 (mtp) cc_final: 0.7224 (ttm) REVERT: 4 33 MET cc_start: -0.0747 (OUTLIER) cc_final: -0.1256 (mtm) REVERT: 4 88 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7530 (ttm-80) REVERT: 4 163 GLU cc_start: 0.8450 (tp30) cc_final: 0.7935 (mp0) REVERT: 5 51 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7292 (mmt180) REVERT: 5 205 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: 6 25 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6994 (ttm) REVERT: 6 88 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7743 (ttp-110) REVERT: 7 25 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6616 (ttp) REVERT: 7 44 LYS cc_start: 0.7915 (tppt) cc_final: 0.7496 (tptp) REVERT: 7 84 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8880 (mmmm) REVERT: 7 205 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.4885 (mp0) outliers start: 104 outliers final: 67 residues processed: 513 average time/residue: 0.1654 time to fit residues: 130.3764 Evaluate side-chains 489 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 411 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 104 ASP 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 C residue 243 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 129 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 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 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 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 87 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 121 SER 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 176 MET Chi-restraints excluded: chain 2 residue 60 VAL 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 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 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 25 MET 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 121 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 0.1980 chunk 177 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN 3 35 ASN ** 3 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 198 GLN 6 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.182133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140627 restraints weight = 26106.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.145370 restraints weight = 16870.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.148530 restraints weight = 12743.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150165 restraints weight = 10597.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.151367 restraints weight = 9475.350| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.842 24143 Z= 0.470 Angle : 0.691 30.030 32571 Z= 0.375 Chirality : 0.047 0.201 3773 Planarity : 0.004 0.046 4193 Dihedral : 6.129 88.414 3414 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.40 % Favored : 96.44 % Rotamer: Outliers : 4.97 % Allowed : 19.18 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3031 helix: 0.93 (0.14), residues: 1252 sheet: -0.37 (0.19), residues: 638 loop : -1.78 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.020 0.002 TYR E 213 PHE 0.032 0.002 PHE 5 211 HIS 0.003 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.01243 (24143) covalent geometry : angle 0.69078 (32571) hydrogen bonds : bond 0.03739 ( 1337) hydrogen bonds : angle 5.20945 ( 3924) *********************** 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 566 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 440 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8179 (mmtp) REVERT: A 183 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 196 MET cc_start: 0.8727 (mmm) cc_final: 0.8394 (tpp) REVERT: B 104 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 121 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 234 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7602 (mp0) REVERT: C 65 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6558 (mm-30) REVERT: C 95 GLU cc_start: 0.8397 (tp30) cc_final: 0.7904 (tp30) REVERT: C 196 MET cc_start: 0.9057 (tpp) cc_final: 0.8793 (tpp) REVERT: D 103 TYR cc_start: 0.9107 (m-80) cc_final: 0.8907 (m-80) REVERT: D 178 GLU cc_start: 0.7655 (tp30) cc_final: 0.7279 (tm-30) REVERT: E 38 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8504 (mt) REVERT: E 71 ASP cc_start: 0.8308 (t0) cc_final: 0.7995 (t0) REVERT: E 222 LYS cc_start: 0.8667 (tttt) cc_final: 0.7883 (tttt) REVERT: E 239 ARG cc_start: 0.7506 (ttt90) cc_final: 0.7069 (tpt-90) REVERT: F 121 GLN cc_start: 0.8577 (tm-30) cc_final: 0.7930 (tm-30) REVERT: F 194 VAL cc_start: 0.8928 (t) cc_final: 0.8703 (m) REVERT: F 198 LEU cc_start: 0.8529 (tp) cc_final: 0.8132 (mt) REVERT: G 60 GLU cc_start: 0.7855 (tt0) cc_final: 0.7596 (tp30) REVERT: G 104 ASP cc_start: 0.8019 (t0) cc_final: 0.7689 (t0) REVERT: G 196 MET cc_start: 0.8763 (tpp) cc_final: 0.8422 (tpp) REVERT: 1 83 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8367 (ttp80) REVERT: 2 163 GLU cc_start: 0.7559 (pm20) cc_final: 0.7129 (pm20) REVERT: 3 51 ARG cc_start: 0.7997 (mmp80) cc_final: 0.7603 (mmp80) REVERT: 3 52 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: 3 106 TYR cc_start: 0.3330 (OUTLIER) cc_final: 0.1350 (t80) REVERT: 4 33 MET cc_start: -0.1009 (OUTLIER) cc_final: -0.1714 (mtm) REVERT: 4 88 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7483 (ttm-80) REVERT: 4 163 GLU cc_start: 0.8453 (tp30) cc_final: 0.7916 (mp0) REVERT: 5 51 ARG cc_start: 0.7933 (mmp80) cc_final: 0.7364 (mmt180) REVERT: 5 110 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8671 (mt) REVERT: 5 156 THR cc_start: 0.8766 (t) cc_final: 0.8412 (m) REVERT: 5 205 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: 6 88 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.7863 (ttp-110) REVERT: 6 152 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7565 (mt-10) REVERT: 6 154 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6504 (mtt-85) REVERT: 7 25 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6748 (ttm) REVERT: 7 44 LYS cc_start: 0.7846 (tppt) cc_final: 0.7427 (tptp) REVERT: 7 84 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8861 (mmmm) REVERT: 7 133 GLU cc_start: 0.8307 (tp30) cc_final: 0.7736 (tp30) REVERT: 7 205 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.4814 (mp0) outliers start: 126 outliers final: 88 residues processed: 519 average time/residue: 0.1747 time to fit residues: 140.7094 Evaluate side-chains 526 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 427 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 166 MET 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 98 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 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 82 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 190 VAL 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 82 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 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 38 ILE 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 214 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 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 58 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET 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 121 SER 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 176 MET Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 72 ILE 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 17 LEU 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 14 THR 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 33 MET 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 136 ASP Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 17 LEU 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 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 136 ASP 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 159 optimal weight: 0.2980 chunk 234 optimal weight: 3.9990 chunk 121 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 288 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 chunk 285 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 96 ASN 4 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.178410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135060 restraints weight = 25893.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140033 restraints weight = 16369.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.143294 restraints weight = 12219.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.145272 restraints weight = 10132.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146710 restraints weight = 8993.164| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.841 24143 Z= 0.441 Angle : 0.639 29.968 32571 Z= 0.347 Chirality : 0.045 0.186 3773 Planarity : 0.004 0.046 4193 Dihedral : 5.864 87.745 3413 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 4.03 % Allowed : 21.19 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3031 helix: 1.15 (0.15), residues: 1244 sheet: -0.37 (0.19), residues: 647 loop : -1.64 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.016 0.001 TYR G 103 PHE 0.031 0.001 PHE 5 211 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01183 (24143) covalent geometry : angle 0.63855 (32571) hydrogen bonds : bond 0.03406 ( 1337) hydrogen bonds : angle 5.03842 ( 3924) *********************** 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 532 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 430 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8160 (mmtp) REVERT: A 183 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 196 MET cc_start: 0.8757 (mmm) cc_final: 0.8387 (tpp) REVERT: B 104 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8153 (t0) REVERT: B 121 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 95 GLU cc_start: 0.8337 (tp30) cc_final: 0.7880 (tp30) REVERT: C 196 MET cc_start: 0.8986 (tpp) cc_final: 0.8731 (tpp) REVERT: C 217 ASP cc_start: 0.8322 (p0) cc_final: 0.8121 (p0) REVERT: D 153 SER cc_start: 0.8808 (t) cc_final: 0.8506 (p) REVERT: D 178 GLU cc_start: 0.7481 (tp30) cc_final: 0.7274 (tm-30) REVERT: E 71 ASP cc_start: 0.8303 (t0) cc_final: 0.7978 (t0) REVERT: E 222 LYS cc_start: 0.8650 (tttt) cc_final: 0.7963 (tttt) REVERT: E 239 ARG cc_start: 0.7492 (ttt90) cc_final: 0.7191 (tpt-90) REVERT: F 121 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7777 (tm-30) REVERT: G 60 GLU cc_start: 0.7804 (tt0) cc_final: 0.7520 (tp30) REVERT: G 104 ASP cc_start: 0.7942 (t0) cc_final: 0.7591 (t0) REVERT: G 196 MET cc_start: 0.8762 (tpp) cc_final: 0.8418 (tpp) REVERT: 1 83 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8326 (mtm-85) REVERT: 2 44 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7424 (tttt) REVERT: 2 121 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8988 (p) REVERT: 2 163 GLU cc_start: 0.7391 (pm20) cc_final: 0.7181 (pm20) REVERT: 3 51 ARG cc_start: 0.8030 (mmp80) cc_final: 0.7575 (mmp80) REVERT: 3 52 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8080 (mtm) REVERT: 3 106 TYR cc_start: 0.3069 (OUTLIER) cc_final: 0.0910 (t80) REVERT: 4 25 MET cc_start: 0.7213 (mtp) cc_final: 0.6912 (ttp) REVERT: 4 33 MET cc_start: -0.0896 (OUTLIER) cc_final: -0.1590 (mtm) REVERT: 4 88 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7718 (ttm-80) REVERT: 4 158 GLU cc_start: 0.7431 (tp30) cc_final: 0.7186 (tp30) REVERT: 4 163 GLU cc_start: 0.8386 (tp30) cc_final: 0.7869 (mp0) REVERT: 5 45 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6211 (mm) REVERT: 5 51 ARG cc_start: 0.7899 (mmp80) cc_final: 0.7417 (mmt180) REVERT: 5 110 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8692 (mt) REVERT: 5 120 LYS cc_start: 0.8215 (mttp) cc_final: 0.7921 (mttp) REVERT: 5 156 THR cc_start: 0.8801 (t) cc_final: 0.8501 (m) REVERT: 5 205 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6593 (tp30) REVERT: 6 154 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6380 (mtt-85) REVERT: 7 44 LYS cc_start: 0.7757 (tppt) cc_final: 0.7325 (tptp) REVERT: 7 51 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.7777 (mmt-90) REVERT: 7 84 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8795 (mmmm) REVERT: 7 133 GLU cc_start: 0.8209 (tp30) cc_final: 0.7651 (tp30) REVERT: 7 205 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.4832 (mp0) outliers start: 102 outliers final: 75 residues processed: 499 average time/residue: 0.1670 time to fit residues: 128.5820 Evaluate side-chains 503 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 417 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 144 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 183 LEU 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 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 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 82 VAL Chi-restraints excluded: chain D residue 98 ILE 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 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 82 VAL 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 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 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 121 SER 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 176 MET Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 72 ILE 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 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 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 55 THR Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 205 GLU 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 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 11 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 78 optimal weight: 0.0000 chunk 39 optimal weight: 0.4980 chunk 85 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 chunk 246 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 249 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 191 optimal weight: 0.5980 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3944 r_free = 0.3944 target = 0.185575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142142 restraints weight = 25999.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.147360 restraints weight = 16169.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.150728 restraints weight = 11955.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.152952 restraints weight = 9805.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.154254 restraints weight = 8671.170| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.840 24143 Z= 0.440 Angle : 0.633 29.952 32571 Z= 0.343 Chirality : 0.045 0.238 3773 Planarity : 0.004 0.045 4193 Dihedral : 5.739 86.889 3411 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 4.58 % Allowed : 20.88 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 3031 helix: 1.24 (0.15), residues: 1253 sheet: -0.33 (0.19), residues: 649 loop : -1.56 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.014 0.001 TYR E 213 PHE 0.030 0.001 PHE 5 211 HIS 0.002 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01181 (24143) covalent geometry : angle 0.63265 (32571) hydrogen bonds : bond 0.03352 ( 1337) hydrogen bonds : angle 4.96209 ( 3924) *********************** 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 543 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 427 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8799 (mmm) cc_final: 0.8384 (tpp) REVERT: B 104 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8097 (t0) REVERT: B 121 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 95 GLU cc_start: 0.8316 (tp30) cc_final: 0.7836 (tp30) REVERT: C 196 MET cc_start: 0.8982 (tpp) cc_final: 0.8704 (tpp) REVERT: C 217 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8125 (p0) REVERT: D 153 SER cc_start: 0.8807 (t) cc_final: 0.8497 (p) REVERT: E 71 ASP cc_start: 0.8352 (t0) cc_final: 0.8007 (t0) REVERT: E 239 ARG cc_start: 0.7498 (ttt90) cc_final: 0.7238 (tpt-90) REVERT: F 121 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 196 MET cc_start: 0.8769 (tpp) cc_final: 0.8445 (tpp) REVERT: G 208 ASN cc_start: 0.7914 (p0) cc_final: 0.7345 (p0) REVERT: 1 83 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8314 (mtm-85) REVERT: 2 121 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8971 (p) REVERT: 3 51 ARG cc_start: 0.8037 (mmp80) cc_final: 0.7569 (mmp80) REVERT: 3 52 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8081 (mtm) REVERT: 3 106 TYR cc_start: 0.3006 (OUTLIER) cc_final: 0.0758 (t80) REVERT: 3 118 GLU cc_start: 0.8155 (pp20) cc_final: 0.7694 (pp20) REVERT: 4 33 MET cc_start: -0.0804 (OUTLIER) cc_final: -0.1512 (mtm) REVERT: 4 88 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7699 (ttm-80) REVERT: 4 163 GLU cc_start: 0.8399 (tp30) cc_final: 0.7862 (mp0) REVERT: 5 51 ARG cc_start: 0.7846 (mmp80) cc_final: 0.7353 (mmt180) REVERT: 5 55 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7517 (p) REVERT: 5 110 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8702 (mt) REVERT: 5 120 LYS cc_start: 0.8219 (mttp) cc_final: 0.7994 (mttp) REVERT: 5 205 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6722 (tp30) REVERT: 6 154 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6369 (mtt-85) REVERT: 7 25 MET cc_start: 0.7012 (mtp) cc_final: 0.6778 (ttm) REVERT: 7 44 LYS cc_start: 0.7744 (tppt) cc_final: 0.7259 (tptp) REVERT: 7 51 ARG cc_start: 0.8212 (mmt-90) cc_final: 0.7087 (mmt180) REVERT: 7 83 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8113 (ttp-170) REVERT: 7 84 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8798 (mmmm) REVERT: 7 133 GLU cc_start: 0.8219 (tp30) cc_final: 0.7705 (tp30) REVERT: 7 205 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.4812 (mp0) outliers start: 116 outliers final: 86 residues processed: 506 average time/residue: 0.1744 time to fit residues: 136.0830 Evaluate side-chains 507 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 410 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 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 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 157 LEU 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 13 THR Chi-restraints excluded: chain D residue 38 ILE 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 204 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 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 82 VAL 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 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 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 132 ILE 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 176 MET Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 72 ILE 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 17 LEU 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 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 55 THR Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 17 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 252 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 159 optimal weight: 0.2980 chunk 289 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN 3 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.175676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.131701 restraints weight = 25902.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136778 restraints weight = 16128.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.140070 restraints weight = 11950.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.142209 restraints weight = 9850.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.143285 restraints weight = 8726.138| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.840 24143 Z= 0.469 Angle : 0.690 29.947 32571 Z= 0.371 Chirality : 0.047 0.232 3773 Planarity : 0.004 0.043 4193 Dihedral : 5.816 88.736 3409 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.85 % Allowed : 21.39 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3031 helix: 1.09 (0.15), residues: 1243 sheet: -0.40 (0.19), residues: 645 loop : -1.58 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.019 0.002 TYR E 213 PHE 0.031 0.002 PHE 5 211 HIS 0.003 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.01244 (24143) covalent geometry : angle 0.68966 (32571) hydrogen bonds : bond 0.03592 ( 1337) hydrogen bonds : angle 5.12895 ( 3924) *********************** 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 551 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 428 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8843 (mmm) cc_final: 0.8383 (tpp) REVERT: B 104 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8248 (t0) REVERT: B 121 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8048 (tm-30) REVERT: C 95 GLU cc_start: 0.8359 (tp30) cc_final: 0.7861 (tp30) REVERT: C 196 MET cc_start: 0.9001 (tpp) cc_final: 0.8720 (tpp) REVERT: E 71 ASP cc_start: 0.8368 (t0) cc_final: 0.8065 (t0) REVERT: F 121 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7845 (tm-30) REVERT: F 198 LEU cc_start: 0.8530 (tp) cc_final: 0.8193 (mp) REVERT: G 104 ASP cc_start: 0.8028 (t0) cc_final: 0.7631 (t0) REVERT: G 196 MET cc_start: 0.8709 (tpp) cc_final: 0.8343 (tpp) REVERT: G 208 ASN cc_start: 0.7919 (p0) cc_final: 0.7449 (p0) REVERT: 1 29 LYS cc_start: 0.8099 (tttt) cc_final: 0.7765 (ttmm) REVERT: 1 83 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8258 (mtm-85) REVERT: 2 163 GLU cc_start: 0.7168 (pm20) cc_final: 0.6449 (pt0) REVERT: 3 52 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8116 (mtm) REVERT: 3 106 TYR cc_start: 0.2933 (OUTLIER) cc_final: 0.0637 (t80) REVERT: 4 33 MET cc_start: -0.0822 (OUTLIER) cc_final: -0.1493 (mtm) REVERT: 4 88 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7813 (ttm-80) REVERT: 4 158 GLU cc_start: 0.7005 (tp30) cc_final: 0.6232 (tp30) REVERT: 4 163 GLU cc_start: 0.8399 (tp30) cc_final: 0.7778 (pm20) REVERT: 5 51 ARG cc_start: 0.7894 (mmp80) cc_final: 0.7267 (mmt180) REVERT: 5 55 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7374 (p) REVERT: 5 110 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8731 (mt) REVERT: 5 205 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6536 (tp30) REVERT: 6 83 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8117 (ptt90) REVERT: 6 133 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7104 (tm-30) REVERT: 6 154 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6467 (mtt-85) REVERT: 7 44 LYS cc_start: 0.7801 (tppt) cc_final: 0.7319 (tptp) REVERT: 7 51 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7165 (mmt-90) REVERT: 7 84 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8789 (mmmm) REVERT: 7 133 GLU cc_start: 0.8188 (tp30) cc_final: 0.7732 (tp30) REVERT: 7 205 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.4977 (mp0) outliers start: 123 outliers final: 99 residues processed: 512 average time/residue: 0.1653 time to fit residues: 131.2927 Evaluate side-chains 532 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 424 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 38 ILE 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 129 VAL 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 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 THR 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 157 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 40 ILE 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 198 LEU Chi-restraints excluded: chain D residue 204 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 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 E residue 149 GLU Chi-restraints excluded: chain E residue 214 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 82 VAL 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 58 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 98 ILE 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 14 THR Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 132 ILE 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 176 MET Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 72 ILE 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 17 LEU Chi-restraints excluded: chain 3 residue 52 MET Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 90 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 45 ILE Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 205 GLU 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 205 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 266 optimal weight: 0.5980 chunk 267 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 178 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3905 r_free = 0.3905 target = 0.181444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138526 restraints weight = 25917.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.143554 restraints weight = 16148.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.146839 restraints weight = 11948.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.148708 restraints weight = 9866.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.150227 restraints weight = 8771.002| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.839 24143 Z= 0.453 Angle : 0.667 29.927 32571 Z= 0.360 Chirality : 0.046 0.249 3773 Planarity : 0.004 0.043 4193 Dihedral : 5.750 89.122 3409 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 4.54 % Allowed : 21.82 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 3031 helix: 1.14 (0.15), residues: 1249 sheet: -0.33 (0.19), residues: 631 loop : -1.53 (0.16), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.018 0.001 TYR F 159 PHE 0.029 0.001 PHE 5 211 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01211 (24143) covalent geometry : angle 0.66737 (32571) hydrogen bonds : bond 0.03449 ( 1337) hydrogen bonds : angle 5.09990 ( 3924) *********************** 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 557 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 442 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8442 (ttpt) REVERT: A 196 MET cc_start: 0.8820 (mmm) cc_final: 0.8373 (tpp) REVERT: B 104 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (t0) REVERT: B 121 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 38 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7877 (mt) REVERT: C 95 GLU cc_start: 0.8325 (tp30) cc_final: 0.7834 (tp30) REVERT: C 196 MET cc_start: 0.8995 (tpp) cc_final: 0.8638 (tpp) REVERT: D 153 SER cc_start: 0.8937 (t) cc_final: 0.8607 (p) REVERT: E 71 ASP cc_start: 0.8385 (t0) cc_final: 0.8040 (t0) REVERT: E 239 ARG cc_start: 0.7550 (ttt90) cc_final: 0.7298 (tpt-90) REVERT: F 121 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7796 (tm-30) REVERT: F 198 LEU cc_start: 0.8511 (tp) cc_final: 0.8235 (mp) REVERT: G 104 ASP cc_start: 0.7992 (t0) cc_final: 0.7647 (t0) REVERT: G 196 MET cc_start: 0.8704 (tpp) cc_final: 0.8390 (tpp) REVERT: G 208 ASN cc_start: 0.7875 (p0) cc_final: 0.7461 (p0) REVERT: 1 29 LYS cc_start: 0.8116 (tttt) cc_final: 0.7769 (ttmm) REVERT: 1 83 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8261 (mtm-85) REVERT: 2 163 GLU cc_start: 0.7237 (pm20) cc_final: 0.6610 (pt0) REVERT: 2 206 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7578 (tp40) REVERT: 3 51 ARG cc_start: 0.8240 (mmp80) cc_final: 0.7967 (mmp80) REVERT: 3 52 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8054 (mtm) REVERT: 3 106 TYR cc_start: 0.3439 (OUTLIER) cc_final: 0.1146 (t80) REVERT: 3 118 GLU cc_start: 0.8005 (pp20) cc_final: 0.7567 (pp20) REVERT: 4 33 MET cc_start: -0.0675 (OUTLIER) cc_final: -0.1457 (mtm) REVERT: 4 54 MET cc_start: 0.7727 (ttt) cc_final: 0.7517 (ttt) REVERT: 4 88 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7779 (ttm-80) REVERT: 4 158 GLU cc_start: 0.6879 (tp30) cc_final: 0.6046 (tp30) REVERT: 4 163 GLU cc_start: 0.8355 (tp30) cc_final: 0.7825 (pm20) REVERT: 5 51 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7330 (mmt180) REVERT: 5 55 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7325 (p) REVERT: 5 110 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8757 (mt) REVERT: 5 205 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6545 (tp30) REVERT: 6 30 ARG cc_start: 0.4713 (OUTLIER) cc_final: 0.3145 (tpm170) REVERT: 6 83 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8024 (ptt90) REVERT: 6 133 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7014 (tm-30) REVERT: 6 154 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6450 (mtt-85) REVERT: 6 158 GLU cc_start: 0.7547 (tp30) cc_final: 0.7174 (tp30) REVERT: 7 44 LYS cc_start: 0.7762 (tppt) cc_final: 0.7208 (tptp) REVERT: 7 51 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.7157 (mmt-90) REVERT: 7 84 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8781 (mmmm) REVERT: 7 205 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.4987 (mp0) REVERT: 7 206 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7743 (tm-30) outliers start: 115 outliers final: 97 residues processed: 521 average time/residue: 0.1752 time to fit residues: 141.8358 Evaluate side-chains 541 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 433 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 38 ILE 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 38 ILE 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 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 190 VAL 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 67 ILE 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 204 LEU Chi-restraints excluded: chain D residue 205 VAL 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 E residue 149 GLU Chi-restraints excluded: chain E residue 214 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 82 VAL 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 98 ILE 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 14 THR Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 132 ILE 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 176 MET Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 72 ILE 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 17 LEU Chi-restraints excluded: chain 3 residue 52 MET 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 87 VAL 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 69 ILE Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 30 ARG 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 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 191 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 280 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 297 optimal weight: 0.8980 chunk 295 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3850 r_free = 0.3850 target = 0.176345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.132767 restraints weight = 26070.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137838 restraints weight = 16166.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.141133 restraints weight = 11941.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.143235 restraints weight = 9838.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.144677 restraints weight = 8673.716| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.838 24143 Z= 0.464 Angle : 0.692 29.918 32571 Z= 0.372 Chirality : 0.047 0.272 3773 Planarity : 0.004 0.042 4193 Dihedral : 5.766 86.065 3409 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 4.62 % Allowed : 21.82 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.15), residues: 3031 helix: 1.03 (0.14), residues: 1256 sheet: -0.38 (0.20), residues: 637 loop : -1.49 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.020 0.002 TYR G 103 PHE 0.029 0.002 PHE 5 211 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01234 (24143) covalent geometry : angle 0.69169 (32571) hydrogen bonds : bond 0.03559 ( 1337) hydrogen bonds : angle 5.17969 ( 3924) ********************** 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 559 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 442 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8245 (ttpt) REVERT: A 196 MET cc_start: 0.8836 (mmm) cc_final: 0.8374 (tpp) REVERT: B 104 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8174 (t0) REVERT: B 121 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 38 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7904 (mt) REVERT: C 95 GLU cc_start: 0.8338 (tp30) cc_final: 0.7881 (tp30) REVERT: C 196 MET cc_start: 0.8961 (tpp) cc_final: 0.8672 (tpp) REVERT: D 153 SER cc_start: 0.8948 (t) cc_final: 0.8604 (p) REVERT: E 204 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8099 (mm) REVERT: E 239 ARG cc_start: 0.7630 (ttt90) cc_final: 0.7344 (tpt-90) REVERT: F 121 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7824 (tm-30) REVERT: F 198 LEU cc_start: 0.8571 (tp) cc_final: 0.8276 (mp) REVERT: G 104 ASP cc_start: 0.8051 (t0) cc_final: 0.7684 (t0) REVERT: G 182 ASP cc_start: 0.7918 (p0) cc_final: 0.7572 (p0) REVERT: G 196 MET cc_start: 0.8722 (tpp) cc_final: 0.8371 (tpp) REVERT: G 208 ASN cc_start: 0.7869 (p0) cc_final: 0.7505 (p0) REVERT: 1 29 LYS cc_start: 0.8131 (tttt) cc_final: 0.7789 (ttmm) REVERT: 1 83 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8260 (mtm-85) REVERT: 2 163 GLU cc_start: 0.7241 (pm20) cc_final: 0.6644 (pt0) REVERT: 3 51 ARG cc_start: 0.8113 (mmp80) cc_final: 0.7797 (mmp80) REVERT: 3 106 TYR cc_start: 0.3443 (OUTLIER) cc_final: 0.1041 (t80) REVERT: 4 33 MET cc_start: -0.0613 (OUTLIER) cc_final: -0.1366 (mtm) REVERT: 4 88 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7877 (ttm-80) REVERT: 4 158 GLU cc_start: 0.7066 (tp30) cc_final: 0.6228 (tp30) REVERT: 4 163 GLU cc_start: 0.8400 (tp30) cc_final: 0.7955 (mp0) REVERT: 5 51 ARG cc_start: 0.7937 (mmp80) cc_final: 0.7699 (mmt180) REVERT: 5 55 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7331 (p) REVERT: 5 110 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8740 (mt) REVERT: 5 205 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6628 (tp30) REVERT: 6 30 ARG cc_start: 0.4773 (OUTLIER) cc_final: 0.3169 (tpm170) REVERT: 6 83 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8075 (ptt90) REVERT: 6 154 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6393 (mtt-85) REVERT: 6 158 GLU cc_start: 0.7600 (tp30) cc_final: 0.7231 (tp30) REVERT: 7 44 LYS cc_start: 0.7855 (tppt) cc_final: 0.7284 (tptp) REVERT: 7 51 ARG cc_start: 0.8372 (mmt-90) cc_final: 0.7248 (mmt-90) REVERT: 7 84 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8795 (mmmm) REVERT: 7 205 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.4940 (mp0) REVERT: 7 206 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7802 (tm-30) outliers start: 117 outliers final: 101 residues processed: 520 average time/residue: 0.1759 time to fit residues: 142.5496 Evaluate side-chains 546 residues out of total 2534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 434 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 38 ILE 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 38 ILE 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 78 THR 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 190 VAL 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 40 ILE 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 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL 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 E residue 149 GLU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 82 VAL 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 G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 98 ILE 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 14 THR Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 132 ILE 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 176 MET Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 72 ILE 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 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 90 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 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 69 ILE Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 25 MET Chi-restraints excluded: chain 6 residue 30 ARG 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 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 288 optimal weight: 0.4980 chunk 287 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 124 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3861 r_free = 0.3861 target = 0.177374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133947 restraints weight = 25780.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.139013 restraints weight = 15984.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.142316 restraints weight = 11813.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.144370 restraints weight = 9726.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.145783 restraints weight = 8598.937| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.837 24143 Z= 0.452 Angle : 0.671 29.917 32571 Z= 0.361 Chirality : 0.046 0.290 3773 Planarity : 0.004 0.043 4193 Dihedral : 5.664 82.962 3409 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 4.50 % Allowed : 22.06 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3031 helix: 1.12 (0.14), residues: 1254 sheet: -0.34 (0.20), residues: 637 loop : -1.44 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.018 0.001 TYR F 159 PHE 0.028 0.001 PHE 5 211 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.01208 (24143) covalent geometry : angle 0.67072 (32571) hydrogen bonds : bond 0.03416 ( 1337) hydrogen bonds : angle 5.13561 ( 3924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4107.85 seconds wall clock time: 71 minutes 51.54 seconds (4311.54 seconds total)