Starting phenix.real_space_refine on Fri Jun 5 22:15:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6he5_0210/06_2026/6he5_0210.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he5_0210/06_2026/6he5_0210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2026/6he5_0210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2026/6he5_0210.map" model { file = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2026/6he5_0210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2026/6he5_0210.cif" } resolution = 4.12 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= 0.003 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 97 5.16 5 C 15633 2.51 5 N 4127 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 412 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24633 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "C" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "D" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "F" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "G" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "1" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'TRANS': 6} Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'TRANS': 7} Time building chain proxies: 6.30, per 1000 atoms: 0.26 Number of scatterers: 24633 At special positions: 0 Unit cell: (131.32, 134, 108.54, 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 97 16.00 O 4776 8.00 N 4127 7.00 C 15633 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 33 sheets defined 40.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.806A pdb=" N LYS A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 34' Processing helix chain 'A' and resid 81 through 103 removed outlier: 3.844A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.561A pdb=" N LYS A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.801A pdb=" N GLU A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.518A pdb=" N ILE A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 225 through 244 removed outlier: 3.651A pdb=" N LYS A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.710A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.513A pdb=" N VAL B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 removed outlier: 3.790A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.631A pdb=" N TYR B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.584A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 201 Processing helix chain 'B' and resid 225 through 245 Proline residue: B 231 - end of helix removed outlier: 4.066A pdb=" N GLU B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 81 through 103 removed outlier: 3.916A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.836A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 201 Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.762A pdb=" N LYS C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Proline residue: C 231 - end of helix removed outlier: 3.638A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.557A 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 103 removed outlier: 3.866A pdb=" N VAL D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.588A pdb=" N GLU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 225 through 243 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: 4.615A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.573A pdb=" N ARG E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.578A pdb=" N ARG E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.717A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.969A pdb=" N LYS E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.627A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.877A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 104 removed outlier: 3.747A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.574A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 225 through 244 removed outlier: 3.597A pdb=" N LYS F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 4.106A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.781A pdb=" N GLU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 104 removed outlier: 3.889A pdb=" N VAL G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.758A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.843A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 229 through 246 removed outlier: 4.077A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain '1' and resid 59 through 82 removed outlier: 3.603A pdb=" N PHE 1 65 " --> pdb=" O GLY 1 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE 1 69 " --> pdb=" O PHE 1 65 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 101 removed outlier: 3.753A pdb=" N ILE 1 90 " --> pdb=" O THR 1 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER 1 95 " --> pdb=" O ALA 1 91 " (cutoff:3.500A) Processing helix chain '1' and resid 143 through 153 removed outlier: 4.660A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 179 removed outlier: 3.608A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP 1 179 " --> pdb=" O ALA 1 175 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 208 removed outlier: 4.326A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE 1 207 " --> pdb=" O GLU 1 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 1 208 " --> pdb=" O VAL 1 204 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.711A pdb=" N ARG 2 68 " --> pdb=" O GLN 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 removed outlier: 3.669A pdb=" N ILE 2 90 " --> pdb=" O THR 2 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 2 96 " --> pdb=" O THR 2 92 " (cutoff:3.500A) Processing helix chain '2' and resid 143 through 153 removed outlier: 3.596A pdb=" N ASP 2 153 " --> pdb=" O GLY 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 177 removed outlier: 3.950A pdb=" N LEU 2 167 " --> pdb=" O GLU 2 163 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS 2 177 " --> pdb=" O TYR 2 173 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 206 removed outlier: 4.225A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 removed outlier: 3.616A pdb=" N ALA 3 63 " --> pdb=" O SER 3 59 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE 3 69 " --> pdb=" O PHE 3 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 3 70 " --> pdb=" O LEU 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 101 Processing helix chain '3' and resid 143 through 154 removed outlier: 4.111A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 3 150 " --> pdb=" O THR 3 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP 3 153 " --> pdb=" O GLY 3 149 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 176 removed outlier: 3.560A pdb=" N GLU 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA 3 175 " --> pdb=" O ALA 3 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET 3 176 " --> pdb=" O ILE 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 200 through 206 Processing helix chain '4' and resid 59 through 82 removed outlier: 3.709A pdb=" N ILE 4 69 " --> pdb=" O PHE 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 Processing helix chain '4' and resid 143 through 154 removed outlier: 3.790A pdb=" N VAL 4 150 " --> pdb=" O THR 4 146 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP 4 153 " --> pdb=" O GLY 4 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 4 154 " --> pdb=" O VAL 4 150 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 removed outlier: 3.885A pdb=" N GLU 4 166 " --> pdb=" O ASP 4 162 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 4 175 " --> pdb=" O ALA 4 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 209 removed outlier: 3.924A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE 4 207 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 82 removed outlier: 3.605A pdb=" N ALA 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE 5 65 " --> pdb=" O GLY 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 152 removed outlier: 3.559A pdb=" N GLU 5 152 " --> pdb=" O TYR 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.908A pdb=" N GLU 5 166 " --> pdb=" O ASP 5 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER 5 174 " --> pdb=" O ARG 5 170 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET 5 176 " --> pdb=" O ILE 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 179 through 184 removed outlier: 3.781A pdb=" N SER 5 182 " --> pdb=" O ASP 5 179 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP 5 184 " --> pdb=" O ALA 5 181 " (cutoff:3.500A) Processing helix chain '5' and resid 199 through 206 removed outlier: 4.443A pdb=" N GLU 5 203 " --> pdb=" O TYR 5 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL 5 204 " --> pdb=" O SER 5 200 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.732A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.511A pdb=" N ILE 6 90 " --> pdb=" O THR 6 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 6 100 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR 6 101 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 155 removed outlier: 3.630A pdb=" N GLY 6 149 " --> pdb=" O LEU 6 145 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.506A pdb=" N ALA 6 164 " --> pdb=" O GLY 6 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 6 166 " --> pdb=" O ASP 6 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE 6 172 " --> pdb=" O ALA 6 168 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.122A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 6 204 " --> pdb=" O SER 6 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN 6 206 " --> pdb=" O GLU 6 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 6 207 " --> pdb=" O GLU 6 203 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 82 Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 154 removed outlier: 3.800A pdb=" N GLY 7 149 " --> pdb=" O LEU 7 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 7 150 " --> pdb=" O THR 7 146 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 163 through 177 removed outlier: 3.837A pdb=" N LEU 7 167 " --> pdb=" O GLU 7 163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG 7 170 " --> pdb=" O GLU 7 166 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS 7 177 " --> pdb=" O TYR 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 205 removed outlier: 4.392A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.659A pdb=" N VAL A 211 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.698A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 147 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.575A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.219A pdb=" N ILE B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 147 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.836A 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: 4.152A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 147 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.150A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.522A pdb=" N GLY E 45 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL E 211 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.553A pdb=" N ALA E 77 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.524A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL F 211 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.565A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 147 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 69 removed outlier: 4.857A pdb=" N GLY F 80 " --> pdb=" O VAL M 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.521A pdb=" N ALA G 37 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AB7, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.508A pdb=" N VAL L 398 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain '1' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain '1' and resid 45 through 49 removed outlier: 6.700A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 125 " --> pdb=" O LEU 1 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY 1 114 " --> pdb=" O SER 1 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER 1 121 " --> pdb=" O GLY 1 114 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 137 through 138 removed outlier: 3.651A pdb=" N ASP 2 187 " --> pdb=" O THR 2 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '2' and resid 32 through 33 Processing sheet with id=AC4, first strand: chain '2' and resid 45 through 49 removed outlier: 6.609A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 2 110 " --> pdb=" O ILE 2 125 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE 2 122 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 14 through 18 removed outlier: 3.540A pdb=" N ALA 3 26 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET 3 25 " --> pdb=" O VAL 3 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP 3 187 " --> pdb=" O THR 3 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 46 through 49 removed outlier: 6.667A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 137 through 138 removed outlier: 4.020A pdb=" N VAL 4 138 " --> pdb=" O GLY 4 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY 4 16 " --> pdb=" O VAL 4 138 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL 4 15 " --> pdb=" O ALA 4 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 46 through 49 removed outlier: 6.555A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 137 through 140 removed outlier: 3.637A pdb=" N ILE 5 191 " --> pdb=" O VAL 5 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 45 through 49 removed outlier: 6.742A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 5 121 " --> pdb=" O GLY 5 114 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 5 132 " --> pdb=" O SER 5 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 14 through 18 removed outlier: 3.722A pdb=" N TYR 6 197 " --> pdb=" O LYS 6 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 31 through 33 removed outlier: 6.738A pdb=" N ALA 6 31 " --> pdb=" O ALA 6 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 45 through 49 removed outlier: 6.824A pdb=" N ILE 6 45 " --> pdb=" O THR 6 56 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR 6 56 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN 6 47 " --> pdb=" O MET 6 54 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET 6 54 " --> pdb=" O GLN 6 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY 6 113 " --> pdb=" O ALA 6 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 6 110 " --> pdb=" O ILE 6 125 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 137 through 141 removed outlier: 5.394A pdb=" N THR 7 13 " --> pdb=" O GLU 7 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU 7 28 " --> pdb=" O THR 7 13 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 7 22 " --> pdb=" O CYS 7 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 7 23 " --> pdb=" O ILE 7 191 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE 7 122 " --> pdb=" O GLU 7 134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3699 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: 4.57 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.23: 1776 1.23 - 1.46: 10918 1.46 - 1.69: 12100 1.69 - 1.92: 167 1.92 - 2.15: 7 Bond restraints: 24968 Sorted by residual: bond pdb=" CZ ARG 5 170 " pdb=" NH2 ARG 5 170 " ideal model delta sigma weight residual 1.330 2.147 -0.817 1.30e-02 5.92e+03 3.95e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.104 -0.720 2.10e-02 2.27e+03 1.17e+03 bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.041 -0.657 2.10e-02 2.27e+03 9.80e+02 bond pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 1.330 1.710 -0.380 1.23e-02 6.61e+03 9.52e+02 bond pdb=" N GLN E 5 " pdb=" CA GLN E 5 " ideal model delta sigma weight residual 1.458 1.000 0.458 1.90e-02 2.77e+03 5.80e+02 ... (remaining 24963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 26571 4.27 - 8.54: 6410 8.54 - 12.81: 642 12.81 - 17.07: 33 17.07 - 21.34: 4 Bond angle restraints: 33660 Sorted by residual: angle pdb=" NE ARG 5 170 " pdb=" CZ ARG 5 170 " pdb=" NH1 ARG 5 170 " ideal model delta sigma weight residual 121.50 101.39 20.11 1.00e+00 1.00e+00 4.05e+02 angle pdb=" N LYS 2 40 " pdb=" CA LYS 2 40 " pdb=" C LYS 2 40 " ideal model delta sigma weight residual 114.62 95.87 18.75 1.14e+00 7.69e-01 2.71e+02 angle pdb=" C GLU E 65 " pdb=" N LYS E 66 " pdb=" CA LYS E 66 " ideal model delta sigma weight residual 120.38 141.72 -21.34 1.37e+00 5.33e-01 2.43e+02 angle pdb=" CA LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 117.22 101.99 15.23 1.17e+00 7.31e-01 1.69e+02 angle pdb=" O LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 122.12 135.88 -13.76 1.06e+00 8.90e-01 1.69e+02 ... (remaining 33655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14375 25.08 - 50.16: 682 50.16 - 75.23: 224 75.23 - 100.31: 60 100.31 - 125.39: 2 Dihedral angle restraints: 15343 sinusoidal: 6204 harmonic: 9139 Sorted by residual: dihedral pdb=" CA GLU A 65 " pdb=" C GLU A 65 " pdb=" N LYS A 66 " pdb=" CA LYS A 66 " ideal model delta harmonic sigma weight residual -180.00 -54.61 -125.39 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA GLY H 394 " pdb=" C GLY H 394 " pdb=" N VAL H 395 " pdb=" CA VAL H 395 " ideal model delta harmonic sigma weight residual -180.00 -70.34 -109.66 0 5.00e+00 4.00e-02 4.81e+02 dihedral pdb=" CA ALA 2 139 " pdb=" C ALA 2 139 " pdb=" N THR 2 140 " pdb=" CA THR 2 140 " ideal model delta harmonic sigma weight residual 180.00 110.18 69.82 0 5.00e+00 4.00e-02 1.95e+02 ... (remaining 15340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 2874 0.225 - 0.450: 890 0.450 - 0.674: 107 0.674 - 0.899: 9 0.899 - 1.124: 1 Chirality restraints: 3881 Sorted by residual: chirality pdb=" CA THR 3 140 " pdb=" N THR 3 140 " pdb=" C THR 3 140 " pdb=" CB THR 3 140 " both_signs ideal model delta sigma weight residual False 2.53 1.40 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASP B 217 " pdb=" N ASP B 217 " pdb=" C ASP B 217 " pdb=" CB ASP B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA GLU D 65 " pdb=" N GLU D 65 " pdb=" C GLU D 65 " pdb=" CB GLU D 65 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3878 not shown) Planarity restraints: 4329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 5 199 " 0.225 2.00e-02 2.50e+03 1.45e-01 4.21e+02 pdb=" CG TYR 5 199 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR 5 199 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR 5 199 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 TYR 5 199 " -0.166 2.00e-02 2.50e+03 pdb=" CE2 TYR 5 199 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR 5 199 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR 5 199 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 123 " 0.214 2.00e-02 2.50e+03 1.28e-01 3.30e+02 pdb=" CG TYR G 123 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 123 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 TYR G 123 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR G 123 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR G 123 " -0.121 2.00e-02 2.50e+03 pdb=" CZ TYR G 123 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR G 123 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 101 " -0.196 2.00e-02 2.50e+03 1.26e-01 3.20e+02 pdb=" CG TYR 3 101 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 101 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 101 " 0.142 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 101 " 0.139 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 101 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR 3 101 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR 3 101 " -0.209 2.00e-02 2.50e+03 ... (remaining 4326 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3223 2.77 - 3.30: 22758 3.30 - 3.83: 39960 3.83 - 4.37: 53183 4.37 - 4.90: 84967 Nonbonded interactions: 204091 Sorted by model distance: nonbonded pdb=" NH2 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.236 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.237 3.340 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE1 PHE 5 211 " model vdw 2.242 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.250 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CZ PHE 5 211 " model vdw 2.251 3.420 ... (remaining 204086 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.740 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 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 : 0.036 0.817 24968 Z= 2.308 Angle : 3.508 21.343 33660 Z= 2.349 Chirality : 0.204 1.124 3881 Planarity : 0.030 0.297 4329 Dihedral : 17.648 125.386 9493 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 2.18 % Allowed : 5.32 % Favored : 92.50 % Rotamer: Outliers : 4.51 % Allowed : 9.74 % Favored : 85.75 % Cbeta Deviations : 6.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 1.10 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.13), residues: 3122 helix: -1.29 (0.13), residues: 1197 sheet: -0.43 (0.20), residues: 563 loop : -2.82 (0.13), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.012 ARG 1 83 TYR 0.243 0.049 TYR F 8 PHE 0.189 0.040 PHE A 221 HIS 0.032 0.015 HIS G 73 Details of bonding type rmsd/Z covalent geometry : bond 0.03648 / 2.31 (24968) covalent geometry : angle 3.50752 / 2.35 (33660) hydrogen bonds : bond 0.28205 / 18.51 ( 1269) hydrogen bonds : angle 9.34882 / 6.51 ( 3699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1303 time to evaluate : 0.961 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6473 (mm-30) REVERT: A 208 ASN cc_start: 0.7788 (p0) cc_final: 0.7357 (p0) REVERT: A 211 VAL cc_start: 0.7891 (t) cc_final: 0.7530 (p) REVERT: A 220 THR cc_start: 0.8239 (m) cc_final: 0.7978 (m) REVERT: B 24 VAL cc_start: 0.8283 (t) cc_final: 0.7917 (t) REVERT: B 152 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: B 208 ASN cc_start: 0.6638 (p0) cc_final: 0.6184 (p0) REVERT: C 23 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8165 (tp40) REVERT: C 41 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8079 (ttpt) REVERT: C 47 ILE cc_start: 0.8472 (mt) cc_final: 0.8255 (mt) REVERT: C 144 VAL cc_start: 0.8745 (m) cc_final: 0.8484 (m) REVERT: C 160 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7659 (mtpt) REVERT: D 82 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8638 (t) REVERT: D 115 LYS cc_start: 0.8472 (mttm) cc_final: 0.7810 (mttt) REVERT: D 121 GLN cc_start: 0.8060 (tm130) cc_final: 0.7740 (tm130) REVERT: D 174 PHE cc_start: 0.7339 (t80) cc_final: 0.6544 (t80) REVERT: D 211 VAL cc_start: 0.8980 (t) cc_final: 0.8744 (t) REVERT: E 25 GLU cc_start: 0.6352 (tp30) cc_final: 0.5639 (tp30) REVERT: E 41 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7074 (ptmt) REVERT: E 49 ILE cc_start: 0.6840 (tt) cc_final: 0.6596 (tt) REVERT: E 68 TYR cc_start: 0.8023 (m-80) cc_final: 0.7697 (m-80) REVERT: E 116 ILE cc_start: 0.8525 (mt) cc_final: 0.8321 (mt) REVERT: E 120 LYS cc_start: 0.7120 (mttt) cc_final: 0.6913 (mttm) REVERT: E 186 ASP cc_start: 0.6779 (m-30) cc_final: 0.6126 (m-30) REVERT: E 235 ARG cc_start: 0.6204 (ttp-170) cc_final: 0.5557 (ttp80) REVERT: F 22 PHE cc_start: 0.6992 (m-80) cc_final: 0.6425 (m-80) REVERT: F 99 ASN cc_start: 0.7780 (t0) cc_final: 0.7489 (t0) REVERT: F 106 PRO cc_start: 0.9192 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: G 5 GLN cc_start: 0.4622 (OUTLIER) cc_final: 0.3616 (pm20) REVERT: G 16 SER cc_start: 0.7583 (p) cc_final: 0.7166 (p) REVERT: G 23 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7964 (tp40) REVERT: G 47 ILE cc_start: 0.8519 (mt) cc_final: 0.7840 (mt) REVERT: G 157 LEU cc_start: 0.7984 (mt) cc_final: 0.7600 (mt) REVERT: G 171 VAL cc_start: 0.5968 (t) cc_final: 0.4307 (t) REVERT: G 200 ILE cc_start: 0.7751 (pt) cc_final: 0.7383 (pt) REVERT: G 224 VAL cc_start: 0.6674 (t) cc_final: 0.6381 (t) REVERT: 1 107 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0699 (pt) REVERT: 2 44 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3394 (mptm) REVERT: 2 162 ASP cc_start: 0.4158 (m-30) cc_final: 0.3664 (m-30) REVERT: 3 24 VAL cc_start: 0.8584 (t) cc_final: 0.8350 (t) REVERT: 3 46 TYR cc_start: 0.7226 (m-80) cc_final: 0.6541 (m-80) REVERT: 3 93 LEU cc_start: 0.8152 (tp) cc_final: 0.7541 (tt) REVERT: 4 70 ILE cc_start: 0.9169 (mt) cc_final: 0.8898 (mt) REVERT: 5 146 THR cc_start: 0.6264 (p) cc_final: 0.5918 (p) REVERT: 6 155 PHE cc_start: 0.3192 (t80) cc_final: 0.2983 (t80) outliers start: 118 outliers final: 19 residues processed: 1361 average time/residue: 0.2062 time to fit residues: 415.4558 Evaluate side-chains 1111 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1088 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 237 ASN G 97 GLN G 99 ASN 1 64 GLN 3 96 ASN 4 99 ASN 7 109 GLN 7 198 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.186175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153757 restraints weight = 36901.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.158305 restraints weight = 21437.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.161391 restraints weight = 14380.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.163370 restraints weight = 10774.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.164808 restraints weight = 8857.416| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24968 Z= 0.258 Angle : 0.881 14.202 33660 Z= 0.482 Chirality : 0.052 0.213 3881 Planarity : 0.006 0.088 4329 Dihedral : 6.552 56.473 3498 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.62 % Favored : 96.06 % Rotamer: Outliers : 0.19 % Allowed : 4.66 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -1.27 (0.14), residues: 3122 helix: -0.06 (0.14), residues: 1242 sheet: 0.12 (0.19), residues: 593 loop : -2.09 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 5 170 TYR 0.039 0.002 TYR 6 46 PHE 0.030 0.003 PHE 4 155 HIS 0.008 0.003 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (24968) covalent geometry : angle 0.88084 / 0.48 (33660) hydrogen bonds : bond 0.05041 / 3.32 ( 1269) hydrogen bonds : angle 5.78466 / 4.08 ( 3699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1299 time to evaluate : 0.967 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: 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: 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: A 121 GLN cc_start: 0.8625 (tp40) cc_final: 0.7661 (tm-30) REVERT: A 172 THR cc_start: 0.8552 (p) cc_final: 0.7797 (p) REVERT: A 186 ASP cc_start: 0.7703 (p0) cc_final: 0.7063 (p0) REVERT: A 208 ASN cc_start: 0.8716 (p0) cc_final: 0.8152 (p0) REVERT: A 211 VAL cc_start: 0.8728 (t) cc_final: 0.7128 (p) REVERT: A 222 LYS cc_start: 0.8499 (tttm) cc_final: 0.8204 (ttmm) REVERT: B 104 ASP cc_start: 0.7156 (m-30) cc_final: 0.6564 (m-30) REVERT: B 176 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 181 ASP cc_start: 0.7762 (m-30) cc_final: 0.7497 (m-30) REVERT: B 186 ASP cc_start: 0.8486 (p0) cc_final: 0.8284 (p0) REVERT: B 201 GLU cc_start: 0.7924 (tm-30) cc_final: 0.6928 (tm-30) REVERT: B 208 ASN cc_start: 0.7419 (p0) cc_final: 0.7119 (p0) REVERT: B 214 VAL cc_start: 0.9423 (t) cc_final: 0.9202 (p) REVERT: B 238 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6727 (mt-10) REVERT: C 57 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8465 (pttm) REVERT: C 123 TYR cc_start: 0.7866 (m-80) cc_final: 0.7487 (m-80) REVERT: C 137 LEU cc_start: 0.9358 (mt) cc_final: 0.8787 (mt) REVERT: C 149 GLU cc_start: 0.8733 (tt0) cc_final: 0.8532 (tt0) REVERT: C 160 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8239 (mtmm) REVERT: C 164 ILE cc_start: 0.9546 (pt) cc_final: 0.9329 (pt) REVERT: C 185 PHE cc_start: 0.8829 (t80) cc_final: 0.8465 (t80) REVERT: C 189 MET cc_start: 0.9141 (ttm) cc_final: 0.8807 (ttm) REVERT: C 202 SER cc_start: 0.8522 (p) cc_final: 0.8093 (p) REVERT: C 208 ASN cc_start: 0.8541 (p0) cc_final: 0.8041 (p0) REVERT: C 209 ILE cc_start: 0.9099 (pt) cc_final: 0.8740 (pt) REVERT: C 214 VAL cc_start: 0.8939 (t) cc_final: 0.8583 (t) REVERT: C 225 SER cc_start: 0.8905 (p) cc_final: 0.7955 (p) REVERT: D 33 ARG cc_start: 0.8540 (ptm160) cc_final: 0.8188 (mtp-110) REVERT: D 60 GLU cc_start: 0.7797 (pp20) cc_final: 0.7540 (pp20) REVERT: D 64 ILE cc_start: 0.6738 (pt) cc_final: 0.6455 (pt) REVERT: D 91 ARG cc_start: 0.8681 (tpt170) cc_final: 0.8204 (tpt90) REVERT: D 95 GLU cc_start: 0.8059 (tt0) cc_final: 0.6847 (tt0) REVERT: D 115 LYS cc_start: 0.8571 (mttm) cc_final: 0.7979 (mtpt) REVERT: D 121 GLN cc_start: 0.7958 (tp40) cc_final: 0.7612 (tm-30) REVERT: D 174 PHE cc_start: 0.8543 (t80) cc_final: 0.8280 (t80) REVERT: D 185 PHE cc_start: 0.7864 (t80) cc_final: 0.7410 (t80) REVERT: D 228 GLU cc_start: 0.7986 (tp30) cc_final: 0.7746 (tp30) REVERT: E 25 GLU cc_start: 0.8074 (tp30) cc_final: 0.6780 (tp30) REVERT: E 65 GLU cc_start: 0.5289 (tt0) cc_final: 0.4639 (tt0) REVERT: E 68 TYR cc_start: 0.8848 (m-80) cc_final: 0.8228 (m-80) REVERT: E 72 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6951 (mt-10) REVERT: E 75 CYS cc_start: 0.9044 (p) cc_final: 0.8819 (p) REVERT: E 88 LEU cc_start: 0.9154 (tp) cc_final: 0.8915 (tt) REVERT: E 93 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8607 (mtp85) REVERT: E 172 THR cc_start: 0.8999 (m) cc_final: 0.8678 (t) REVERT: E 221 PHE cc_start: 0.8443 (t80) cc_final: 0.8021 (t80) REVERT: F 9 ASP cc_start: 0.8620 (p0) cc_final: 0.8345 (p0) REVERT: F 26 TYR cc_start: 0.9231 (m-10) cc_final: 0.8710 (m-10) REVERT: F 99 ASN cc_start: 0.9044 (t0) cc_final: 0.8814 (t0) REVERT: F 150 THR cc_start: 0.8562 (p) cc_final: 0.8251 (p) REVERT: F 151 ASP cc_start: 0.7869 (m-30) cc_final: 0.7662 (m-30) REVERT: F 187 ASP cc_start: 0.8543 (m-30) cc_final: 0.7964 (m-30) REVERT: F 196 MET cc_start: 0.9127 (tpp) cc_final: 0.8778 (tpp) REVERT: F 210 GLU cc_start: 0.7922 (tt0) cc_final: 0.7027 (tt0) REVERT: F 228 GLU cc_start: 0.8413 (tp30) cc_final: 0.8102 (tp30) REVERT: G 23 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8411 (tp40) REVERT: G 33 ARG cc_start: 0.7198 (ptp-170) cc_final: 0.6845 (mtm180) REVERT: G 44 GLU cc_start: 0.7826 (mp0) cc_final: 0.7570 (mp0) REVERT: G 47 ILE cc_start: 0.9298 (mt) cc_final: 0.9029 (mt) REVERT: G 89 ILE cc_start: 0.9334 (mm) cc_final: 0.9076 (mm) REVERT: G 93 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8421 (mtt-85) REVERT: G 104 ASP cc_start: 0.7929 (t70) cc_final: 0.7335 (t0) REVERT: G 171 VAL cc_start: 0.8673 (t) cc_final: 0.7361 (p) REVERT: G 187 ASP cc_start: 0.8190 (m-30) cc_final: 0.7988 (m-30) REVERT: G 209 ILE cc_start: 0.9158 (pt) cc_final: 0.8902 (pt) REVERT: 1 44 LYS cc_start: 0.8124 (tttt) cc_final: 0.7908 (tptt) REVERT: 1 111 LEU cc_start: 0.9013 (mt) cc_final: 0.8672 (mt) REVERT: 1 116 ASP cc_start: 0.8818 (p0) cc_final: 0.8574 (p0) REVERT: 1 122 ILE cc_start: 0.8377 (mm) cc_final: 0.7768 (mm) REVERT: 1 135 LYS cc_start: 0.7779 (mppt) cc_final: 0.7477 (mppt) REVERT: 1 173 TYR cc_start: 0.8482 (t80) cc_final: 0.7968 (t80) REVERT: 1 190 LYS cc_start: 0.8562 (ptpp) cc_final: 0.7982 (ptpp) REVERT: 1 208 LEU cc_start: 0.4755 (pp) cc_final: 0.4217 (pp) REVERT: 2 19 CYS cc_start: 0.6861 (m) cc_final: 0.6390 (m) REVERT: 2 72 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8713 (mp) REVERT: 2 159 ILE cc_start: 0.8296 (tt) cc_final: 0.7862 (tt) REVERT: 2 162 ASP cc_start: 0.5839 (m-30) cc_final: 0.5474 (m-30) REVERT: 2 163 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7029 (mp0) REVERT: 2 190 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8705 (tttt) REVERT: 2 203 GLU cc_start: 0.7393 (pt0) cc_final: 0.6959 (pt0) REVERT: 3 46 TYR cc_start: 0.7337 (m-80) cc_final: 0.6498 (m-10) REVERT: 3 48 ILE cc_start: 0.8949 (mm) cc_final: 0.8725 (tp) REVERT: 3 84 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7662 (mptt) REVERT: 3 90 ILE cc_start: 0.9477 (mm) cc_final: 0.8998 (tt) REVERT: 3 188 VAL cc_start: 0.7533 (t) cc_final: 0.7293 (t) REVERT: 4 48 ILE cc_start: 0.9307 (mm) cc_final: 0.8592 (mm) REVERT: 4 80 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8336 (mtp180) REVERT: 4 87 VAL cc_start: 0.9376 (t) cc_final: 0.9008 (t) REVERT: 4 88 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7973 (ttp-170) REVERT: 4 132 ILE cc_start: 0.8878 (mt) cc_final: 0.8661 (mt) REVERT: 4 190 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7868 (ptmm) REVERT: 5 79 ILE cc_start: 0.8899 (mt) cc_final: 0.8507 (mt) REVERT: 5 92 THR cc_start: 0.8796 (p) cc_final: 0.8576 (p) REVERT: 5 122 ILE cc_start: 0.8985 (mt) cc_final: 0.8354 (mt) REVERT: 5 132 ILE cc_start: 0.8491 (mt) cc_final: 0.8136 (mt) REVERT: 5 134 GLU cc_start: 0.7043 (mp0) cc_final: 0.6729 (mp0) REVERT: 6 33 MET cc_start: 0.1424 (pmm) cc_final: 0.1210 (pmm) REVERT: 6 68 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.7057 (mtm-85) REVERT: 6 72 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8505 (mp) REVERT: 6 81 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8097 (tpp80) REVERT: 6 137 ILE cc_start: 0.8282 (mm) cc_final: 0.7632 (mp) REVERT: 7 44 LYS cc_start: 0.6346 (tppt) cc_final: 0.5917 (tppt) REVERT: 7 75 ASN cc_start: 0.8920 (m-40) cc_final: 0.8644 (m-40) REVERT: 7 120 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8233 (mtmm) REVERT: 7 152 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6923 (mt-10) outliers start: 5 outliers final: 0 residues processed: 1301 average time/residue: 0.1899 time to fit residues: 372.6523 Evaluate side-chains 1116 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1114 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 179 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 148 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN 3 75 ASN 6 96 ASN 6 198 GLN 7 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.182175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.149745 restraints weight = 36746.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.154223 restraints weight = 21182.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.157192 restraints weight = 14175.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159325 restraints weight = 10662.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.160562 restraints weight = 8699.525| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24968 Z= 0.187 Angle : 0.741 14.351 33660 Z= 0.404 Chirality : 0.049 0.226 3881 Planarity : 0.005 0.067 4329 Dihedral : 5.886 59.514 3498 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.00 % Favored : 95.68 % Rotamer: Outliers : 0.31 % Allowed : 3.40 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.89 (0.14), residues: 3122 helix: 0.14 (0.14), residues: 1239 sheet: 0.37 (0.19), residues: 585 loop : -1.74 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 4 81 TYR 0.031 0.002 TYR 6 148 PHE 0.023 0.002 PHE 5 155 HIS 0.005 0.002 HIS G 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (24968) covalent geometry : angle 0.74108 / 0.40 (33660) hydrogen bonds : bond 0.04253 / 2.79 ( 1269) hydrogen bonds : angle 5.36534 / 3.79 ( 3699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1252 time to evaluate : 1.035 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: 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: 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 117 CYS cc_start: 0.8384 (m) cc_final: 0.8147 (m) REVERT: A 121 GLN cc_start: 0.8157 (tp40) cc_final: 0.7663 (tm-30) REVERT: A 172 THR cc_start: 0.8794 (p) cc_final: 0.8577 (p) REVERT: A 182 ASP cc_start: 0.7244 (p0) cc_final: 0.7022 (p0) REVERT: A 186 ASP cc_start: 0.7575 (p0) cc_final: 0.6810 (p0) REVERT: A 208 ASN cc_start: 0.8765 (p0) cc_final: 0.8207 (p0) REVERT: A 211 VAL cc_start: 0.8937 (t) cc_final: 0.7404 (p) REVERT: A 222 LYS cc_start: 0.8553 (tttm) cc_final: 0.8331 (ttmm) REVERT: B 38 ILE cc_start: 0.8960 (mt) cc_final: 0.8500 (mt) REVERT: B 47 ILE cc_start: 0.8911 (mt) cc_final: 0.8209 (mt) REVERT: B 93 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8097 (mtt-85) REVERT: B 116 ILE cc_start: 0.9353 (tt) cc_final: 0.9091 (tt) REVERT: B 151 ASP cc_start: 0.9156 (t0) cc_final: 0.8695 (t0) REVERT: B 152 PRO cc_start: 0.9615 (Cg_exo) cc_final: 0.9299 (Cg_endo) REVERT: B 174 PHE cc_start: 0.7995 (t80) cc_final: 0.7444 (t80) REVERT: B 176 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 187 ASP cc_start: 0.7744 (m-30) cc_final: 0.7319 (m-30) REVERT: B 189 MET cc_start: 0.8280 (tpt) cc_final: 0.7872 (tpt) REVERT: B 196 MET cc_start: 0.8607 (mmm) cc_final: 0.8129 (mmm) REVERT: B 201 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 207 GLU cc_start: 0.7326 (mp0) cc_final: 0.6942 (mp0) REVERT: B 208 ASN cc_start: 0.7491 (p0) cc_final: 0.7260 (p0) REVERT: B 234 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8622 (mt-10) REVERT: C 26 TYR cc_start: 0.8710 (m-10) cc_final: 0.8000 (m-10) REVERT: C 44 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5837 (tm-30) REVERT: C 52 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8463 (ttpt) REVERT: C 57 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8467 (pttm) REVERT: C 103 TYR cc_start: 0.8439 (m-80) cc_final: 0.8058 (m-10) REVERT: C 123 TYR cc_start: 0.7377 (m-80) cc_final: 0.7023 (m-80) REVERT: C 160 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8275 (mtmm) REVERT: C 175 PHE cc_start: 0.9045 (m-80) cc_final: 0.8830 (m-80) REVERT: C 185 PHE cc_start: 0.8455 (t80) cc_final: 0.8224 (t80) REVERT: C 189 MET cc_start: 0.8981 (ttm) cc_final: 0.8769 (ttm) REVERT: C 202 SER cc_start: 0.8651 (p) cc_final: 0.8391 (p) REVERT: C 203 GLU cc_start: 0.6011 (pm20) cc_final: 0.5747 (pm20) REVERT: C 208 ASN cc_start: 0.8503 (p0) cc_final: 0.7845 (p0) REVERT: C 222 LYS cc_start: 0.8349 (tttt) cc_final: 0.8103 (ttmm) REVERT: D 33 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8173 (mtp-110) REVERT: D 38 ILE cc_start: 0.9141 (mt) cc_final: 0.8764 (mt) REVERT: D 57 LYS cc_start: 0.8668 (pttm) cc_final: 0.8014 (mppt) REVERT: D 64 ILE cc_start: 0.6761 (pt) cc_final: 0.6430 (pt) REVERT: D 67 ILE cc_start: 0.9228 (mm) cc_final: 0.8999 (mm) REVERT: D 68 TYR cc_start: 0.7711 (m-80) cc_final: 0.7507 (m-80) REVERT: D 91 ARG cc_start: 0.8727 (tpt170) cc_final: 0.8478 (tpt90) REVERT: D 95 GLU cc_start: 0.8222 (tt0) cc_final: 0.7951 (tt0) REVERT: D 115 LYS cc_start: 0.8730 (mttm) cc_final: 0.8143 (mtmt) REVERT: D 174 PHE cc_start: 0.8694 (t80) cc_final: 0.8304 (t80) REVERT: D 178 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7454 (mt-10) REVERT: E 25 GLU cc_start: 0.8169 (tp30) cc_final: 0.6809 (tp30) REVERT: E 68 TYR cc_start: 0.8761 (m-80) cc_final: 0.8191 (m-80) REVERT: E 159 TYR cc_start: 0.9009 (m-80) cc_final: 0.8675 (m-80) REVERT: E 172 THR cc_start: 0.9115 (m) cc_final: 0.8834 (t) REVERT: E 218 ASP cc_start: 0.8927 (p0) cc_final: 0.8267 (p0) REVERT: E 222 LYS cc_start: 0.8410 (mttt) cc_final: 0.8036 (mttp) REVERT: F 9 ASP cc_start: 0.8519 (p0) cc_final: 0.8000 (p0) REVERT: F 26 TYR cc_start: 0.9201 (m-10) cc_final: 0.8749 (m-10) REVERT: F 99 ASN cc_start: 0.9113 (t0) cc_final: 0.8877 (t0) REVERT: F 120 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8279 (ttmm) REVERT: F 142 ASP cc_start: 0.6990 (p0) cc_final: 0.6433 (p0) REVERT: F 150 THR cc_start: 0.8626 (p) cc_final: 0.8271 (p) REVERT: F 173 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7631 (tm-30) REVERT: F 193 LEU cc_start: 0.9274 (mm) cc_final: 0.9049 (mm) REVERT: F 210 GLU cc_start: 0.6997 (tt0) cc_final: 0.6628 (tt0) REVERT: F 223 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 33 ARG cc_start: 0.7115 (ptp-170) cc_final: 0.6909 (mtm180) REVERT: G 66 LYS cc_start: 0.8560 (tptt) cc_final: 0.7432 (mptt) REVERT: G 68 TYR cc_start: 0.8385 (m-80) cc_final: 0.8165 (m-80) REVERT: G 73 HIS cc_start: 0.8053 (p-80) cc_final: 0.7645 (p-80) REVERT: G 104 ASP cc_start: 0.7634 (t70) cc_final: 0.6906 (t0) REVERT: G 114 LYS cc_start: 0.8360 (mttp) cc_final: 0.7941 (mmtm) REVERT: G 171 VAL cc_start: 0.8743 (t) cc_final: 0.8356 (m) REVERT: G 187 ASP cc_start: 0.8290 (m-30) cc_final: 0.7997 (m-30) REVERT: G 211 VAL cc_start: 0.9273 (t) cc_final: 0.9053 (t) REVERT: G 234 GLU cc_start: 0.8317 (pp20) cc_final: 0.8027 (pp20) REVERT: G 237 ASN cc_start: 0.7451 (m110) cc_final: 0.6816 (m110) REVERT: 1 80 ARG cc_start: 0.8932 (mtm180) cc_final: 0.8507 (mtt180) REVERT: 1 88 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8566 (mmm-85) REVERT: 1 111 LEU cc_start: 0.8998 (mt) cc_final: 0.8598 (mt) REVERT: 1 122 ILE cc_start: 0.8520 (mm) cc_final: 0.7900 (mm) REVERT: 1 123 TYR cc_start: 0.8439 (m-80) cc_final: 0.8111 (m-80) REVERT: 1 135 LYS cc_start: 0.7846 (mppt) cc_final: 0.7575 (mppt) REVERT: 1 173 TYR cc_start: 0.8505 (t80) cc_final: 0.7906 (t80) REVERT: 1 208 LEU cc_start: 0.5226 (pp) cc_final: 0.4699 (pp) REVERT: 2 19 CYS cc_start: 0.7056 (m) cc_final: 0.6740 (m) REVERT: 2 72 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8565 (mp) REVERT: 2 95 SER cc_start: 0.8240 (m) cc_final: 0.7978 (t) REVERT: 2 159 ILE cc_start: 0.8151 (tt) cc_final: 0.7784 (mt) REVERT: 2 190 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8839 (tttt) REVERT: 3 46 TYR cc_start: 0.7164 (m-80) cc_final: 0.6250 (m-80) REVERT: 3 84 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7801 (mptt) REVERT: 3 90 ILE cc_start: 0.9403 (mm) cc_final: 0.8888 (tt) REVERT: 4 44 LYS cc_start: 0.6371 (tppt) cc_final: 0.6115 (tppt) REVERT: 4 48 ILE cc_start: 0.9377 (mm) cc_final: 0.9026 (mm) REVERT: 4 52 MET cc_start: 0.8335 (ttm) cc_final: 0.8095 (ttm) REVERT: 4 80 ARG cc_start: 0.8749 (mtp180) cc_final: 0.7912 (mtp180) REVERT: 4 83 ARG cc_start: 0.8564 (ptm160) cc_final: 0.7738 (ptm160) REVERT: 4 88 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7907 (ttp-170) REVERT: 4 109 GLN cc_start: 0.6821 (mp10) cc_final: 0.6549 (mp10) REVERT: 4 123 TYR cc_start: 0.9063 (m-80) cc_final: 0.8612 (m-80) REVERT: 4 135 LYS cc_start: 0.8090 (tppt) cc_final: 0.7457 (ttpt) REVERT: 4 152 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8346 (mm-30) REVERT: 4 190 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7979 (ptmm) REVERT: 5 33 MET cc_start: -0.1122 (mtt) cc_final: -0.1917 (ttm) REVERT: 5 46 TYR cc_start: 0.7633 (m-80) cc_final: 0.6606 (m-10) REVERT: 5 73 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8102 (mm-30) REVERT: 5 87 VAL cc_start: 0.9411 (t) cc_final: 0.9056 (m) REVERT: 5 92 THR cc_start: 0.8813 (p) cc_final: 0.8605 (p) REVERT: 5 115 ILE cc_start: 0.7245 (pt) cc_final: 0.6807 (pt) REVERT: 5 134 GLU cc_start: 0.7373 (mp0) cc_final: 0.7024 (mp0) REVERT: 5 165 VAL cc_start: 0.8814 (m) cc_final: 0.8330 (m) REVERT: 6 68 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.6993 (ttp-110) REVERT: 6 72 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8602 (mp) REVERT: 6 79 ILE cc_start: 0.9597 (mt) cc_final: 0.9282 (mt) REVERT: 6 81 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8209 (tpp80) REVERT: 6 122 ILE cc_start: 0.9219 (tp) cc_final: 0.8855 (tp) REVERT: 6 163 GLU cc_start: 0.7926 (mp0) cc_final: 0.7378 (pm20) REVERT: 6 170 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: 7 44 LYS cc_start: 0.6630 (tppt) cc_final: 0.6165 (tppt) REVERT: 7 77 TYR cc_start: 0.8051 (t80) cc_final: 0.7812 (t80) REVERT: 7 120 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8100 (mtmm) REVERT: 7 122 ILE cc_start: 0.9004 (tp) cc_final: 0.8767 (tp) REVERT: 7 193 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 8 outliers final: 1 residues processed: 1256 average time/residue: 0.1836 time to fit residues: 354.7870 Evaluate side-chains 1131 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1128 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 190 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 211 optimal weight: 0.0670 chunk 162 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN 3 75 ASN 3 198 GLN 4 75 ASN 4 96 ASN 6 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.176126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.143776 restraints weight = 36929.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.148088 restraints weight = 21279.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.150970 restraints weight = 14282.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.152991 restraints weight = 10789.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.154187 restraints weight = 8838.083| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24968 Z= 0.231 Angle : 0.747 14.672 33660 Z= 0.404 Chirality : 0.049 0.212 3881 Planarity : 0.005 0.161 4329 Dihedral : 5.771 59.203 3498 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.20 % Favored : 95.48 % Rotamer: Outliers : 0.27 % Allowed : 3.78 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.77 (0.14), residues: 3122 helix: 0.27 (0.14), residues: 1223 sheet: 0.06 (0.19), residues: 628 loop : -1.54 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 88 TYR 0.031 0.002 TYR 6 46 PHE 0.023 0.002 PHE 5 196 HIS 0.006 0.002 HIS G 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (24968) covalent geometry : angle 0.74677 / 0.40 (33660) hydrogen bonds : bond 0.04072 / 2.70 ( 1269) hydrogen bonds : angle 5.29671 / 3.74 ( 3699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1273 time to evaluate : 0.982 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: 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: symmetry clash REVERT: A 51 ASP cc_start: 0.8634 (t70) cc_final: 0.8418 (t0) REVERT: A 98 ILE cc_start: 0.8905 (mt) cc_final: 0.8503 (mt) REVERT: A 121 GLN cc_start: 0.8555 (tp40) cc_final: 0.7772 (tm-30) REVERT: A 146 LYS cc_start: 0.8666 (mttt) cc_final: 0.8395 (mttp) REVERT: A 166 MET cc_start: 0.8325 (mtp) cc_final: 0.8055 (ttt) REVERT: A 186 ASP cc_start: 0.7589 (p0) cc_final: 0.6771 (p0) REVERT: A 187 ASP cc_start: 0.7920 (m-30) cc_final: 0.7690 (m-30) REVERT: A 208 ASN cc_start: 0.8837 (p0) cc_final: 0.8270 (p0) REVERT: A 211 VAL cc_start: 0.9034 (t) cc_final: 0.7354 (p) REVERT: A 213 TYR cc_start: 0.8814 (p90) cc_final: 0.8369 (p90) REVERT: A 222 LYS cc_start: 0.8721 (tttm) cc_final: 0.8353 (ttmm) REVERT: B 32 LYS cc_start: 0.8320 (mmtp) cc_final: 0.8109 (mmmm) REVERT: B 51 ASP cc_start: 0.7289 (m-30) cc_final: 0.7026 (m-30) REVERT: B 60 GLU cc_start: 0.8017 (tp30) cc_final: 0.7677 (tp30) REVERT: B 151 ASP cc_start: 0.9294 (t0) cc_final: 0.8859 (t0) REVERT: B 152 PRO cc_start: 0.9706 (Cg_exo) cc_final: 0.9379 (Cg_endo) REVERT: B 201 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 207 GLU cc_start: 0.7559 (mp0) cc_final: 0.7309 (mp0) REVERT: B 208 ASN cc_start: 0.7606 (p0) cc_final: 0.7398 (p0) REVERT: B 214 VAL cc_start: 0.9436 (t) cc_final: 0.9147 (t) REVERT: B 230 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8821 (ttpt) REVERT: B 239 ARG cc_start: 0.7491 (ttp-170) cc_final: 0.7168 (ttp-170) REVERT: C 9 ASP cc_start: 0.7830 (p0) cc_final: 0.7472 (p0) REVERT: C 44 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 52 LYS cc_start: 0.8765 (ttpt) cc_final: 0.8464 (ttmm) REVERT: C 110 LYS cc_start: 0.9499 (tptp) cc_final: 0.9183 (tptt) REVERT: C 123 TYR cc_start: 0.7501 (m-80) cc_final: 0.7070 (m-80) REVERT: C 148 TYR cc_start: 0.9325 (m-80) cc_final: 0.9064 (m-10) REVERT: C 175 PHE cc_start: 0.9078 (m-80) cc_final: 0.8773 (m-80) REVERT: C 185 PHE cc_start: 0.8558 (t80) cc_final: 0.8329 (t80) REVERT: C 189 MET cc_start: 0.9064 (ttm) cc_final: 0.8702 (ttm) REVERT: C 208 ASN cc_start: 0.8536 (p0) cc_final: 0.8035 (p0) REVERT: C 210 GLU cc_start: 0.6972 (tt0) cc_final: 0.6199 (tt0) REVERT: C 211 VAL cc_start: 0.9108 (t) cc_final: 0.8900 (p) REVERT: C 214 VAL cc_start: 0.8938 (t) cc_final: 0.8666 (t) REVERT: C 215 LYS cc_start: 0.8114 (mttt) cc_final: 0.7911 (mttp) REVERT: C 222 LYS cc_start: 0.8678 (tttt) cc_final: 0.8287 (ttmm) REVERT: C 225 SER cc_start: 0.8859 (p) cc_final: 0.7614 (t) REVERT: D 20 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7934 (ttp-110) REVERT: D 33 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8426 (mtp-110) REVERT: D 57 LYS cc_start: 0.8626 (pttm) cc_final: 0.7957 (mppt) REVERT: D 64 ILE cc_start: 0.6930 (pt) cc_final: 0.6552 (pt) REVERT: D 171 VAL cc_start: 0.9656 (t) cc_final: 0.9294 (p) REVERT: D 196 MET cc_start: 0.8932 (mmm) cc_final: 0.8508 (tpp) REVERT: D 200 ILE cc_start: 0.8825 (pt) cc_final: 0.8570 (pt) REVERT: D 227 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8241 (tm-30) REVERT: D 228 GLU cc_start: 0.7874 (tp30) cc_final: 0.7627 (tp30) REVERT: D 240 ILE cc_start: 0.8735 (pt) cc_final: 0.8479 (pt) REVERT: E 6 MET cc_start: 0.6499 (ttm) cc_final: 0.5995 (ttm) REVERT: E 8 TYR cc_start: 0.7836 (m-10) cc_final: 0.7362 (m-80) REVERT: E 25 GLU cc_start: 0.8278 (tp30) cc_final: 0.6987 (tp30) REVERT: E 52 LYS cc_start: 0.9261 (ttpp) cc_final: 0.9029 (ttpp) REVERT: E 68 TYR cc_start: 0.8787 (m-80) cc_final: 0.8235 (m-10) REVERT: E 108 THR cc_start: 0.9078 (m) cc_final: 0.8669 (m) REVERT: E 112 LEU cc_start: 0.9485 (tp) cc_final: 0.9268 (tp) REVERT: E 148 TYR cc_start: 0.9009 (m-80) cc_final: 0.8523 (m-10) REVERT: E 172 THR cc_start: 0.9160 (m) cc_final: 0.8937 (t) REVERT: E 218 ASP cc_start: 0.8988 (p0) cc_final: 0.8429 (p0) REVERT: E 222 LYS cc_start: 0.8453 (mttt) cc_final: 0.8124 (mttp) REVERT: E 234 GLU cc_start: 0.8424 (tp30) cc_final: 0.8189 (tp30) REVERT: F 9 ASP cc_start: 0.8379 (p0) cc_final: 0.8108 (p0) REVERT: F 26 TYR cc_start: 0.9144 (m-10) cc_final: 0.8739 (m-10) REVERT: F 52 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8438 (mtpp) REVERT: F 71 ASP cc_start: 0.8318 (t70) cc_final: 0.8028 (t70) REVERT: F 99 ASN cc_start: 0.9178 (t0) cc_final: 0.8767 (t0) REVERT: F 150 THR cc_start: 0.8830 (p) cc_final: 0.8603 (p) REVERT: F 158 GLU cc_start: 0.6730 (tt0) cc_final: 0.6212 (tt0) REVERT: F 173 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7457 (tm-30) REVERT: F 211 VAL cc_start: 0.9152 (t) cc_final: 0.8929 (t) REVERT: F 228 GLU cc_start: 0.8448 (tp30) cc_final: 0.8235 (tp30) REVERT: F 229 LEU cc_start: 0.9134 (tt) cc_final: 0.8790 (tt) REVERT: F 232 TYR cc_start: 0.8919 (m-80) cc_final: 0.8554 (m-10) REVERT: F 241 ARG cc_start: 0.7560 (ptp-110) cc_final: 0.6903 (mtm110) REVERT: G 16 SER cc_start: 0.8866 (p) cc_final: 0.8645 (t) REVERT: G 47 ILE cc_start: 0.9253 (mt) cc_final: 0.8988 (mt) REVERT: G 51 ASP cc_start: 0.8945 (t0) cc_final: 0.8513 (t0) REVERT: G 66 LYS cc_start: 0.8961 (tppp) cc_final: 0.8233 (mptt) REVERT: G 73 HIS cc_start: 0.8458 (p-80) cc_final: 0.7834 (p-80) REVERT: G 104 ASP cc_start: 0.7674 (t70) cc_final: 0.6623 (t0) REVERT: G 114 LYS cc_start: 0.8477 (mttm) cc_final: 0.8272 (mmtm) REVERT: G 169 ASN cc_start: 0.8338 (m-40) cc_final: 0.8031 (m110) REVERT: G 171 VAL cc_start: 0.9031 (t) cc_final: 0.7810 (p) REVERT: G 172 THR cc_start: 0.8554 (p) cc_final: 0.8099 (p) REVERT: G 187 ASP cc_start: 0.8443 (m-30) cc_final: 0.8089 (m-30) REVERT: G 211 VAL cc_start: 0.9276 (t) cc_final: 0.8703 (t) REVERT: G 234 GLU cc_start: 0.8560 (pp20) cc_final: 0.8144 (pp20) REVERT: G 237 ASN cc_start: 0.7806 (m110) cc_final: 0.7212 (m110) REVERT: 1 17 LEU cc_start: 0.9151 (pt) cc_final: 0.8883 (pt) REVERT: 1 25 MET cc_start: 0.7880 (mtm) cc_final: 0.7239 (ttm) REVERT: 1 88 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8515 (mmm-85) REVERT: 1 111 LEU cc_start: 0.8990 (mt) cc_final: 0.8404 (mt) REVERT: 1 122 ILE cc_start: 0.8775 (mm) cc_final: 0.8341 (mm) REVERT: 1 170 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8615 (mtm-85) REVERT: 1 173 TYR cc_start: 0.8506 (t80) cc_final: 0.7978 (t80) REVERT: 1 190 LYS cc_start: 0.8270 (ptmt) cc_final: 0.8008 (ptmm) REVERT: 1 208 LEU cc_start: 0.4864 (pp) cc_final: 0.4316 (pp) REVERT: 2 45 ILE cc_start: 0.8354 (tt) cc_final: 0.7911 (tt) REVERT: 2 48 ILE cc_start: 0.8938 (mm) cc_final: 0.8651 (mm) REVERT: 2 72 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8446 (mp) REVERT: 2 116 ASP cc_start: 0.5437 (p0) cc_final: 0.5142 (p0) REVERT: 2 162 ASP cc_start: 0.6294 (m-30) cc_final: 0.5575 (m-30) REVERT: 2 190 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8625 (tttt) REVERT: 2 192 THR cc_start: 0.7626 (t) cc_final: 0.6944 (t) REVERT: 3 46 TYR cc_start: 0.7188 (m-80) cc_final: 0.6577 (m-80) REVERT: 3 48 ILE cc_start: 0.8899 (tp) cc_final: 0.8672 (tp) REVERT: 3 88 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7776 (ttm110) REVERT: 3 90 ILE cc_start: 0.9547 (mm) cc_final: 0.9014 (tt) REVERT: 3 123 TYR cc_start: 0.8387 (m-80) cc_final: 0.7985 (m-80) REVERT: 3 188 VAL cc_start: 0.8085 (t) cc_final: 0.7881 (t) REVERT: 4 33 MET cc_start: 0.5006 (ttm) cc_final: 0.4410 (ttm) REVERT: 4 48 ILE cc_start: 0.9334 (mm) cc_final: 0.8760 (mm) REVERT: 4 52 MET cc_start: 0.8272 (ttm) cc_final: 0.7946 (ttm) REVERT: 4 80 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8425 (mtp180) REVERT: 4 87 VAL cc_start: 0.9217 (t) cc_final: 0.8995 (t) REVERT: 4 88 ARG cc_start: 0.8249 (ttp80) cc_final: 0.8016 (ttp-170) REVERT: 4 109 GLN cc_start: 0.6574 (mp10) cc_final: 0.6134 (mp10) REVERT: 4 123 TYR cc_start: 0.9084 (m-80) cc_final: 0.8417 (m-80) REVERT: 4 134 GLU cc_start: 0.7455 (mp0) cc_final: 0.7045 (mp0) REVERT: 4 135 LYS cc_start: 0.8124 (tppt) cc_final: 0.7520 (ttpt) REVERT: 4 152 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8250 (mm-30) REVERT: 4 190 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8186 (ptmm) REVERT: 5 43 LYS cc_start: 0.7665 (tptt) cc_final: 0.7431 (tptt) REVERT: 5 46 TYR cc_start: 0.8093 (m-80) cc_final: 0.7223 (m-10) REVERT: 5 73 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8014 (mm-30) REVERT: 5 121 SER cc_start: 0.8613 (p) cc_final: 0.8401 (p) REVERT: 5 134 GLU cc_start: 0.7348 (mp0) cc_final: 0.6955 (mp0) REVERT: 5 152 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7815 (tm-30) REVERT: 5 165 VAL cc_start: 0.8519 (m) cc_final: 0.8274 (m) REVERT: 5 193 GLU cc_start: 0.8550 (mp0) cc_final: 0.8337 (mp0) REVERT: 6 28 GLU cc_start: 0.7924 (pm20) cc_final: 0.7688 (pm20) REVERT: 6 68 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7171 (ttp-110) REVERT: 6 72 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8833 (mp) REVERT: 6 79 ILE cc_start: 0.9428 (mt) cc_final: 0.8867 (mt) REVERT: 6 81 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7971 (tpp80) REVERT: 6 122 ILE cc_start: 0.9251 (tp) cc_final: 0.8976 (tp) REVERT: 6 163 GLU cc_start: 0.7933 (mp0) cc_final: 0.7379 (pm20) REVERT: 6 173 TYR cc_start: 0.7329 (t80) cc_final: 0.6973 (t80) REVERT: 7 44 LYS cc_start: 0.6727 (tppt) cc_final: 0.6302 (tppt) REVERT: 7 75 ASN cc_start: 0.8789 (m-40) cc_final: 0.8539 (m-40) REVERT: 7 193 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7433 (tm-30) REVERT: H 396 MET cc_start: 0.7877 (ptp) cc_final: 0.7456 (ptp) outliers start: 7 outliers final: 0 residues processed: 1275 average time/residue: 0.1837 time to fit residues: 360.4465 Evaluate side-chains 1165 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1163 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 109 optimal weight: 0.6980 chunk 84 optimal weight: 0.0040 chunk 218 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 164 optimal weight: 0.0970 chunk 243 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 280 optimal weight: 0.0060 chunk 285 optimal weight: 0.2980 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN F 5 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN 3 75 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 99 ASN 3 198 GLN 4 75 ASN ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 75 ASN ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.180180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.148388 restraints weight = 36393.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.152740 restraints weight = 20836.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.155750 restraints weight = 13948.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.157559 restraints weight = 10448.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159081 restraints weight = 8609.116| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24968 Z= 0.146 Angle : 0.685 14.125 33660 Z= 0.368 Chirality : 0.047 0.186 3881 Planarity : 0.004 0.051 4329 Dihedral : 5.548 55.139 3498 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.68 % Favored : 96.12 % Rotamer: Outliers : 0.23 % Allowed : 1.60 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.60 (0.14), residues: 3122 helix: 0.44 (0.15), residues: 1233 sheet: 0.20 (0.19), residues: 604 loop : -1.50 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 91 TYR 0.032 0.002 TYR 2 46 PHE 0.028 0.002 PHE A 175 HIS 0.005 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (24968) covalent geometry : angle 0.68529 / 0.37 (33660) hydrogen bonds : bond 0.03739 / 2.46 ( 1269) hydrogen bonds : angle 5.08845 / 3.57 ( 3699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1214 time to evaluate : 0.906 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: 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: symmetry clash REVERT: A 44 GLU cc_start: 0.8424 (pm20) cc_final: 0.8062 (pm20) REVERT: A 53 ARG cc_start: 0.7517 (tmt170) cc_final: 0.7315 (tmt170) REVERT: A 98 ILE cc_start: 0.8815 (mt) cc_final: 0.8408 (mt) REVERT: A 186 ASP cc_start: 0.7631 (p0) cc_final: 0.6925 (p0) REVERT: A 187 ASP cc_start: 0.7811 (m-30) cc_final: 0.7556 (m-30) REVERT: A 205 VAL cc_start: 0.8130 (t) cc_final: 0.7908 (t) REVERT: A 208 ASN cc_start: 0.8793 (p0) cc_final: 0.8148 (p0) REVERT: A 211 VAL cc_start: 0.8981 (t) cc_final: 0.7490 (p) REVERT: B 20 ARG cc_start: 0.8227 (ptp-110) cc_final: 0.7651 (ptp-170) REVERT: B 93 ARG cc_start: 0.8770 (mtt-85) cc_final: 0.8474 (mtt-85) REVERT: B 104 ASP cc_start: 0.7707 (t70) cc_final: 0.7434 (t0) REVERT: B 151 ASP cc_start: 0.9108 (t0) cc_final: 0.8898 (t0) REVERT: B 196 MET cc_start: 0.8401 (mmm) cc_final: 0.7902 (mmm) REVERT: B 201 GLU cc_start: 0.7730 (tm-30) cc_final: 0.6721 (tm-30) REVERT: B 208 ASN cc_start: 0.7565 (p0) cc_final: 0.7291 (p0) REVERT: B 214 VAL cc_start: 0.9394 (t) cc_final: 0.9105 (t) REVERT: C 9 ASP cc_start: 0.7709 (p0) cc_final: 0.7444 (p0) REVERT: C 44 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6385 (tm-30) REVERT: C 52 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8530 (ttmm) REVERT: C 110 LYS cc_start: 0.9433 (tptp) cc_final: 0.9081 (tptt) REVERT: C 148 TYR cc_start: 0.9212 (m-80) cc_final: 0.9001 (m-10) REVERT: C 175 PHE cc_start: 0.8991 (m-80) cc_final: 0.8743 (m-80) REVERT: C 185 PHE cc_start: 0.8471 (t80) cc_final: 0.8235 (t80) REVERT: C 189 MET cc_start: 0.8972 (ttm) cc_final: 0.8653 (ttm) REVERT: C 202 SER cc_start: 0.9091 (m) cc_final: 0.8674 (p) REVERT: C 203 GLU cc_start: 0.5964 (pm20) cc_final: 0.5668 (pm20) REVERT: C 208 ASN cc_start: 0.8534 (p0) cc_final: 0.7983 (p0) REVERT: C 210 GLU cc_start: 0.6731 (tt0) cc_final: 0.6191 (tt0) REVERT: C 211 VAL cc_start: 0.9147 (t) cc_final: 0.8917 (p) REVERT: C 214 VAL cc_start: 0.8900 (t) cc_final: 0.8593 (t) REVERT: C 219 ARG cc_start: 0.7419 (mtt-85) cc_final: 0.7150 (mtt90) REVERT: C 222 LYS cc_start: 0.8573 (tttt) cc_final: 0.8238 (tttp) REVERT: D 41 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8470 (ttpp) REVERT: D 57 LYS cc_start: 0.8630 (pttm) cc_final: 0.7880 (mppt) REVERT: D 64 ILE cc_start: 0.6657 (pt) cc_final: 0.6351 (pt) REVERT: D 67 ILE cc_start: 0.9398 (mm) cc_final: 0.9189 (mm) REVERT: D 115 LYS cc_start: 0.8475 (mttm) cc_final: 0.7289 (mtpt) REVERT: D 196 MET cc_start: 0.8851 (mmm) cc_final: 0.8534 (mmm) REVERT: D 200 ILE cc_start: 0.8966 (pt) cc_final: 0.8723 (pt) REVERT: D 227 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 6 MET cc_start: 0.6515 (ttm) cc_final: 0.5954 (ttm) REVERT: E 25 GLU cc_start: 0.8236 (tp30) cc_final: 0.6853 (tp30) REVERT: E 44 GLU cc_start: 0.7247 (pm20) cc_final: 0.6911 (pt0) REVERT: E 52 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8884 (ttpp) REVERT: E 86 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7403 (mmt180) REVERT: E 108 THR cc_start: 0.8994 (m) cc_final: 0.8729 (m) REVERT: E 148 TYR cc_start: 0.9043 (m-80) cc_final: 0.7987 (m-10) REVERT: E 158 GLU cc_start: 0.6991 (tt0) cc_final: 0.6741 (tt0) REVERT: E 164 ILE cc_start: 0.9143 (pt) cc_final: 0.8759 (pt) REVERT: E 186 ASP cc_start: 0.8110 (m-30) cc_final: 0.7748 (m-30) REVERT: E 218 ASP cc_start: 0.8874 (p0) cc_final: 0.8521 (p0) REVERT: E 222 LYS cc_start: 0.8452 (mttt) cc_final: 0.8048 (tptm) REVERT: E 234 GLU cc_start: 0.8334 (tp30) cc_final: 0.8096 (tp30) REVERT: F 9 ASP cc_start: 0.8445 (p0) cc_final: 0.7848 (p0) REVERT: F 26 TYR cc_start: 0.8958 (m-10) cc_final: 0.8744 (m-10) REVERT: F 107 ILE cc_start: 0.9165 (tt) cc_final: 0.8884 (tt) REVERT: F 112 LEU cc_start: 0.9285 (tp) cc_final: 0.8994 (tp) REVERT: F 158 GLU cc_start: 0.6434 (tt0) cc_final: 0.5773 (tt0) REVERT: F 173 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7325 (tm-30) REVERT: F 193 LEU cc_start: 0.9366 (mm) cc_final: 0.9136 (mm) REVERT: F 199 SER cc_start: 0.8661 (t) cc_final: 0.8270 (t) REVERT: F 211 VAL cc_start: 0.9047 (t) cc_final: 0.8813 (t) REVERT: F 229 LEU cc_start: 0.9064 (tt) cc_final: 0.8853 (tt) REVERT: F 232 TYR cc_start: 0.8850 (m-80) cc_final: 0.8569 (m-10) REVERT: G 47 ILE cc_start: 0.9239 (mt) cc_final: 0.9020 (mt) REVERT: G 51 ASP cc_start: 0.8560 (t0) cc_final: 0.8284 (t0) REVERT: G 58 LEU cc_start: 0.8538 (mp) cc_final: 0.8332 (mp) REVERT: G 66 LYS cc_start: 0.8893 (tppp) cc_final: 0.8357 (mptt) REVERT: G 112 LEU cc_start: 0.9157 (tp) cc_final: 0.8939 (tp) REVERT: G 171 VAL cc_start: 0.8971 (t) cc_final: 0.7757 (p) REVERT: G 187 ASP cc_start: 0.8457 (m-30) cc_final: 0.8098 (m-30) REVERT: G 191 LEU cc_start: 0.9279 (tp) cc_final: 0.9010 (tp) REVERT: G 234 GLU cc_start: 0.8490 (pp20) cc_final: 0.7963 (pp20) REVERT: 1 17 LEU cc_start: 0.9215 (pt) cc_final: 0.8956 (pt) REVERT: 1 25 MET cc_start: 0.7938 (mtm) cc_final: 0.7250 (ttm) REVERT: 1 111 LEU cc_start: 0.8936 (mt) cc_final: 0.8235 (mt) REVERT: 1 122 ILE cc_start: 0.8593 (mm) cc_final: 0.7843 (mm) REVERT: 1 173 TYR cc_start: 0.8511 (t80) cc_final: 0.7768 (t80) REVERT: 1 190 LYS cc_start: 0.7921 (ptmt) cc_final: 0.7681 (ptmm) REVERT: 2 45 ILE cc_start: 0.7822 (tt) cc_final: 0.7287 (tt) REVERT: 2 48 ILE cc_start: 0.8827 (mm) cc_final: 0.8577 (mm) REVERT: 2 72 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (mp) REVERT: 2 83 ARG cc_start: 0.7999 (ptm160) cc_final: 0.7534 (ptt180) REVERT: 2 162 ASP cc_start: 0.6278 (m-30) cc_final: 0.5673 (m-30) REVERT: 2 190 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8598 (ptmt) REVERT: 3 33 MET cc_start: 0.3426 (mtm) cc_final: 0.2812 (ptp) REVERT: 3 46 TYR cc_start: 0.7070 (m-80) cc_final: 0.6709 (m-80) REVERT: 3 48 ILE cc_start: 0.8962 (tp) cc_final: 0.8742 (tp) REVERT: 3 90 ILE cc_start: 0.9430 (mm) cc_final: 0.8941 (tt) REVERT: 3 123 TYR cc_start: 0.8026 (m-80) cc_final: 0.7604 (m-80) REVERT: 3 188 VAL cc_start: 0.7984 (t) cc_final: 0.7778 (t) REVERT: 3 190 LYS cc_start: 0.7476 (ttmm) cc_final: 0.7062 (ptmm) REVERT: 4 44 LYS cc_start: 0.6670 (tppt) cc_final: 0.6112 (tttt) REVERT: 4 48 ILE cc_start: 0.9306 (mm) cc_final: 0.8735 (mm) REVERT: 4 52 MET cc_start: 0.8284 (ttm) cc_final: 0.7901 (ttm) REVERT: 4 80 ARG cc_start: 0.8964 (mtp180) cc_final: 0.8265 (mtp180) REVERT: 4 88 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7836 (ttp-170) REVERT: 4 116 ASP cc_start: 0.7571 (p0) cc_final: 0.7296 (p0) REVERT: 4 135 LYS cc_start: 0.8143 (tppt) cc_final: 0.7606 (ttpt) REVERT: 4 190 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7977 (ptmm) REVERT: 5 46 TYR cc_start: 0.7983 (m-80) cc_final: 0.7298 (m-10) REVERT: 5 134 GLU cc_start: 0.7462 (mp0) cc_final: 0.7077 (mp0) REVERT: 6 28 GLU cc_start: 0.7991 (pm20) cc_final: 0.7665 (pm20) REVERT: 6 68 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7141 (ttp-110) REVERT: 6 72 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8813 (mp) REVERT: 6 81 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7897 (tpp80) REVERT: 6 122 ILE cc_start: 0.9202 (tp) cc_final: 0.8988 (tp) REVERT: 6 163 GLU cc_start: 0.7903 (mp0) cc_final: 0.7444 (pm20) REVERT: 7 193 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7131 (tm-30) REVERT: H 396 MET cc_start: 0.8065 (ptp) cc_final: 0.7785 (mtm) outliers start: 6 outliers final: 0 residues processed: 1217 average time/residue: 0.1767 time to fit residues: 333.0831 Evaluate side-chains 1102 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1100 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 22 optimal weight: 0.0370 chunk 137 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 198 GLN ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.178375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.145861 restraints weight = 36577.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.150197 restraints weight = 21106.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.153167 restraints weight = 14239.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.155129 restraints weight = 10744.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.156506 restraints weight = 8827.097| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24968 Z= 0.171 Angle : 0.698 14.074 33660 Z= 0.373 Chirality : 0.048 0.209 3881 Planarity : 0.004 0.048 4329 Dihedral : 5.492 52.578 3498 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.61 (0.14), residues: 3122 helix: 0.46 (0.15), residues: 1223 sheet: 0.15 (0.19), residues: 609 loop : -1.49 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 170 TYR 0.036 0.002 TYR 5 197 PHE 0.029 0.002 PHE B 175 HIS 0.005 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (24968) covalent geometry : angle 0.69807 / 0.37 (33660) hydrogen bonds : bond 0.03780 / 2.49 ( 1269) hydrogen bonds : angle 5.12767 / 3.60 ( 3699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1214 time to evaluate : 1.108 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: 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: A 25 GLU cc_start: 0.7924 (tt0) cc_final: 0.7665 (tt0) REVERT: A 98 ILE cc_start: 0.8853 (mt) cc_final: 0.8434 (mt) REVERT: A 166 MET cc_start: 0.8125 (mtp) cc_final: 0.7740 (ttp) REVERT: A 186 ASP cc_start: 0.7670 (p0) cc_final: 0.7006 (p0) REVERT: A 208 ASN cc_start: 0.8809 (p0) cc_final: 0.8367 (p0) REVERT: A 211 VAL cc_start: 0.8972 (t) cc_final: 0.7579 (p) REVERT: B 25 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 44 GLU cc_start: 0.8249 (tt0) cc_final: 0.7930 (tt0) REVERT: B 60 GLU cc_start: 0.8008 (tp30) cc_final: 0.7468 (tp30) REVERT: B 93 ARG cc_start: 0.8809 (mtt-85) cc_final: 0.8512 (mtt-85) REVERT: B 178 GLU cc_start: 0.7113 (tt0) cc_final: 0.6779 (tt0) REVERT: B 186 ASP cc_start: 0.8427 (p0) cc_final: 0.8208 (p0) REVERT: B 201 GLU cc_start: 0.7877 (tm-30) cc_final: 0.6717 (tm-30) REVERT: B 214 VAL cc_start: 0.9435 (t) cc_final: 0.9144 (t) REVERT: B 238 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7055 (mt-10) REVERT: C 9 ASP cc_start: 0.7660 (p0) cc_final: 0.7429 (p0) REVERT: C 44 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6699 (tm-30) REVERT: C 51 ASP cc_start: 0.9089 (t0) cc_final: 0.8590 (t0) REVERT: C 110 LYS cc_start: 0.9424 (tptp) cc_final: 0.9006 (tptt) REVERT: C 172 THR cc_start: 0.9376 (m) cc_final: 0.9019 (t) REVERT: C 175 PHE cc_start: 0.9049 (m-80) cc_final: 0.8771 (m-80) REVERT: C 189 MET cc_start: 0.8985 (ttm) cc_final: 0.8631 (ttm) REVERT: C 208 ASN cc_start: 0.8604 (p0) cc_final: 0.8288 (p0) REVERT: C 214 VAL cc_start: 0.8965 (t) cc_final: 0.8557 (p) REVERT: C 219 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.6815 (mtt-85) REVERT: C 222 LYS cc_start: 0.8652 (tttt) cc_final: 0.8366 (tttp) REVERT: D 20 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8072 (mtp85) REVERT: D 57 LYS cc_start: 0.8573 (pttm) cc_final: 0.7750 (mppt) REVERT: D 60 GLU cc_start: 0.7527 (pp20) cc_final: 0.6417 (pm20) REVERT: D 81 LEU cc_start: 0.9134 (mp) cc_final: 0.8797 (mp) REVERT: D 91 ARG cc_start: 0.8840 (tpt90) cc_final: 0.8416 (tpt170) REVERT: D 115 LYS cc_start: 0.8260 (mttm) cc_final: 0.7225 (mtpt) REVERT: D 130 ARG cc_start: 0.8445 (ptt-90) cc_final: 0.8210 (ptt-90) REVERT: D 151 ASP cc_start: 0.8777 (t0) cc_final: 0.8317 (t0) REVERT: D 174 PHE cc_start: 0.8529 (t80) cc_final: 0.7562 (t80) REVERT: D 185 PHE cc_start: 0.8059 (t80) cc_final: 0.7591 (t80) REVERT: D 227 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 234 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7400 (tm-30) REVERT: D 240 ILE cc_start: 0.8688 (pt) cc_final: 0.8430 (pt) REVERT: E 6 MET cc_start: 0.6381 (ttm) cc_final: 0.5805 (ttm) REVERT: E 8 TYR cc_start: 0.8028 (m-80) cc_final: 0.7092 (m-80) REVERT: E 25 GLU cc_start: 0.8278 (tp30) cc_final: 0.6929 (tp30) REVERT: E 28 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8508 (mmm160) REVERT: E 33 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8394 (ttt90) REVERT: E 44 GLU cc_start: 0.6969 (pm20) cc_final: 0.6762 (pt0) REVERT: E 86 ARG cc_start: 0.7799 (mmt180) cc_final: 0.7512 (mmt180) REVERT: E 108 THR cc_start: 0.9092 (m) cc_final: 0.8878 (m) REVERT: E 132 PHE cc_start: 0.9001 (m-80) cc_final: 0.8666 (m-10) REVERT: E 186 ASP cc_start: 0.8103 (m-30) cc_final: 0.7843 (m-30) REVERT: E 218 ASP cc_start: 0.8870 (p0) cc_final: 0.8501 (p0) REVERT: E 222 LYS cc_start: 0.8476 (mttt) cc_final: 0.8014 (tptm) REVERT: E 234 GLU cc_start: 0.7935 (tp30) cc_final: 0.7669 (tp30) REVERT: F 9 ASP cc_start: 0.8428 (p0) cc_final: 0.7920 (p0) REVERT: F 22 PHE cc_start: 0.9019 (m-80) cc_final: 0.8814 (m-10) REVERT: F 25 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8472 (mm-30) REVERT: F 26 TYR cc_start: 0.9073 (m-10) cc_final: 0.8791 (m-10) REVERT: F 33 ARG cc_start: 0.7824 (tpt90) cc_final: 0.7362 (mmm-85) REVERT: F 52 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8654 (mtpt) REVERT: F 151 ASP cc_start: 0.7961 (m-30) cc_final: 0.7727 (m-30) REVERT: F 158 GLU cc_start: 0.6604 (tt0) cc_final: 0.6065 (tt0) REVERT: F 173 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7379 (tm-30) REVERT: F 185 PHE cc_start: 0.8017 (t80) cc_final: 0.7751 (t80) REVERT: F 199 SER cc_start: 0.8704 (t) cc_final: 0.8407 (t) REVERT: F 211 VAL cc_start: 0.9024 (t) cc_final: 0.8661 (t) REVERT: F 227 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7485 (tp30) REVERT: F 234 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7413 (mt-10) REVERT: G 51 ASP cc_start: 0.8685 (t0) cc_final: 0.8422 (t0) REVERT: G 66 LYS cc_start: 0.8774 (tppp) cc_final: 0.8426 (mptt) REVERT: G 73 HIS cc_start: 0.8517 (p-80) cc_final: 0.7576 (p90) REVERT: G 89 ILE cc_start: 0.9380 (mm) cc_final: 0.9098 (mm) REVERT: G 104 ASP cc_start: 0.7721 (t70) cc_final: 0.7132 (t0) REVERT: G 171 VAL cc_start: 0.9097 (t) cc_final: 0.7936 (p) REVERT: G 187 ASP cc_start: 0.8565 (m-30) cc_final: 0.8036 (m-30) REVERT: G 191 LEU cc_start: 0.9281 (tp) cc_final: 0.8879 (tp) REVERT: G 234 GLU cc_start: 0.8439 (pp20) cc_final: 0.7892 (pp20) REVERT: G 237 ASN cc_start: 0.7331 (m110) cc_final: 0.7094 (m110) REVERT: 1 25 MET cc_start: 0.8008 (mtm) cc_final: 0.7333 (ttm) REVERT: 1 111 LEU cc_start: 0.8951 (mt) cc_final: 0.8276 (mt) REVERT: 1 122 ILE cc_start: 0.8659 (mm) cc_final: 0.7856 (mm) REVERT: 1 173 TYR cc_start: 0.8552 (t80) cc_final: 0.7829 (t80) REVERT: 1 193 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7725 (tm-30) REVERT: 2 45 ILE cc_start: 0.7915 (tt) cc_final: 0.7396 (tt) REVERT: 2 48 ILE cc_start: 0.8817 (mm) cc_final: 0.8484 (mm) REVERT: 2 83 ARG cc_start: 0.8086 (ptm160) cc_final: 0.7611 (ptt180) REVERT: 2 151 LEU cc_start: 0.9175 (mt) cc_final: 0.8900 (mt) REVERT: 3 29 LYS cc_start: 0.6026 (mttt) cc_final: 0.5094 (mptt) REVERT: 3 46 TYR cc_start: 0.6963 (m-80) cc_final: 0.6510 (m-80) REVERT: 3 90 ILE cc_start: 0.9410 (mm) cc_final: 0.9023 (tt) REVERT: 3 120 LYS cc_start: 0.8793 (mttm) cc_final: 0.8574 (mttp) REVERT: 3 123 TYR cc_start: 0.8325 (m-80) cc_final: 0.7585 (m-10) REVERT: 3 190 LYS cc_start: 0.7628 (ttmm) cc_final: 0.7051 (pttt) REVERT: 4 44 LYS cc_start: 0.6842 (tppt) cc_final: 0.6173 (tttt) REVERT: 4 52 MET cc_start: 0.8295 (ttm) cc_final: 0.8042 (ttm) REVERT: 4 87 VAL cc_start: 0.9246 (t) cc_final: 0.8942 (t) REVERT: 4 88 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7906 (ttp-170) REVERT: 4 133 GLU cc_start: 0.7407 (tt0) cc_final: 0.7092 (tt0) REVERT: 4 135 LYS cc_start: 0.8084 (tppt) cc_final: 0.7570 (ttpt) REVERT: 4 190 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8175 (ptmm) REVERT: 4 195 GLU cc_start: 0.7585 (tt0) cc_final: 0.7380 (tt0) REVERT: 5 46 TYR cc_start: 0.8115 (m-80) cc_final: 0.7526 (m-10) REVERT: 5 134 GLU cc_start: 0.7361 (mp0) cc_final: 0.7050 (mp0) REVERT: 5 203 GLU cc_start: 0.7510 (pm20) cc_final: 0.7136 (pm20) REVERT: 6 28 GLU cc_start: 0.8082 (pm20) cc_final: 0.7185 (pm20) REVERT: 6 81 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7819 (tpp80) REVERT: 6 173 TYR cc_start: 0.7083 (t80) cc_final: 0.6280 (t80) REVERT: 7 190 LYS cc_start: 0.8642 (pttp) cc_final: 0.8314 (pttp) REVERT: 7 193 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7145 (tm-30) REVERT: H 396 MET cc_start: 0.8181 (ptp) cc_final: 0.7956 (ptp) outliers start: 0 outliers final: 0 residues processed: 1214 average time/residue: 0.1743 time to fit residues: 329.5709 Evaluate side-chains 1117 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1117 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 113 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 110 optimal weight: 0.0970 chunk 163 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN 3 75 ASN 3 96 ASN ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 109 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.177151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.144571 restraints weight = 36585.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.148915 restraints weight = 21064.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151893 restraints weight = 14174.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153872 restraints weight = 10699.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.155260 restraints weight = 8764.775| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24968 Z= 0.171 Angle : 0.707 13.958 33660 Z= 0.378 Chirality : 0.048 0.261 3881 Planarity : 0.004 0.049 4329 Dihedral : 5.444 50.902 3498 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.61 (0.14), residues: 3122 helix: 0.43 (0.15), residues: 1221 sheet: 0.12 (0.19), residues: 608 loop : -1.43 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 86 TYR 0.032 0.002 TYR 7 148 PHE 0.021 0.002 PHE D 175 HIS 0.005 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (24968) covalent geometry : angle 0.70703 / 0.38 (33660) hydrogen bonds : bond 0.03787 / 2.48 ( 1269) hydrogen bonds : angle 5.18840 / 3.63 ( 3699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1217 time to evaluate : 0.987 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: 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: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7912 (tt0) cc_final: 0.7656 (tt0) REVERT: A 44 GLU cc_start: 0.8520 (pm20) cc_final: 0.8311 (pm20) REVERT: A 71 ASP cc_start: 0.8307 (t0) cc_final: 0.8082 (t0) REVERT: A 100 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8517 (ttm-80) REVERT: A 130 ARG cc_start: 0.8708 (ptt-90) cc_final: 0.8462 (ptt-90) REVERT: A 186 ASP cc_start: 0.7472 (p0) cc_final: 0.6812 (p0) REVERT: A 208 ASN cc_start: 0.8915 (p0) cc_final: 0.8608 (p0) REVERT: A 211 VAL cc_start: 0.8797 (t) cc_final: 0.7777 (p) REVERT: B 38 ILE cc_start: 0.9267 (mt) cc_final: 0.8968 (mt) REVERT: B 44 GLU cc_start: 0.8267 (tt0) cc_final: 0.7905 (tt0) REVERT: B 60 GLU cc_start: 0.8065 (tp30) cc_final: 0.7489 (tp30) REVERT: B 93 ARG cc_start: 0.8788 (mtt-85) cc_final: 0.8546 (mtt-85) REVERT: B 196 MET cc_start: 0.8774 (mmm) cc_final: 0.8373 (mmm) REVERT: B 214 VAL cc_start: 0.9450 (t) cc_final: 0.9159 (t) REVERT: B 238 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7120 (mt-10) REVERT: C 9 ASP cc_start: 0.7527 (p0) cc_final: 0.7318 (p0) REVERT: C 44 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 172 THR cc_start: 0.9415 (m) cc_final: 0.9052 (t) REVERT: C 189 MET cc_start: 0.9043 (ttm) cc_final: 0.8650 (ttm) REVERT: C 208 ASN cc_start: 0.8643 (p0) cc_final: 0.8176 (p0) REVERT: C 209 ILE cc_start: 0.9345 (pt) cc_final: 0.9076 (pt) REVERT: C 211 VAL cc_start: 0.9074 (t) cc_final: 0.8771 (p) REVERT: C 214 VAL cc_start: 0.8957 (t) cc_final: 0.8509 (p) REVERT: C 219 ARG cc_start: 0.7450 (mtt-85) cc_final: 0.7243 (mtt90) REVERT: C 222 LYS cc_start: 0.8625 (tttt) cc_final: 0.8320 (ttmm) REVERT: D 57 LYS cc_start: 0.8597 (pttm) cc_final: 0.7694 (mppt) REVERT: D 64 ILE cc_start: 0.6812 (pt) cc_final: 0.6484 (pt) REVERT: D 81 LEU cc_start: 0.9096 (mp) cc_final: 0.8821 (mp) REVERT: D 91 ARG cc_start: 0.8799 (tpt90) cc_final: 0.8313 (tpt170) REVERT: D 115 LYS cc_start: 0.8267 (mttm) cc_final: 0.7274 (mtpt) REVERT: D 196 MET cc_start: 0.8836 (mmm) cc_final: 0.8558 (mmm) REVERT: D 227 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 234 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 6 MET cc_start: 0.6183 (ttm) cc_final: 0.5648 (ttm) REVERT: E 8 TYR cc_start: 0.8029 (m-80) cc_final: 0.7077 (m-80) REVERT: E 25 GLU cc_start: 0.8355 (tp30) cc_final: 0.6980 (tp30) REVERT: E 28 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.7937 (mmm160) REVERT: E 33 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8156 (ttt-90) REVERT: E 86 ARG cc_start: 0.7834 (mmt180) cc_final: 0.7557 (mmt180) REVERT: E 148 TYR cc_start: 0.9032 (m-80) cc_final: 0.8309 (m-10) REVERT: E 186 ASP cc_start: 0.8066 (m-30) cc_final: 0.7824 (m-30) REVERT: E 218 ASP cc_start: 0.8967 (p0) cc_final: 0.8679 (p0) REVERT: E 222 LYS cc_start: 0.8462 (mttt) cc_final: 0.7979 (tptm) REVERT: E 234 GLU cc_start: 0.8036 (tp30) cc_final: 0.7745 (tp30) REVERT: F 9 ASP cc_start: 0.8500 (p0) cc_final: 0.8026 (p0) REVERT: F 25 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8471 (mm-30) REVERT: F 26 TYR cc_start: 0.9037 (m-10) cc_final: 0.8773 (m-10) REVERT: F 52 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8581 (mtpp) REVERT: F 64 ILE cc_start: 0.8983 (tt) cc_final: 0.8751 (tt) REVERT: F 99 ASN cc_start: 0.8818 (t0) cc_final: 0.8516 (t0) REVERT: F 151 ASP cc_start: 0.7975 (m-30) cc_final: 0.7686 (m-30) REVERT: F 158 GLU cc_start: 0.6671 (tt0) cc_final: 0.6025 (tt0) REVERT: F 193 LEU cc_start: 0.9497 (mm) cc_final: 0.9210 (mm) REVERT: F 199 SER cc_start: 0.8765 (t) cc_final: 0.8413 (t) REVERT: F 211 VAL cc_start: 0.8981 (t) cc_final: 0.8704 (t) REVERT: F 222 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7995 (tttt) REVERT: F 234 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7396 (mt-10) REVERT: G 9 ASP cc_start: 0.8045 (p0) cc_final: 0.7472 (p0) REVERT: G 51 ASP cc_start: 0.8968 (t0) cc_final: 0.8641 (t0) REVERT: G 66 LYS cc_start: 0.8835 (tppp) cc_final: 0.8417 (mptt) REVERT: G 73 HIS cc_start: 0.8512 (p-80) cc_final: 0.8187 (p90) REVERT: G 93 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8219 (mtt-85) REVERT: G 171 VAL cc_start: 0.9160 (t) cc_final: 0.8835 (m) REVERT: G 191 LEU cc_start: 0.9213 (tp) cc_final: 0.8653 (tp) REVERT: G 234 GLU cc_start: 0.8446 (pp20) cc_final: 0.7951 (pp20) REVERT: G 237 ASN cc_start: 0.7761 (m110) cc_final: 0.7442 (m-40) REVERT: 1 17 LEU cc_start: 0.9229 (pt) cc_final: 0.8999 (pt) REVERT: 1 25 MET cc_start: 0.8094 (mtm) cc_final: 0.7396 (ttm) REVERT: 1 111 LEU cc_start: 0.8932 (mt) cc_final: 0.8273 (mt) REVERT: 1 122 ILE cc_start: 0.8640 (mm) cc_final: 0.7857 (mm) REVERT: 1 173 TYR cc_start: 0.8645 (t80) cc_final: 0.7991 (t80) REVERT: 1 190 LYS cc_start: 0.8036 (ptmt) cc_final: 0.7748 (ptmm) REVERT: 1 193 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7744 (tm-30) REVERT: 2 45 ILE cc_start: 0.8031 (tt) cc_final: 0.7499 (tt) REVERT: 2 48 ILE cc_start: 0.8779 (mm) cc_final: 0.8320 (mm) REVERT: 2 52 MET cc_start: 0.8108 (ttm) cc_final: 0.7684 (ttm) REVERT: 2 83 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7627 (ptt180) REVERT: 2 151 LEU cc_start: 0.9219 (mt) cc_final: 0.8956 (mt) REVERT: 2 190 LYS cc_start: 0.9309 (tttt) cc_final: 0.8525 (tttt) REVERT: 3 46 TYR cc_start: 0.6923 (m-80) cc_final: 0.6380 (m-80) REVERT: 3 90 ILE cc_start: 0.9417 (mm) cc_final: 0.9014 (tt) REVERT: 3 120 LYS cc_start: 0.8819 (mttm) cc_final: 0.8545 (mttp) REVERT: 3 123 TYR cc_start: 0.8569 (m-80) cc_final: 0.7722 (m-80) REVERT: 3 202 GLU cc_start: 0.8170 (pm20) cc_final: 0.7961 (pm20) REVERT: 4 28 GLU cc_start: 0.5792 (pp20) cc_final: 0.5576 (pm20) REVERT: 4 44 LYS cc_start: 0.7092 (tppt) cc_final: 0.6300 (tttm) REVERT: 4 52 MET cc_start: 0.8291 (ttm) cc_final: 0.8025 (ttm) REVERT: 4 80 ARG cc_start: 0.9036 (mtp180) cc_final: 0.8659 (mtp180) REVERT: 4 87 VAL cc_start: 0.9261 (t) cc_final: 0.9008 (t) REVERT: 4 123 TYR cc_start: 0.8900 (m-80) cc_final: 0.7072 (m-80) REVERT: 4 133 GLU cc_start: 0.7233 (tt0) cc_final: 0.6914 (tt0) REVERT: 4 134 GLU cc_start: 0.7720 (mp0) cc_final: 0.7509 (mp0) REVERT: 4 135 LYS cc_start: 0.8157 (tppt) cc_final: 0.7566 (ttpt) REVERT: 4 151 LEU cc_start: 0.9156 (tp) cc_final: 0.8955 (tp) REVERT: 4 190 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8202 (ptmm) REVERT: 5 25 MET cc_start: 0.7465 (mtp) cc_final: 0.6944 (ttm) REVERT: 5 46 TYR cc_start: 0.8110 (m-80) cc_final: 0.7714 (m-10) REVERT: 5 55 THR cc_start: 0.7605 (p) cc_final: 0.7186 (p) REVERT: 5 134 GLU cc_start: 0.7691 (mp0) cc_final: 0.7398 (mp0) REVERT: 6 28 GLU cc_start: 0.8195 (pm20) cc_final: 0.7347 (pm20) REVERT: 6 79 ILE cc_start: 0.9593 (mt) cc_final: 0.9383 (mt) REVERT: 6 172 ILE cc_start: 0.8399 (tt) cc_final: 0.8054 (tt) REVERT: 6 173 TYR cc_start: 0.7069 (t80) cc_final: 0.6478 (t80) REVERT: 7 190 LYS cc_start: 0.8640 (pttp) cc_final: 0.8115 (pttp) REVERT: 7 193 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7161 (tm-30) REVERT: H 396 MET cc_start: 0.8278 (ptp) cc_final: 0.7840 (mtm) outliers start: 0 outliers final: 0 residues processed: 1217 average time/residue: 0.1704 time to fit residues: 322.9147 Evaluate side-chains 1120 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1120 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 213 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 196 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 251 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.175376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.142557 restraints weight = 36725.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.146761 restraints weight = 21224.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.149642 restraints weight = 14389.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.151592 restraints weight = 10895.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152886 restraints weight = 9001.220| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24968 Z= 0.192 Angle : 0.731 13.867 33660 Z= 0.388 Chirality : 0.049 0.259 3881 Planarity : 0.004 0.045 4329 Dihedral : 5.501 50.104 3498 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.64 (0.14), residues: 3122 helix: 0.32 (0.15), residues: 1242 sheet: 0.10 (0.19), residues: 618 loop : -1.38 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.038 0.002 TYR 5 197 PHE 0.024 0.002 PHE A 119 HIS 0.005 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (24968) covalent geometry : angle 0.73095 / 0.39 (33660) hydrogen bonds : bond 0.03865 / 2.55 ( 1269) hydrogen bonds : angle 5.27088 / 3.70 ( 3699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1206 time to evaluate : 1.003 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: 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: A 98 ILE cc_start: 0.8735 (mt) cc_final: 0.8350 (mt) REVERT: A 186 ASP cc_start: 0.7299 (p0) cc_final: 0.6891 (p0) REVERT: A 196 MET cc_start: 0.9062 (mmm) cc_final: 0.8440 (mmm) REVERT: A 208 ASN cc_start: 0.9049 (p0) cc_final: 0.8769 (p0) REVERT: A 211 VAL cc_start: 0.8981 (t) cc_final: 0.7846 (p) REVERT: A 222 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8510 (ttmm) REVERT: A 235 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7528 (ttm170) REVERT: B 58 LEU cc_start: 0.9116 (mt) cc_final: 0.8914 (mt) REVERT: B 60 GLU cc_start: 0.8123 (tp30) cc_final: 0.7519 (tp30) REVERT: B 72 GLU cc_start: 0.7542 (tt0) cc_final: 0.7336 (tt0) REVERT: B 93 ARG cc_start: 0.8759 (mtt-85) cc_final: 0.8522 (mtt-85) REVERT: B 214 VAL cc_start: 0.9458 (t) cc_final: 0.9117 (t) REVERT: C 9 ASP cc_start: 0.7559 (p0) cc_final: 0.7102 (p0) REVERT: C 44 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7282 (tm-30) REVERT: C 71 ASP cc_start: 0.8717 (t70) cc_final: 0.8507 (t70) REVERT: C 110 LYS cc_start: 0.9348 (tmtt) cc_final: 0.8926 (tptt) REVERT: C 172 THR cc_start: 0.9410 (m) cc_final: 0.9154 (t) REVERT: C 175 PHE cc_start: 0.9171 (m-80) cc_final: 0.8897 (m-80) REVERT: C 189 MET cc_start: 0.9056 (ttm) cc_final: 0.8667 (ttm) REVERT: C 208 ASN cc_start: 0.8604 (p0) cc_final: 0.8183 (p0) REVERT: C 211 VAL cc_start: 0.9084 (t) cc_final: 0.8824 (p) REVERT: C 214 VAL cc_start: 0.9003 (t) cc_final: 0.8553 (p) REVERT: C 219 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7351 (mtt90) REVERT: C 222 LYS cc_start: 0.8707 (tttt) cc_final: 0.8364 (ttmm) REVERT: D 24 VAL cc_start: 0.9069 (t) cc_final: 0.8857 (t) REVERT: D 64 ILE cc_start: 0.7076 (pt) cc_final: 0.6871 (pt) REVERT: D 91 ARG cc_start: 0.8845 (tpt90) cc_final: 0.8304 (tpt170) REVERT: D 112 LEU cc_start: 0.9190 (tp) cc_final: 0.8988 (tp) REVERT: D 115 LYS cc_start: 0.8253 (mttm) cc_final: 0.7258 (mtpt) REVERT: D 130 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8340 (ptt-90) REVERT: D 196 MET cc_start: 0.8784 (mmm) cc_final: 0.8570 (mmm) REVERT: D 222 LYS cc_start: 0.8879 (ptmt) cc_final: 0.8612 (ptmt) REVERT: D 227 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 228 GLU cc_start: 0.7900 (tp30) cc_final: 0.7656 (tp30) REVERT: D 234 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7443 (tm-30) REVERT: E 8 TYR cc_start: 0.8065 (m-80) cc_final: 0.7120 (m-80) REVERT: E 25 GLU cc_start: 0.8343 (tp30) cc_final: 0.6991 (tp30) REVERT: E 28 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8067 (mmm160) REVERT: E 33 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8244 (ttt-90) REVERT: E 86 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7620 (mmt180) REVERT: E 148 TYR cc_start: 0.9046 (m-80) cc_final: 0.8210 (m-10) REVERT: E 158 GLU cc_start: 0.7174 (tt0) cc_final: 0.6809 (tt0) REVERT: E 186 ASP cc_start: 0.8138 (m-30) cc_final: 0.7891 (m-30) REVERT: E 222 LYS cc_start: 0.8467 (mttt) cc_final: 0.8182 (mttp) REVERT: E 234 GLU cc_start: 0.8077 (tp30) cc_final: 0.7853 (tp30) REVERT: F 9 ASP cc_start: 0.8589 (p0) cc_final: 0.8102 (p0) REVERT: F 26 TYR cc_start: 0.9000 (m-10) cc_final: 0.8742 (m-10) REVERT: F 52 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8625 (mtpt) REVERT: F 95 GLU cc_start: 0.8131 (tp30) cc_final: 0.7702 (tp30) REVERT: F 158 GLU cc_start: 0.6757 (tt0) cc_final: 0.6199 (tt0) REVERT: F 173 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7640 (tm-30) REVERT: F 211 VAL cc_start: 0.8992 (t) cc_final: 0.8584 (t) REVERT: F 234 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7422 (mt-10) REVERT: G 9 ASP cc_start: 0.8108 (p0) cc_final: 0.7553 (p0) REVERT: G 51 ASP cc_start: 0.9039 (t0) cc_final: 0.8612 (t0) REVERT: G 73 HIS cc_start: 0.8536 (p-80) cc_final: 0.8180 (p90) REVERT: G 89 ILE cc_start: 0.9307 (mm) cc_final: 0.9042 (mm) REVERT: G 93 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8277 (mtt-85) REVERT: G 104 ASP cc_start: 0.7533 (t70) cc_final: 0.7231 (t70) REVERT: G 110 LYS cc_start: 0.8836 (tttt) cc_final: 0.8568 (tptp) REVERT: G 171 VAL cc_start: 0.9271 (t) cc_final: 0.8989 (m) REVERT: G 174 PHE cc_start: 0.8583 (t80) cc_final: 0.8077 (t80) REVERT: G 186 ASP cc_start: 0.8198 (m-30) cc_final: 0.7790 (p0) REVERT: G 191 LEU cc_start: 0.9126 (tp) cc_final: 0.8836 (tp) REVERT: G 234 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7817 (tm-30) REVERT: G 237 ASN cc_start: 0.7599 (m110) cc_final: 0.7256 (m110) REVERT: 1 17 LEU cc_start: 0.9233 (pt) cc_final: 0.9007 (pt) REVERT: 1 25 MET cc_start: 0.7970 (mtm) cc_final: 0.7283 (ttm) REVERT: 1 52 MET cc_start: 0.8254 (ttp) cc_final: 0.8038 (ttp) REVERT: 1 111 LEU cc_start: 0.8932 (mt) cc_final: 0.8247 (mt) REVERT: 1 122 ILE cc_start: 0.8602 (mm) cc_final: 0.7835 (mm) REVERT: 1 123 TYR cc_start: 0.8635 (m-80) cc_final: 0.8356 (m-80) REVERT: 1 172 ILE cc_start: 0.8349 (mm) cc_final: 0.7744 (mm) REVERT: 1 173 TYR cc_start: 0.8713 (t80) cc_final: 0.8048 (t80) REVERT: 1 190 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7875 (ptmm) REVERT: 1 193 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7619 (tm-30) REVERT: 2 45 ILE cc_start: 0.8097 (tt) cc_final: 0.7509 (tt) REVERT: 2 48 ILE cc_start: 0.8841 (mm) cc_final: 0.8580 (mm) REVERT: 2 83 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7669 (ptt180) REVERT: 3 46 TYR cc_start: 0.7078 (m-80) cc_final: 0.6562 (m-80) REVERT: 3 83 ARG cc_start: 0.7063 (ptp-170) cc_final: 0.6697 (ptp-170) REVERT: 3 90 ILE cc_start: 0.9407 (mm) cc_final: 0.9056 (tt) REVERT: 3 110 LEU cc_start: 0.9415 (mt) cc_final: 0.9131 (mt) REVERT: 3 120 LYS cc_start: 0.8864 (mttm) cc_final: 0.8409 (mttp) REVERT: 3 123 TYR cc_start: 0.8463 (m-80) cc_final: 0.7809 (m-80) REVERT: 3 202 GLU cc_start: 0.8380 (pm20) cc_final: 0.8127 (pm20) REVERT: 4 17 LEU cc_start: 0.8988 (mt) cc_final: 0.8753 (mt) REVERT: 4 20 LYS cc_start: 0.8357 (tptm) cc_final: 0.7683 (pttm) REVERT: 4 44 LYS cc_start: 0.7212 (tppt) cc_final: 0.6432 (tttt) REVERT: 4 52 MET cc_start: 0.8300 (ttm) cc_final: 0.8024 (ttm) REVERT: 4 87 VAL cc_start: 0.9312 (t) cc_final: 0.9030 (t) REVERT: 4 123 TYR cc_start: 0.8992 (m-80) cc_final: 0.7301 (m-80) REVERT: 4 133 GLU cc_start: 0.7210 (tt0) cc_final: 0.6993 (tt0) REVERT: 4 135 LYS cc_start: 0.8315 (tppt) cc_final: 0.7626 (ttpt) REVERT: 4 137 ILE cc_start: 0.8432 (mm) cc_final: 0.7643 (tt) REVERT: 4 190 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8224 (ptmm) REVERT: 5 25 MET cc_start: 0.7514 (mtp) cc_final: 0.7019 (ttm) REVERT: 5 55 THR cc_start: 0.7690 (p) cc_final: 0.7255 (p) REVERT: 5 123 TYR cc_start: 0.8617 (m-80) cc_final: 0.7959 (m-10) REVERT: 5 134 GLU cc_start: 0.7828 (mp0) cc_final: 0.7453 (mp0) REVERT: 5 191 ILE cc_start: 0.8120 (mt) cc_final: 0.7899 (mt) REVERT: 6 28 GLU cc_start: 0.8382 (pm20) cc_final: 0.7658 (pm20) REVERT: 6 81 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7778 (mmt90) REVERT: 6 120 LYS cc_start: 0.7848 (mttm) cc_final: 0.7522 (mtpt) REVERT: 6 122 ILE cc_start: 0.9007 (tp) cc_final: 0.8624 (tp) REVERT: 6 163 GLU cc_start: 0.7982 (pm20) cc_final: 0.7753 (pm20) REVERT: 6 173 TYR cc_start: 0.7321 (t80) cc_final: 0.6702 (t80) REVERT: 7 75 ASN cc_start: 0.8831 (m-40) cc_final: 0.8460 (t0) REVERT: 7 120 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8257 (mtmt) REVERT: 7 190 LYS cc_start: 0.8484 (pttp) cc_final: 0.7888 (pttp) REVERT: 7 193 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6977 (tm-30) REVERT: H 396 MET cc_start: 0.8443 (ptp) cc_final: 0.7879 (ptp) outliers start: 0 outliers final: 0 residues processed: 1206 average time/residue: 0.1761 time to fit residues: 331.6999 Evaluate side-chains 1117 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1117 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 180 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 224 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN 2 198 GLN 3 75 ASN ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 75 ASN 6 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.174422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.141706 restraints weight = 36864.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.145860 restraints weight = 21459.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.148601 restraints weight = 14562.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.150405 restraints weight = 11174.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151770 restraints weight = 9315.207| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24968 Z= 0.201 Angle : 0.754 13.751 33660 Z= 0.400 Chirality : 0.049 0.263 3881 Planarity : 0.004 0.069 4329 Dihedral : 5.584 47.159 3498 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.67 (0.14), residues: 3122 helix: 0.31 (0.15), residues: 1230 sheet: 0.10 (0.19), residues: 610 loop : -1.41 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 1 80 TYR 0.035 0.002 TYR 7 148 PHE 0.036 0.002 PHE D 185 HIS 0.005 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (24968) covalent geometry : angle 0.75385 / 0.40 (33660) hydrogen bonds : bond 0.03853 / 2.54 ( 1269) hydrogen bonds : angle 5.32569 / 3.72 ( 3699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1216 time to evaluate : 0.973 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: 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: symmetry clash REVERT: A 44 GLU cc_start: 0.8537 (pm20) cc_final: 0.8246 (pm20) REVERT: A 98 ILE cc_start: 0.8787 (mt) cc_final: 0.8368 (mt) REVERT: A 117 CYS cc_start: 0.8468 (m) cc_final: 0.8266 (m) REVERT: A 130 ARG cc_start: 0.8298 (ptt90) cc_final: 0.8001 (ptt-90) REVERT: A 186 ASP cc_start: 0.7500 (p0) cc_final: 0.6649 (p0) REVERT: A 196 MET cc_start: 0.9051 (mmm) cc_final: 0.8360 (mmm) REVERT: A 208 ASN cc_start: 0.9024 (p0) cc_final: 0.8758 (p0) REVERT: A 211 VAL cc_start: 0.8744 (t) cc_final: 0.7939 (p) REVERT: A 214 VAL cc_start: 0.9009 (t) cc_final: 0.8785 (t) REVERT: A 222 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8554 (ttmm) REVERT: B 8 TYR cc_start: 0.8447 (m-80) cc_final: 0.8181 (m-80) REVERT: B 58 LEU cc_start: 0.9107 (mt) cc_final: 0.8902 (mt) REVERT: B 60 GLU cc_start: 0.8108 (tp30) cc_final: 0.7467 (tp30) REVERT: B 72 GLU cc_start: 0.7551 (tt0) cc_final: 0.7256 (tt0) REVERT: B 93 ARG cc_start: 0.8700 (mtt-85) cc_final: 0.8486 (mtt-85) REVERT: B 134 VAL cc_start: 0.8951 (p) cc_final: 0.8750 (p) REVERT: B 137 LEU cc_start: 0.9308 (mt) cc_final: 0.9093 (mm) REVERT: B 186 ASP cc_start: 0.8460 (p0) cc_final: 0.8039 (p0) REVERT: B 201 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 208 ASN cc_start: 0.7695 (p0) cc_final: 0.7487 (p0) REVERT: B 214 VAL cc_start: 0.9400 (t) cc_final: 0.9117 (t) REVERT: B 215 LYS cc_start: 0.8772 (tppp) cc_final: 0.8550 (tppp) REVERT: B 232 TYR cc_start: 0.8616 (m-80) cc_final: 0.8318 (m-80) REVERT: C 44 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 110 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8914 (tptt) REVERT: C 172 THR cc_start: 0.9402 (m) cc_final: 0.9137 (t) REVERT: C 175 PHE cc_start: 0.9274 (m-80) cc_final: 0.8985 (m-80) REVERT: C 189 MET cc_start: 0.9046 (ttm) cc_final: 0.8593 (ttm) REVERT: C 208 ASN cc_start: 0.8622 (p0) cc_final: 0.8208 (p0) REVERT: C 209 ILE cc_start: 0.9365 (pt) cc_final: 0.9131 (pt) REVERT: C 214 VAL cc_start: 0.8956 (t) cc_final: 0.8477 (p) REVERT: C 217 ASP cc_start: 0.8675 (p0) cc_final: 0.8451 (p0) REVERT: C 218 ASP cc_start: 0.8167 (p0) cc_final: 0.7398 (p0) REVERT: C 220 THR cc_start: 0.8106 (p) cc_final: 0.7792 (p) REVERT: C 222 LYS cc_start: 0.8633 (tttt) cc_final: 0.8374 (ttmm) REVERT: D 64 ILE cc_start: 0.7107 (pt) cc_final: 0.6881 (pt) REVERT: D 91 ARG cc_start: 0.8840 (tpt90) cc_final: 0.8240 (tpt170) REVERT: D 112 LEU cc_start: 0.9189 (tp) cc_final: 0.8891 (tp) REVERT: D 115 LYS cc_start: 0.8202 (mttm) cc_final: 0.7254 (mtpt) REVERT: D 196 MET cc_start: 0.8797 (mmm) cc_final: 0.8499 (mmm) REVERT: D 227 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8103 (tm-30) REVERT: D 228 GLU cc_start: 0.7814 (tp30) cc_final: 0.7595 (tp30) REVERT: D 234 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7567 (tm-30) REVERT: E 9 ASP cc_start: 0.6831 (p0) cc_final: 0.5805 (p0) REVERT: E 25 GLU cc_start: 0.8286 (tp30) cc_final: 0.7033 (tp30) REVERT: E 28 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7800 (mmm160) REVERT: E 33 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8179 (ttt-90) REVERT: E 107 ILE cc_start: 0.9128 (tt) cc_final: 0.8914 (tt) REVERT: E 148 TYR cc_start: 0.8996 (m-80) cc_final: 0.8069 (m-10) REVERT: E 158 GLU cc_start: 0.7111 (tt0) cc_final: 0.6846 (tt0) REVERT: E 189 MET cc_start: 0.8415 (ttp) cc_final: 0.7984 (ttp) REVERT: E 213 TYR cc_start: 0.8484 (p90) cc_final: 0.8274 (p90) REVERT: E 222 LYS cc_start: 0.8441 (mttt) cc_final: 0.7953 (tptm) REVERT: F 9 ASP cc_start: 0.8646 (p0) cc_final: 0.8157 (p0) REVERT: F 26 TYR cc_start: 0.8966 (m-10) cc_final: 0.8713 (m-10) REVERT: F 52 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8550 (mtpt) REVERT: F 95 GLU cc_start: 0.8449 (tp30) cc_final: 0.7866 (tp30) REVERT: F 99 ASN cc_start: 0.8898 (t0) cc_final: 0.8526 (t0) REVERT: F 107 ILE cc_start: 0.9334 (tt) cc_final: 0.8990 (tt) REVERT: F 112 LEU cc_start: 0.9240 (tp) cc_final: 0.8878 (tp) REVERT: F 158 GLU cc_start: 0.6895 (tt0) cc_final: 0.6357 (tt0) REVERT: F 173 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7565 (tm-30) REVERT: F 222 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8018 (ptmm) REVERT: G 9 ASP cc_start: 0.8125 (p0) cc_final: 0.7591 (p0) REVERT: G 51 ASP cc_start: 0.8991 (t0) cc_final: 0.8610 (t0) REVERT: G 73 HIS cc_start: 0.8560 (p-80) cc_final: 0.7519 (p90) REVERT: G 110 LYS cc_start: 0.8838 (tttt) cc_final: 0.8637 (tptm) REVERT: G 112 LEU cc_start: 0.9254 (tp) cc_final: 0.8981 (tp) REVERT: G 174 PHE cc_start: 0.8488 (t80) cc_final: 0.8287 (t80) REVERT: G 191 LEU cc_start: 0.9223 (tp) cc_final: 0.8816 (tp) REVERT: G 234 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7527 (tm-30) REVERT: G 237 ASN cc_start: 0.7668 (m110) cc_final: 0.7254 (m110) REVERT: 1 17 LEU cc_start: 0.9322 (pt) cc_final: 0.8893 (pt) REVERT: 1 25 MET cc_start: 0.7976 (mtm) cc_final: 0.7249 (ttm) REVERT: 1 52 MET cc_start: 0.8428 (ttp) cc_final: 0.8070 (ttp) REVERT: 1 111 LEU cc_start: 0.8912 (mt) cc_final: 0.8226 (mt) REVERT: 1 122 ILE cc_start: 0.8660 (mm) cc_final: 0.7821 (mm) REVERT: 1 172 ILE cc_start: 0.8584 (mm) cc_final: 0.7797 (mm) REVERT: 1 173 TYR cc_start: 0.8700 (t80) cc_final: 0.8024 (t80) REVERT: 1 190 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7616 (ptmm) REVERT: 1 193 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7539 (tm-30) REVERT: 2 45 ILE cc_start: 0.7985 (tt) cc_final: 0.7424 (tt) REVERT: 2 48 ILE cc_start: 0.8866 (mm) cc_final: 0.8524 (mm) REVERT: 2 83 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7637 (ptt180) REVERT: 2 190 LYS cc_start: 0.8795 (tptm) cc_final: 0.8475 (tptt) REVERT: 3 46 TYR cc_start: 0.7039 (m-80) cc_final: 0.6509 (m-80) REVERT: 3 54 MET cc_start: 0.8073 (ttp) cc_final: 0.7660 (ttp) REVERT: 3 90 ILE cc_start: 0.9520 (mm) cc_final: 0.9073 (tt) REVERT: 3 110 LEU cc_start: 0.9358 (mt) cc_final: 0.8895 (mt) REVERT: 3 123 TYR cc_start: 0.8522 (m-80) cc_final: 0.7900 (m-80) REVERT: 3 154 ARG cc_start: 0.5733 (ptp-170) cc_final: 0.5453 (ptp-170) REVERT: 3 202 GLU cc_start: 0.8234 (pm20) cc_final: 0.8026 (pm20) REVERT: 4 20 LYS cc_start: 0.8456 (tptm) cc_final: 0.7769 (pttm) REVERT: 4 44 LYS cc_start: 0.7339 (tppt) cc_final: 0.6515 (tttt) REVERT: 4 52 MET cc_start: 0.8313 (ttm) cc_final: 0.8062 (ttm) REVERT: 4 87 VAL cc_start: 0.9319 (t) cc_final: 0.9042 (t) REVERT: 4 123 TYR cc_start: 0.8994 (m-80) cc_final: 0.7231 (m-80) REVERT: 4 133 GLU cc_start: 0.7203 (tt0) cc_final: 0.6992 (tt0) REVERT: 4 134 GLU cc_start: 0.7763 (mp0) cc_final: 0.7494 (mp0) REVERT: 4 135 LYS cc_start: 0.8392 (tppt) cc_final: 0.7642 (ttpt) REVERT: 4 137 ILE cc_start: 0.8344 (mm) cc_final: 0.7948 (mm) REVERT: 4 190 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8250 (ptmm) REVERT: 5 25 MET cc_start: 0.7811 (mtp) cc_final: 0.7324 (ttm) REVERT: 5 46 TYR cc_start: 0.8247 (m-80) cc_final: 0.7810 (m-80) REVERT: 5 55 THR cc_start: 0.7866 (p) cc_final: 0.7475 (p) REVERT: 5 123 TYR cc_start: 0.8532 (m-80) cc_final: 0.8251 (m-10) REVERT: 5 134 GLU cc_start: 0.7849 (mp0) cc_final: 0.7531 (mp0) REVERT: 6 28 GLU cc_start: 0.8401 (pm20) cc_final: 0.7647 (pm20) REVERT: 6 79 ILE cc_start: 0.9378 (mt) cc_final: 0.8668 (mt) REVERT: 6 81 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7729 (mmt90) REVERT: 6 122 ILE cc_start: 0.9055 (tp) cc_final: 0.8665 (tp) REVERT: 6 133 GLU cc_start: 0.8385 (tt0) cc_final: 0.8160 (tt0) REVERT: 6 163 GLU cc_start: 0.7985 (pm20) cc_final: 0.7696 (pm20) REVERT: 6 172 ILE cc_start: 0.8158 (tt) cc_final: 0.7956 (tt) REVERT: 6 173 TYR cc_start: 0.7348 (t80) cc_final: 0.6710 (t80) REVERT: 7 75 ASN cc_start: 0.8875 (m-40) cc_final: 0.8464 (t0) REVERT: 7 120 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8152 (mtmt) REVERT: 7 190 LYS cc_start: 0.8571 (pttp) cc_final: 0.8153 (pttp) REVERT: 7 193 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6906 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1216 average time/residue: 0.1748 time to fit residues: 332.2101 Evaluate side-chains 1124 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1124 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 189 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 284 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN 3 75 ASN 3 198 GLN ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.174646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.142026 restraints weight = 36768.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.146291 restraints weight = 21242.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149164 restraints weight = 14311.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.151038 restraints weight = 10868.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.152221 restraints weight = 8984.604| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24968 Z= 0.188 Angle : 0.755 13.467 33660 Z= 0.400 Chirality : 0.050 0.274 3881 Planarity : 0.004 0.058 4329 Dihedral : 5.602 42.811 3498 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.71 (0.14), residues: 3122 helix: 0.24 (0.15), residues: 1231 sheet: 0.09 (0.20), residues: 603 loop : -1.39 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 4 68 TYR 0.035 0.002 TYR 7 148 PHE 0.044 0.002 PHE 2 196 HIS 0.006 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (24968) covalent geometry : angle 0.75525 / 0.40 (33660) hydrogen bonds : bond 0.03925 / 2.57 ( 1269) hydrogen bonds : angle 5.39877 / 3.77 ( 3699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1201 time to evaluate : 0.983 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: 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: A 25 GLU cc_start: 0.7900 (tt0) cc_final: 0.7588 (tt0) REVERT: A 43 LYS cc_start: 0.8610 (tmtt) cc_final: 0.8321 (tttm) REVERT: A 71 ASP cc_start: 0.8397 (t0) cc_final: 0.8146 (t0) REVERT: A 95 GLU cc_start: 0.8345 (tp30) cc_final: 0.8109 (tp30) REVERT: A 98 ILE cc_start: 0.8781 (mt) cc_final: 0.8331 (mt) REVERT: A 117 CYS cc_start: 0.8497 (m) cc_final: 0.8273 (m) REVERT: A 130 ARG cc_start: 0.8301 (ptt90) cc_final: 0.7839 (ptt-90) REVERT: A 186 ASP cc_start: 0.7366 (p0) cc_final: 0.6605 (p0) REVERT: A 196 MET cc_start: 0.9063 (mmm) cc_final: 0.8328 (mmm) REVERT: A 208 ASN cc_start: 0.9036 (p0) cc_final: 0.8752 (p0) REVERT: A 211 VAL cc_start: 0.8980 (t) cc_final: 0.7968 (p) REVERT: A 222 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8365 (ttmm) REVERT: B 8 TYR cc_start: 0.8272 (m-80) cc_final: 0.8038 (m-80) REVERT: B 20 ARG cc_start: 0.8253 (ptp-110) cc_final: 0.7931 (ptm-80) REVERT: B 58 LEU cc_start: 0.9072 (mt) cc_final: 0.8842 (mt) REVERT: B 60 GLU cc_start: 0.8094 (tp30) cc_final: 0.7421 (tp30) REVERT: B 137 LEU cc_start: 0.9288 (mt) cc_final: 0.9088 (mm) REVERT: B 180 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: B 181 ASP cc_start: 0.7630 (m-30) cc_final: 0.7323 (m-30) REVERT: B 186 ASP cc_start: 0.8507 (p0) cc_final: 0.8080 (p0) REVERT: B 187 ASP cc_start: 0.8280 (m-30) cc_final: 0.8070 (m-30) REVERT: B 201 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 214 VAL cc_start: 0.9368 (t) cc_final: 0.8959 (p) REVERT: B 232 TYR cc_start: 0.8688 (m-80) cc_final: 0.8463 (m-80) REVERT: B 239 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7517 (ttp-170) REVERT: C 9 ASP cc_start: 0.7360 (p0) cc_final: 0.7066 (p0) REVERT: C 14 VAL cc_start: 0.8911 (t) cc_final: 0.8581 (t) REVERT: C 68 TYR cc_start: 0.8626 (m-10) cc_final: 0.8328 (m-10) REVERT: C 110 LYS cc_start: 0.9279 (tptp) cc_final: 0.8935 (tptt) REVERT: C 175 PHE cc_start: 0.9310 (m-80) cc_final: 0.9066 (m-80) REVERT: C 189 MET cc_start: 0.9060 (ttm) cc_final: 0.8605 (ttm) REVERT: C 208 ASN cc_start: 0.8653 (p0) cc_final: 0.8180 (p0) REVERT: C 214 VAL cc_start: 0.8947 (t) cc_final: 0.8521 (p) REVERT: C 222 LYS cc_start: 0.8602 (tttt) cc_final: 0.8306 (ttmm) REVERT: D 64 ILE cc_start: 0.7098 (pt) cc_final: 0.6885 (pt) REVERT: D 81 LEU cc_start: 0.9079 (mp) cc_final: 0.8819 (mp) REVERT: D 91 ARG cc_start: 0.9002 (tpt90) cc_final: 0.8248 (tpt170) REVERT: D 130 ARG cc_start: 0.8817 (ptt-90) cc_final: 0.8425 (ptt-90) REVERT: D 185 PHE cc_start: 0.8157 (t80) cc_final: 0.7883 (t80) REVERT: D 234 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 9 ASP cc_start: 0.7044 (p0) cc_final: 0.5994 (p0) REVERT: E 25 GLU cc_start: 0.8291 (tp30) cc_final: 0.7027 (tp30) REVERT: E 28 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.7795 (mmm160) REVERT: E 33 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8158 (ttt-90) REVERT: E 74 ILE cc_start: 0.9289 (mp) cc_final: 0.9054 (mp) REVERT: E 148 TYR cc_start: 0.8990 (m-80) cc_final: 0.7936 (m-10) REVERT: E 158 GLU cc_start: 0.6909 (tt0) cc_final: 0.6442 (tt0) REVERT: E 210 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7468 (mm-30) REVERT: F 9 ASP cc_start: 0.8626 (p0) cc_final: 0.8070 (p0) REVERT: F 95 GLU cc_start: 0.8513 (tp30) cc_final: 0.7896 (tp30) REVERT: F 107 ILE cc_start: 0.9282 (tt) cc_final: 0.9014 (tt) REVERT: F 112 LEU cc_start: 0.9170 (tp) cc_final: 0.8795 (tp) REVERT: F 158 GLU cc_start: 0.7003 (tt0) cc_final: 0.6411 (tt0) REVERT: F 193 LEU cc_start: 0.9418 (mm) cc_final: 0.9188 (mm) REVERT: F 196 MET cc_start: 0.9051 (tpp) cc_final: 0.8601 (tpp) REVERT: F 211 VAL cc_start: 0.9157 (t) cc_final: 0.8896 (t) REVERT: F 213 TYR cc_start: 0.8343 (p90) cc_final: 0.8109 (p90) REVERT: F 222 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8012 (ptmm) REVERT: F 234 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7335 (mt-10) REVERT: G 9 ASP cc_start: 0.8132 (p0) cc_final: 0.7608 (p0) REVERT: G 51 ASP cc_start: 0.9179 (t0) cc_final: 0.8693 (t0) REVERT: G 66 LYS cc_start: 0.9000 (tppp) cc_final: 0.8468 (mptt) REVERT: G 112 LEU cc_start: 0.9264 (tp) cc_final: 0.9004 (tp) REVERT: G 186 ASP cc_start: 0.8560 (m-30) cc_final: 0.8128 (p0) REVERT: G 191 LEU cc_start: 0.9191 (tp) cc_final: 0.8756 (tp) REVERT: G 237 ASN cc_start: 0.7430 (m110) cc_final: 0.7178 (m110) REVERT: 1 17 LEU cc_start: 0.9222 (pt) cc_final: 0.8714 (pt) REVERT: 1 25 MET cc_start: 0.7935 (mtm) cc_final: 0.7197 (ttm) REVERT: 1 111 LEU cc_start: 0.8913 (mt) cc_final: 0.8241 (mt) REVERT: 1 122 ILE cc_start: 0.8620 (mm) cc_final: 0.7807 (mm) REVERT: 1 172 ILE cc_start: 0.8325 (mm) cc_final: 0.7795 (mm) REVERT: 1 173 TYR cc_start: 0.8655 (t80) cc_final: 0.7954 (t80) REVERT: 1 190 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7876 (ptmm) REVERT: 1 193 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7598 (tm-30) REVERT: 1 208 LEU cc_start: 0.6172 (pp) cc_final: 0.5968 (pp) REVERT: 2 45 ILE cc_start: 0.7939 (tt) cc_final: 0.7416 (tt) REVERT: 2 52 MET cc_start: 0.8189 (ttm) cc_final: 0.7453 (ttm) REVERT: 2 83 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7591 (ptt180) REVERT: 3 40 LYS cc_start: 0.4307 (mttt) cc_final: 0.4041 (mttt) REVERT: 3 46 TYR cc_start: 0.7084 (m-80) cc_final: 0.6578 (m-80) REVERT: 3 54 MET cc_start: 0.8105 (ttp) cc_final: 0.7711 (ttp) REVERT: 3 110 LEU cc_start: 0.9382 (mt) cc_final: 0.8917 (mt) REVERT: 3 123 TYR cc_start: 0.8514 (m-80) cc_final: 0.7946 (m-80) REVERT: 3 154 ARG cc_start: 0.5745 (ptp-170) cc_final: 0.5405 (ptp-170) REVERT: 3 202 GLU cc_start: 0.8352 (pm20) cc_final: 0.8123 (pm20) REVERT: 4 17 LEU cc_start: 0.8982 (mt) cc_final: 0.8706 (mt) REVERT: 4 20 LYS cc_start: 0.8215 (tptm) cc_final: 0.7566 (pttm) REVERT: 4 28 GLU cc_start: 0.6042 (pp20) cc_final: 0.5733 (pm20) REVERT: 4 44 LYS cc_start: 0.7702 (tppt) cc_final: 0.7138 (tttt) REVERT: 4 52 MET cc_start: 0.8295 (ttm) cc_final: 0.8005 (ttm) REVERT: 4 87 VAL cc_start: 0.9318 (t) cc_final: 0.9014 (t) REVERT: 4 123 TYR cc_start: 0.8953 (m-80) cc_final: 0.7248 (m-10) REVERT: 4 135 LYS cc_start: 0.8454 (tppt) cc_final: 0.7706 (ttpt) REVERT: 4 137 ILE cc_start: 0.8333 (mm) cc_final: 0.7595 (tt) REVERT: 4 190 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8319 (ptmm) REVERT: 5 25 MET cc_start: 0.7725 (mtp) cc_final: 0.7312 (ttm) REVERT: 5 55 THR cc_start: 0.7917 (p) cc_final: 0.7487 (p) REVERT: 5 73 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8063 (mm-30) REVERT: 5 123 TYR cc_start: 0.8507 (m-80) cc_final: 0.8229 (m-10) REVERT: 5 134 GLU cc_start: 0.7858 (mp0) cc_final: 0.7529 (mp0) REVERT: 5 163 GLU cc_start: 0.7956 (pm20) cc_final: 0.7155 (tp30) REVERT: 5 193 GLU cc_start: 0.7918 (mp0) cc_final: 0.7632 (mp0) REVERT: 6 28 GLU cc_start: 0.8592 (pm20) cc_final: 0.7822 (pm20) REVERT: 6 81 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7618 (mmt90) REVERT: 6 122 ILE cc_start: 0.8957 (tp) cc_final: 0.8533 (tp) REVERT: 6 133 GLU cc_start: 0.8364 (tt0) cc_final: 0.8128 (tt0) REVERT: 6 163 GLU cc_start: 0.7946 (pm20) cc_final: 0.7612 (pm20) REVERT: 7 75 ASN cc_start: 0.8852 (m-40) cc_final: 0.8478 (t0) REVERT: 7 81 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7151 (tmm-80) REVERT: 7 120 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8108 (mtmt) REVERT: 7 190 LYS cc_start: 0.8589 (pttp) cc_final: 0.8162 (pttp) REVERT: 7 193 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6955 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1201 average time/residue: 0.1740 time to fit residues: 326.9827 Evaluate side-chains 1105 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1105 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 298 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 264 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 280 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 296 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 253 optimal weight: 0.8980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 1 75 ASN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 64 GLN 4 198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.177075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.145174 restraints weight = 36659.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.149438 restraints weight = 21015.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.152298 restraints weight = 14058.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.154208 restraints weight = 10606.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.155285 restraints weight = 8770.273| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24968 Z= 0.163 Angle : 0.739 13.054 33660 Z= 0.391 Chirality : 0.049 0.293 3881 Planarity : 0.004 0.058 4329 Dihedral : 5.526 40.158 3498 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 are not related in a simple way. whole: -0.65 (0.15), residues: 3122 helix: 0.28 (0.15), residues: 1230 sheet: 0.10 (0.19), residues: 616 loop : -1.34 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 80 TYR 0.041 0.002 TYR 4 46 PHE 0.035 0.002 PHE 2 196 HIS 0.005 0.002 HIS G 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (24968) covalent geometry : angle 0.73930 / 0.39 (33660) hydrogen bonds : bond 0.03786 / 2.47 ( 1269) hydrogen bonds : angle 5.33206 / 3.71 ( 3699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6388.15 seconds wall clock time: 110 minutes 24.13 seconds (6624.13 seconds total)