Starting phenix.real_space_refine on Fri Jun 20 21:51:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6he5_0210/06_2025/6he5_0210.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he5_0210/06_2025/6he5_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_2025/6he5_0210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2025/6he5_0210.map" model { file = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2025/6he5_0210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he5_0210/06_2025/6he5_0210.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.89, per 1000 atoms: 0.65 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: 7.34 Conformation dependent library (CDL) restraints added in 3.2 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: 3.21 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: 8.48 Time building geometry restraints manager: 7.00 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: 0.02 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.130 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (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 HIS 0.032 0.015 HIS G 73 PHE 0.189 0.040 PHE A 221 TYR 0.243 0.049 TYR F 8 ARG 0.091 0.012 ARG 1 83 Details of bonding type rmsd hydrogen bonds : bond 0.28205 ( 1269) hydrogen bonds : angle 9.34882 ( 3699) covalent geometry : bond 0.03648 (24968) covalent geometry : angle 3.50752 (33660) *********************** 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 : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6469 (mm-30) REVERT: A 208 ASN cc_start: 0.7788 (p0) cc_final: 0.7355 (p0) REVERT: A 211 VAL cc_start: 0.7891 (t) cc_final: 0.7541 (p) REVERT: A 220 THR cc_start: 0.8239 (m) cc_final: 0.8001 (m) REVERT: B 24 VAL cc_start: 0.8283 (t) cc_final: 0.7918 (t) REVERT: B 152 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8594 (Cg_endo) REVERT: B 208 ASN cc_start: 0.6638 (p0) cc_final: 0.6217 (p0) REVERT: C 23 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8165 (tp40) REVERT: C 41 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8068 (ttpt) REVERT: C 47 ILE cc_start: 0.8472 (mt) cc_final: 0.8268 (mt) REVERT: C 66 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8238 (tppt) REVERT: C 144 VAL cc_start: 0.8745 (m) cc_final: 0.8487 (m) REVERT: C 160 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7672 (mtpt) REVERT: D 82 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8625 (t) REVERT: D 89 ILE cc_start: 0.9190 (tp) cc_final: 0.8989 (tp) REVERT: D 115 LYS cc_start: 0.8472 (mttm) cc_final: 0.7842 (mttt) REVERT: D 121 GLN cc_start: 0.8060 (tm130) cc_final: 0.7739 (tm130) REVERT: D 174 PHE cc_start: 0.7339 (t80) cc_final: 0.6543 (t80) REVERT: D 211 VAL cc_start: 0.8980 (t) cc_final: 0.8740 (t) REVERT: E 25 GLU cc_start: 0.6352 (tp30) cc_final: 0.5641 (tp30) REVERT: E 41 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7080 (ptmt) REVERT: E 49 ILE cc_start: 0.6840 (tt) cc_final: 0.6612 (tt) REVERT: E 68 TYR cc_start: 0.8023 (m-80) cc_final: 0.7711 (m-80) REVERT: E 116 ILE cc_start: 0.8525 (mt) cc_final: 0.8311 (mt) REVERT: E 120 LYS cc_start: 0.7119 (mttt) cc_final: 0.6897 (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: 0.5559 (ttp80) REVERT: F 22 PHE cc_start: 0.6992 (m-80) cc_final: 0.6426 (m-80) REVERT: F 99 ASN cc_start: 0.7781 (t0) cc_final: 0.7479 (t0) REVERT: F 106 PRO cc_start: 0.9192 (Cg_exo) cc_final: 0.8719 (Cg_endo) REVERT: G 5 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.3614 (pm20) REVERT: G 16 SER cc_start: 0.7584 (p) cc_final: 0.7164 (p) REVERT: G 23 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7965 (tp40) REVERT: G 47 ILE cc_start: 0.8519 (mt) cc_final: 0.7807 (mt) REVERT: G 157 LEU cc_start: 0.7984 (mt) cc_final: 0.7609 (mt) REVERT: G 171 VAL cc_start: 0.5969 (t) cc_final: 0.4258 (t) REVERT: G 200 ILE cc_start: 0.7751 (pt) cc_final: 0.7388 (pt) REVERT: G 224 VAL cc_start: 0.6674 (t) cc_final: 0.6304 (t) REVERT: 1 107 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0710 (pt) REVERT: 2 44 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3402 (mptm) REVERT: 2 162 ASP cc_start: 0.4157 (m-30) cc_final: 0.3663 (m-30) REVERT: 3 46 TYR cc_start: 0.7226 (m-80) cc_final: 0.6548 (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: 0.8903 (mt) REVERT: 5 146 THR cc_start: 0.6265 (p) cc_final: 0.5914 (p) REVERT: 6 155 PHE cc_start: 0.3192 (t80) cc_final: 0.2981 (t80) outliers start: 118 outliers final: 19 residues processed: 1361 average time/residue: 0.4239 time to fit residues: 848.5692 Evaluate side-chains 1112 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1088 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.186325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.154212 restraints weight = 36738.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.158651 restraints weight = 21449.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.161717 restraints weight = 14478.953| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 24968 Z= 0.253 Angle : 0.872 14.225 33660 Z= 0.478 Chirality : 0.052 0.223 3881 Planarity : 0.006 0.065 4329 Dihedral : 6.542 56.674 3498 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.59 % Favored : 96.09 % Rotamer: Outliers : 0.19 % Allowed : 4.78 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3122 helix: -0.08 (0.14), residues: 1242 sheet: 0.11 (0.19), residues: 591 loop : -2.11 (0.15), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 73 PHE 0.027 0.003 PHE 4 155 TYR 0.041 0.003 TYR 6 46 ARG 0.016 0.001 ARG 7 154 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 1269) hydrogen bonds : angle 5.78197 ( 3699) covalent geometry : bond 0.00535 (24968) covalent geometry : angle 0.87215 (33660) *********************** 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 1302 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1297 time to evaluate : 2.841 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: A 121 GLN cc_start: 0.8595 (tp40) cc_final: 0.7658 (tm-30) REVERT: A 172 THR cc_start: 0.8579 (p) cc_final: 0.7836 (p) REVERT: A 186 ASP cc_start: 0.7745 (p0) cc_final: 0.7184 (p0) REVERT: A 208 ASN cc_start: 0.8731 (p0) cc_final: 0.8176 (p0) REVERT: A 211 VAL cc_start: 0.8695 (t) cc_final: 0.7130 (p) REVERT: A 222 LYS cc_start: 0.8489 (tttm) cc_final: 0.8216 (ttmm) REVERT: B 104 ASP cc_start: 0.7160 (m-30) cc_final: 0.6611 (m-30) REVERT: B 176 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 186 ASP cc_start: 0.8514 (p0) cc_final: 0.8299 (p0) REVERT: B 201 GLU cc_start: 0.7979 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 208 ASN cc_start: 0.7450 (p0) cc_final: 0.7162 (p0) REVERT: B 214 VAL cc_start: 0.9442 (t) cc_final: 0.9205 (p) REVERT: B 238 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6776 (mt-10) REVERT: C 8 TYR cc_start: 0.8260 (m-80) cc_final: 0.7627 (m-10) REVERT: C 9 ASP cc_start: 0.7859 (p0) cc_final: 0.7625 (p0) REVERT: C 20 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7402 (ttp80) REVERT: C 57 LYS cc_start: 0.8763 (ptmm) cc_final: 0.8421 (pttm) REVERT: C 72 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 137 LEU cc_start: 0.9363 (mt) cc_final: 0.8768 (mt) REVERT: C 149 GLU cc_start: 0.8753 (tt0) cc_final: 0.8512 (tt0) REVERT: C 160 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8237 (mtmm) REVERT: C 164 ILE cc_start: 0.9543 (pt) cc_final: 0.9312 (pt) REVERT: C 185 PHE cc_start: 0.8823 (t80) cc_final: 0.8392 (t80) REVERT: C 189 MET cc_start: 0.9129 (ttm) cc_final: 0.8870 (ttm) REVERT: C 196 MET cc_start: 0.8207 (ttm) cc_final: 0.7813 (ttm) REVERT: C 202 SER cc_start: 0.8552 (p) cc_final: 0.7976 (p) REVERT: C 208 ASN cc_start: 0.8552 (p0) cc_final: 0.8021 (p0) REVERT: C 209 ILE cc_start: 0.9134 (pt) cc_final: 0.8749 (pt) REVERT: C 214 VAL cc_start: 0.8955 (t) cc_final: 0.8619 (t) REVERT: C 225 SER cc_start: 0.8910 (p) cc_final: 0.8311 (p) REVERT: C 229 LEU cc_start: 0.9154 (mt) cc_final: 0.8954 (mt) REVERT: D 33 ARG cc_start: 0.8471 (ptm160) cc_final: 0.8131 (mtp-110) REVERT: D 60 GLU cc_start: 0.7975 (pp20) cc_final: 0.7618 (pp20) REVERT: D 64 ILE cc_start: 0.6697 (pt) cc_final: 0.6426 (pt) REVERT: D 91 ARG cc_start: 0.8684 (tpt170) cc_final: 0.8256 (tpt90) REVERT: D 95 GLU cc_start: 0.8051 (tt0) cc_final: 0.6830 (tt0) REVERT: D 115 LYS cc_start: 0.8622 (mttm) cc_final: 0.7915 (mtpt) REVERT: D 121 GLN cc_start: 0.7984 (tp40) cc_final: 0.7647 (tm-30) REVERT: D 151 ASP cc_start: 0.7634 (m-30) cc_final: 0.7362 (m-30) REVERT: D 174 PHE cc_start: 0.8545 (t80) cc_final: 0.8259 (t80) REVERT: D 185 PHE cc_start: 0.7867 (t80) cc_final: 0.7356 (t80) REVERT: D 228 GLU cc_start: 0.7968 (tp30) cc_final: 0.7718 (tp30) REVERT: E 28 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8450 (mmm-85) REVERT: E 65 GLU cc_start: 0.5374 (tt0) cc_final: 0.4730 (tt0) REVERT: E 68 TYR cc_start: 0.8860 (m-80) cc_final: 0.8350 (m-80) REVERT: E 72 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6931 (mt-10) REVERT: E 75 CYS cc_start: 0.9100 (p) cc_final: 0.8830 (p) REVERT: E 93 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8640 (mtp85) REVERT: E 172 THR cc_start: 0.8996 (m) cc_final: 0.8707 (t) REVERT: E 221 PHE cc_start: 0.8467 (t80) cc_final: 0.8040 (t80) REVERT: F 25 GLU cc_start: 0.8265 (tt0) cc_final: 0.8025 (tt0) REVERT: F 26 TYR cc_start: 0.9214 (m-10) cc_final: 0.8675 (m-10) REVERT: F 99 ASN cc_start: 0.9037 (t0) cc_final: 0.8821 (t0) REVERT: F 150 THR cc_start: 0.8543 (p) cc_final: 0.8222 (p) REVERT: F 173 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7206 (tm-30) REVERT: F 187 ASP cc_start: 0.8583 (m-30) cc_final: 0.8042 (m-30) REVERT: F 196 MET cc_start: 0.9146 (tpp) cc_final: 0.8786 (tpp) REVERT: F 210 GLU cc_start: 0.7778 (tt0) cc_final: 0.6945 (tt0) REVERT: F 228 GLU cc_start: 0.8478 (tp30) cc_final: 0.8251 (tp30) REVERT: F 229 LEU cc_start: 0.8916 (tt) cc_final: 0.8669 (tt) REVERT: F 232 TYR cc_start: 0.8813 (m-10) cc_final: 0.8596 (m-80) REVERT: F 237 ASN cc_start: 0.7695 (m-40) cc_final: 0.5626 (m-40) REVERT: F 241 ARG cc_start: 0.7666 (ptp-110) cc_final: 0.7090 (mtm110) REVERT: G 23 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8394 (tp40) REVERT: G 33 ARG cc_start: 0.7217 (ptp-170) cc_final: 0.6930 (mtm180) REVERT: G 44 GLU cc_start: 0.7801 (mp0) cc_final: 0.7569 (mp0) REVERT: G 47 ILE cc_start: 0.9342 (mt) cc_final: 0.9069 (mt) REVERT: G 89 ILE cc_start: 0.9362 (mm) cc_final: 0.9110 (mm) REVERT: G 104 ASP cc_start: 0.7829 (t70) cc_final: 0.7294 (t0) REVERT: G 108 THR cc_start: 0.8591 (p) cc_final: 0.8369 (p) REVERT: G 171 VAL cc_start: 0.8629 (t) cc_final: 0.7219 (p) REVERT: G 187 ASP cc_start: 0.8321 (m-30) cc_final: 0.8054 (m-30) REVERT: 1 44 LYS cc_start: 0.8151 (tttt) cc_final: 0.7930 (tptt) REVERT: 1 111 LEU cc_start: 0.9011 (mt) cc_final: 0.8667 (mt) REVERT: 1 116 ASP cc_start: 0.8851 (p0) cc_final: 0.8623 (p0) REVERT: 1 122 ILE cc_start: 0.8369 (mm) cc_final: 0.7794 (mm) REVERT: 1 135 LYS cc_start: 0.7819 (mppt) cc_final: 0.7512 (mppt) REVERT: 1 190 LYS cc_start: 0.8597 (ptpp) cc_final: 0.7886 (ptpp) REVERT: 1 197 TYR cc_start: 0.6752 (t80) cc_final: 0.6337 (t80) REVERT: 1 208 LEU cc_start: 0.4922 (pp) cc_final: 0.4448 (pp) REVERT: 2 19 CYS cc_start: 0.6905 (m) cc_final: 0.6431 (m) REVERT: 2 72 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8533 (mp) REVERT: 2 159 ILE cc_start: 0.8321 (tt) cc_final: 0.7885 (tt) REVERT: 2 162 ASP cc_start: 0.5870 (m-30) cc_final: 0.5471 (m-30) REVERT: 2 163 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7031 (mp0) REVERT: 2 190 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8688 (tttt) REVERT: 3 46 TYR cc_start: 0.7250 (m-80) cc_final: 0.6472 (m-10) REVERT: 3 48 ILE cc_start: 0.8959 (mm) cc_final: 0.8746 (tp) REVERT: 3 84 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7671 (mptt) REVERT: 3 90 ILE cc_start: 0.9488 (mm) cc_final: 0.9013 (tt) REVERT: 3 188 VAL cc_start: 0.7537 (t) cc_final: 0.7299 (t) REVERT: 4 48 ILE cc_start: 0.9331 (mm) cc_final: 0.8625 (mm) REVERT: 4 87 VAL cc_start: 0.9355 (t) cc_final: 0.8983 (t) REVERT: 4 88 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8030 (ttp-170) REVERT: 4 132 ILE cc_start: 0.8916 (mt) cc_final: 0.8708 (mt) REVERT: 4 190 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7848 (ptmm) REVERT: 5 46 TYR cc_start: 0.7229 (m-80) cc_final: 0.6491 (m-80) REVERT: 5 79 ILE cc_start: 0.8917 (mt) cc_final: 0.8524 (mt) REVERT: 5 92 THR cc_start: 0.8796 (p) cc_final: 0.8570 (p) REVERT: 5 122 ILE cc_start: 0.8968 (mt) cc_final: 0.8382 (mt) REVERT: 5 134 GLU cc_start: 0.7046 (mp0) cc_final: 0.6677 (mp0) REVERT: 6 28 GLU cc_start: 0.7052 (pm20) cc_final: 0.6516 (pm20) REVERT: 6 33 MET cc_start: 0.1439 (pmm) cc_final: 0.1234 (pmm) REVERT: 6 72 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8533 (mp) REVERT: 6 81 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8070 (tpp80) REVERT: 6 137 ILE cc_start: 0.8320 (mm) cc_final: 0.7686 (mp) REVERT: 7 52 MET cc_start: 0.8625 (ttm) cc_final: 0.8410 (ttm) REVERT: 7 75 ASN cc_start: 0.8922 (m-40) cc_final: 0.8633 (m-40) REVERT: 7 152 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6999 (mt-10) REVERT: 7 154 ARG cc_start: 0.6830 (ptp-110) cc_final: 0.6619 (ptp90) outliers start: 5 outliers final: 0 residues processed: 1299 average time/residue: 0.4028 time to fit residues: 784.7228 Evaluate side-chains 1111 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1109 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 229 optimal weight: 0.9980 chunk 204 optimal weight: 0.0770 chunk 233 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 282 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.3974 r_free = 0.3974 target = 0.183591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.151641 restraints weight = 36361.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156063 restraints weight = 20963.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.159120 restraints weight = 14086.640| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24968 Z= 0.175 Angle : 0.738 14.094 33660 Z= 0.401 Chirality : 0.049 0.220 3881 Planarity : 0.005 0.068 4329 Dihedral : 5.906 59.788 3498 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.81 % Favored : 95.87 % Rotamer: Outliers : 0.27 % Allowed : 3.25 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3122 helix: 0.16 (0.14), residues: 1247 sheet: 0.20 (0.19), residues: 597 loop : -1.68 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 73 PHE 0.024 0.002 PHE 5 155 TYR 0.031 0.002 TYR 6 46 ARG 0.009 0.001 ARG 4 81 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1269) hydrogen bonds : angle 5.33000 ( 3699) covalent geometry : bond 0.00383 (24968) covalent geometry : angle 0.73777 (33660) *********************** 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 1237 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1230 time to evaluate : 3.564 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 121 GLN cc_start: 0.8297 (tp40) cc_final: 0.7699 (tm-30) REVERT: A 172 THR cc_start: 0.8771 (p) cc_final: 0.8404 (p) REVERT: A 186 ASP cc_start: 0.7836 (p0) cc_final: 0.6970 (p0) REVERT: A 187 ASP cc_start: 0.7884 (m-30) cc_final: 0.7631 (m-30) REVERT: A 191 LEU cc_start: 0.9166 (tp) cc_final: 0.8942 (tp) REVERT: A 208 ASN cc_start: 0.8703 (p0) cc_final: 0.8215 (p0) REVERT: A 211 VAL cc_start: 0.8918 (t) cc_final: 0.7435 (p) REVERT: A 223 GLU cc_start: 0.7457 (tt0) cc_final: 0.7105 (tt0) REVERT: B 38 ILE cc_start: 0.8894 (mt) cc_final: 0.8334 (mt) REVERT: B 151 ASP cc_start: 0.9085 (t0) cc_final: 0.8715 (t0) REVERT: B 152 PRO cc_start: 0.9619 (Cg_exo) cc_final: 0.9287 (Cg_endo) REVERT: B 176 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 187 ASP cc_start: 0.7842 (m-30) cc_final: 0.7272 (m-30) REVERT: B 196 MET cc_start: 0.8667 (mmm) cc_final: 0.8054 (mmm) REVERT: B 201 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7107 (tm-30) REVERT: B 208 ASN cc_start: 0.7478 (p0) cc_final: 0.7165 (p0) REVERT: B 214 VAL cc_start: 0.9395 (t) cc_final: 0.9173 (p) REVERT: B 230 LYS cc_start: 0.9230 (ttpt) cc_final: 0.8903 (ttpt) REVERT: C 9 ASP cc_start: 0.8055 (p0) cc_final: 0.7755 (p0) REVERT: C 44 GLU cc_start: 0.6250 (tm-30) cc_final: 0.5829 (tm-30) REVERT: C 57 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8428 (pttm) REVERT: C 103 TYR cc_start: 0.8436 (m-80) cc_final: 0.8063 (m-10) REVERT: C 123 TYR cc_start: 0.7374 (m-80) cc_final: 0.6965 (m-80) REVERT: C 160 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8306 (mtmm) REVERT: C 175 PHE cc_start: 0.9013 (m-80) cc_final: 0.8698 (m-80) REVERT: C 185 PHE cc_start: 0.8586 (t80) cc_final: 0.8292 (t80) REVERT: C 186 ASP cc_start: 0.8688 (m-30) cc_final: 0.8446 (m-30) REVERT: C 202 SER cc_start: 0.8341 (p) cc_final: 0.8012 (p) REVERT: C 203 GLU cc_start: 0.5962 (pm20) cc_final: 0.5694 (pm20) REVERT: C 208 ASN cc_start: 0.8501 (p0) cc_final: 0.7926 (p0) REVERT: C 213 TYR cc_start: 0.8163 (p90) cc_final: 0.7580 (p90) REVERT: C 215 LYS cc_start: 0.7685 (mttt) cc_final: 0.7466 (mttp) REVERT: C 222 LYS cc_start: 0.8438 (tttt) cc_final: 0.8127 (ttmm) REVERT: D 20 ARG cc_start: 0.8477 (ptm160) cc_final: 0.7949 (ttp-110) REVERT: D 38 ILE cc_start: 0.9039 (mt) cc_final: 0.8709 (mt) REVERT: D 57 LYS cc_start: 0.8683 (pttm) cc_final: 0.7954 (mppt) REVERT: D 64 ILE cc_start: 0.6616 (pt) cc_final: 0.6337 (pt) REVERT: D 67 ILE cc_start: 0.9020 (mm) cc_final: 0.8785 (mm) REVERT: D 91 ARG cc_start: 0.8773 (tpt170) cc_final: 0.8327 (tpt90) REVERT: D 95 GLU cc_start: 0.8199 (tt0) cc_final: 0.7611 (tt0) REVERT: D 115 LYS cc_start: 0.8729 (mttm) cc_final: 0.8331 (mtmt) REVERT: D 174 PHE cc_start: 0.8658 (t80) cc_final: 0.8276 (t80) REVERT: D 178 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7426 (mt-10) REVERT: D 219 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7339 (tpp80) REVERT: D 228 GLU cc_start: 0.7812 (tp30) cc_final: 0.7607 (tp30) REVERT: D 240 ILE cc_start: 0.8659 (pt) cc_final: 0.8453 (pt) REVERT: E 8 TYR cc_start: 0.7920 (m-10) cc_final: 0.7020 (m-80) REVERT: E 52 LYS cc_start: 0.9177 (tmmt) cc_final: 0.8819 (ttpp) REVERT: E 68 TYR cc_start: 0.8625 (m-80) cc_final: 0.8083 (m-80) REVERT: E 172 THR cc_start: 0.9096 (m) cc_final: 0.8850 (t) REVERT: E 218 ASP cc_start: 0.8913 (p0) cc_final: 0.8299 (p0) REVERT: E 222 LYS cc_start: 0.8398 (mttt) cc_final: 0.8082 (mttp) REVERT: F 9 ASP cc_start: 0.7957 (p0) cc_final: 0.7344 (p0) REVERT: F 22 PHE cc_start: 0.8735 (m-80) cc_final: 0.8487 (m-80) REVERT: F 26 TYR cc_start: 0.9182 (m-10) cc_final: 0.8668 (m-10) REVERT: F 120 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8339 (ttmm) REVERT: F 150 THR cc_start: 0.8556 (p) cc_final: 0.8198 (p) REVERT: F 210 GLU cc_start: 0.7140 (tt0) cc_final: 0.6791 (tt0) REVERT: F 223 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8026 (mm-30) REVERT: F 228 GLU cc_start: 0.8454 (tp30) cc_final: 0.8172 (tp30) REVERT: G 73 HIS cc_start: 0.8063 (p-80) cc_final: 0.7677 (p-80) REVERT: G 104 ASP cc_start: 0.7575 (t70) cc_final: 0.6882 (t0) REVERT: G 171 VAL cc_start: 0.8679 (t) cc_final: 0.8370 (m) REVERT: G 187 ASP cc_start: 0.8410 (m-30) cc_final: 0.8031 (m-30) REVERT: G 211 VAL cc_start: 0.9191 (t) cc_final: 0.8961 (t) REVERT: G 237 ASN cc_start: 0.6987 (m110) cc_final: 0.6694 (m110) REVERT: 1 80 ARG cc_start: 0.8923 (mtm-85) cc_final: 0.8434 (mtt180) REVERT: 1 88 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8547 (mmm-85) REVERT: 1 111 LEU cc_start: 0.8986 (mt) cc_final: 0.8562 (mt) REVERT: 1 122 ILE cc_start: 0.8299 (mm) cc_final: 0.7523 (mm) REVERT: 1 123 TYR cc_start: 0.8420 (m-80) cc_final: 0.8091 (m-80) REVERT: 1 135 LYS cc_start: 0.7832 (mppt) cc_final: 0.7539 (mppt) REVERT: 1 173 TYR cc_start: 0.8623 (t80) cc_final: 0.8141 (t80) REVERT: 1 208 LEU cc_start: 0.5229 (pp) cc_final: 0.4718 (pp) REVERT: 2 19 CYS cc_start: 0.7009 (m) cc_final: 0.6618 (m) REVERT: 2 52 MET cc_start: 0.8356 (ttm) cc_final: 0.8123 (ttm) REVERT: 2 72 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8515 (mp) REVERT: 2 81 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8377 (mmt90) REVERT: 2 159 ILE cc_start: 0.8181 (tt) cc_final: 0.7786 (mt) REVERT: 2 190 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8837 (tttt) REVERT: 2 203 GLU cc_start: 0.7640 (pt0) cc_final: 0.7234 (pt0) REVERT: 3 33 MET cc_start: 0.3142 (mtm) cc_final: 0.2535 (ptp) REVERT: 3 46 TYR cc_start: 0.7156 (m-80) cc_final: 0.6361 (m-80) REVERT: 3 90 ILE cc_start: 0.9482 (mm) cc_final: 0.9019 (tt) REVERT: 3 158 GLU cc_start: 0.7902 (pm20) cc_final: 0.7540 (mp0) REVERT: 4 44 LYS cc_start: 0.6289 (tppt) cc_final: 0.6053 (tppt) REVERT: 4 48 ILE cc_start: 0.9385 (mm) cc_final: 0.8976 (mm) REVERT: 4 52 MET cc_start: 0.8337 (ttm) cc_final: 0.8009 (ttm) REVERT: 4 80 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8044 (mtp180) REVERT: 4 83 ARG cc_start: 0.8509 (ptm160) cc_final: 0.7760 (ptm160) REVERT: 4 88 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7942 (ttp-170) REVERT: 4 109 GLN cc_start: 0.6918 (mp10) cc_final: 0.6619 (mp10) REVERT: 4 123 TYR cc_start: 0.9060 (m-80) cc_final: 0.8619 (m-80) REVERT: 4 152 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8373 (mm-30) REVERT: 4 190 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7930 (ptmm) REVERT: 5 33 MET cc_start: -0.1304 (mtt) cc_final: -0.1826 (ttm) REVERT: 5 73 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8122 (mm-30) REVERT: 5 92 THR cc_start: 0.8863 (p) cc_final: 0.8629 (p) REVERT: 5 134 GLU cc_start: 0.7353 (mp0) cc_final: 0.7015 (mp0) REVERT: 5 193 GLU cc_start: 0.8369 (mp0) cc_final: 0.8150 (mp0) REVERT: 6 72 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8558 (mp) REVERT: 6 79 ILE cc_start: 0.9574 (mt) cc_final: 0.9261 (mt) REVERT: 6 81 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8166 (tpp80) REVERT: 6 122 ILE cc_start: 0.9216 (tp) cc_final: 0.8869 (tp) REVERT: 6 163 GLU cc_start: 0.7934 (mp0) cc_final: 0.7402 (pm20) REVERT: 6 170 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8203 (mmm-85) REVERT: 7 44 LYS cc_start: 0.6765 (tppt) cc_final: 0.6280 (tppt) REVERT: 7 75 ASN cc_start: 0.8755 (m-40) cc_final: 0.8314 (m-40) REVERT: 7 122 ILE cc_start: 0.9054 (tp) cc_final: 0.8798 (tp) REVERT: 7 193 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7502 (tm-30) outliers start: 7 outliers final: 1 residues processed: 1234 average time/residue: 0.3889 time to fit residues: 732.6711 Evaluate side-chains 1125 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1122 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 196 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 239 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 93 optimal weight: 0.0370 chunk 80 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 169 ASN F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 3 75 ASN 3 198 GLN 4 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.182504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.149828 restraints weight = 36972.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.154416 restraints weight = 21158.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.157510 restraints weight = 14109.676| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 24968 Z= 0.163 Angle : 0.700 14.228 33660 Z= 0.378 Chirality : 0.048 0.212 3881 Planarity : 0.005 0.052 4329 Dihedral : 5.690 58.037 3498 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.46 % Favored : 96.22 % Rotamer: Outliers : 0.15 % Allowed : 2.90 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3122 helix: 0.34 (0.15), residues: 1232 sheet: 0.16 (0.19), residues: 611 loop : -1.52 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 73 PHE 0.020 0.002 PHE 5 196 TYR 0.035 0.002 TYR 6 46 ARG 0.014 0.001 ARG G 33 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 1269) hydrogen bonds : angle 5.20776 ( 3699) covalent geometry : bond 0.00370 (24968) covalent geometry : angle 0.69980 (33660) *********************** 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 1209 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1205 time to evaluate : 2.571 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: 0.8285 (pm20) cc_final: 0.7930 (pm20) REVERT: A 51 ASP cc_start: 0.8476 (t0) cc_final: 0.8202 (t0) REVERT: A 98 ILE cc_start: 0.8820 (mt) cc_final: 0.8411 (mt) REVERT: A 121 GLN cc_start: 0.8434 (tp40) cc_final: 0.7842 (tm-30) REVERT: A 186 ASP cc_start: 0.7708 (p0) cc_final: 0.6845 (p0) REVERT: A 187 ASP cc_start: 0.7941 (m-30) cc_final: 0.7629 (m-30) REVERT: A 196 MET cc_start: 0.8828 (mmm) cc_final: 0.8586 (tpp) REVERT: A 208 ASN cc_start: 0.8840 (p0) cc_final: 0.8176 (p0) REVERT: A 211 VAL cc_start: 0.8941 (t) cc_final: 0.7385 (p) REVERT: A 223 GLU cc_start: 0.7755 (tt0) cc_final: 0.7432 (tt0) REVERT: B 38 ILE cc_start: 0.8819 (mt) cc_final: 0.8309 (mt) REVERT: B 51 ASP cc_start: 0.7414 (m-30) cc_final: 0.6845 (m-30) REVERT: B 93 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8238 (mtt-85) REVERT: B 100 ARG cc_start: 0.8857 (mmt180) cc_final: 0.8186 (ttm110) REVERT: B 116 ILE cc_start: 0.9374 (tt) cc_final: 0.9166 (tt) REVERT: B 152 PRO cc_start: 0.9613 (Cg_exo) cc_final: 0.9380 (Cg_endo) REVERT: B 176 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 196 MET cc_start: 0.8548 (mmm) cc_final: 0.8210 (mmm) REVERT: B 201 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 207 GLU cc_start: 0.7468 (mp0) cc_final: 0.7201 (mp0) REVERT: B 208 ASN cc_start: 0.7494 (p0) cc_final: 0.7256 (p0) REVERT: B 214 VAL cc_start: 0.9402 (t) cc_final: 0.9125 (t) REVERT: B 238 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 9 ASP cc_start: 0.7942 (p0) cc_final: 0.7553 (p0) REVERT: C 44 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6175 (tm-30) REVERT: C 57 LYS cc_start: 0.8796 (ptmm) cc_final: 0.8406 (pttm) REVERT: C 123 TYR cc_start: 0.7294 (m-80) cc_final: 0.6917 (m-80) REVERT: C 148 TYR cc_start: 0.9268 (m-80) cc_final: 0.9039 (m-10) REVERT: C 160 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8532 (mtmm) REVERT: C 175 PHE cc_start: 0.8998 (m-80) cc_final: 0.8721 (m-80) REVERT: C 185 PHE cc_start: 0.8501 (t80) cc_final: 0.8264 (t80) REVERT: C 199 SER cc_start: 0.9087 (t) cc_final: 0.8872 (t) REVERT: C 208 ASN cc_start: 0.8511 (p0) cc_final: 0.8022 (p0) REVERT: C 210 GLU cc_start: 0.6356 (tt0) cc_final: 0.6061 (tt0) REVERT: C 211 VAL cc_start: 0.9085 (t) cc_final: 0.8765 (m) REVERT: C 213 TYR cc_start: 0.8188 (p90) cc_final: 0.7528 (p90) REVERT: C 214 VAL cc_start: 0.8974 (t) cc_final: 0.8699 (t) REVERT: C 222 LYS cc_start: 0.8535 (tttt) cc_final: 0.8153 (ttmm) REVERT: C 225 SER cc_start: 0.8983 (p) cc_final: 0.8495 (p) REVERT: C 230 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8587 (mtpp) REVERT: D 20 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7946 (ttp-110) REVERT: D 38 ILE cc_start: 0.9151 (mt) cc_final: 0.8950 (mt) REVERT: D 57 LYS cc_start: 0.8665 (pttm) cc_final: 0.7975 (mppt) REVERT: D 67 ILE cc_start: 0.9119 (mm) cc_final: 0.8870 (mm) REVERT: D 115 LYS cc_start: 0.8606 (mttm) cc_final: 0.7364 (mtpt) REVERT: D 156 LEU cc_start: 0.9534 (tp) cc_final: 0.9324 (tp) REVERT: D 171 VAL cc_start: 0.9634 (t) cc_final: 0.9375 (p) REVERT: D 174 PHE cc_start: 0.8600 (t80) cc_final: 0.8028 (t80) REVERT: D 196 MET cc_start: 0.8942 (mmm) cc_final: 0.8457 (tpp) REVERT: D 227 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8242 (tm-30) REVERT: E 8 TYR cc_start: 0.7992 (m-10) cc_final: 0.6987 (m-80) REVERT: E 21 LEU cc_start: 0.7361 (mp) cc_final: 0.7051 (mp) REVERT: E 33 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8312 (ttt-90) REVERT: E 68 TYR cc_start: 0.8623 (m-80) cc_final: 0.8028 (m-80) REVERT: E 159 TYR cc_start: 0.8564 (m-10) cc_final: 0.8220 (m-10) REVERT: E 172 THR cc_start: 0.9132 (m) cc_final: 0.8867 (t) REVERT: E 218 ASP cc_start: 0.8970 (p0) cc_final: 0.8417 (p0) REVERT: E 222 LYS cc_start: 0.8388 (mttt) cc_final: 0.8167 (mttp) REVERT: F 9 ASP cc_start: 0.8002 (p0) cc_final: 0.7486 (p0) REVERT: F 25 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7650 (mt-10) REVERT: F 26 TYR cc_start: 0.9149 (m-10) cc_final: 0.8692 (m-10) REVERT: F 64 ILE cc_start: 0.8888 (tt) cc_final: 0.8666 (tt) REVERT: F 121 GLN cc_start: 0.6821 (tp40) cc_final: 0.6267 (tp40) REVERT: F 150 THR cc_start: 0.8649 (p) cc_final: 0.8386 (p) REVERT: F 151 ASP cc_start: 0.7932 (m-30) cc_final: 0.7686 (m-30) REVERT: F 158 GLU cc_start: 0.6376 (tt0) cc_final: 0.5702 (tt0) REVERT: F 175 PHE cc_start: 0.9331 (m-80) cc_final: 0.9123 (m-80) REVERT: F 193 LEU cc_start: 0.9323 (mm) cc_final: 0.9075 (mm) REVERT: F 211 VAL cc_start: 0.9154 (t) cc_final: 0.8946 (t) REVERT: F 234 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7519 (mt-10) REVERT: G 47 ILE cc_start: 0.9267 (mt) cc_final: 0.9030 (mt) REVERT: G 73 HIS cc_start: 0.8281 (p-80) cc_final: 0.7855 (p-80) REVERT: G 104 ASP cc_start: 0.7689 (t70) cc_final: 0.6782 (t0) REVERT: G 143 GLU cc_start: 0.7426 (pm20) cc_final: 0.7022 (pm20) REVERT: G 171 VAL cc_start: 0.8877 (t) cc_final: 0.7717 (p) REVERT: G 174 PHE cc_start: 0.7665 (t80) cc_final: 0.7219 (t80) REVERT: G 187 ASP cc_start: 0.8569 (m-30) cc_final: 0.8052 (m-30) REVERT: G 191 LEU cc_start: 0.9004 (tp) cc_final: 0.8422 (tp) REVERT: G 211 VAL cc_start: 0.9323 (t) cc_final: 0.8762 (t) REVERT: G 237 ASN cc_start: 0.7269 (m110) cc_final: 0.6860 (m110) REVERT: G 242 GLU cc_start: 0.8779 (pt0) cc_final: 0.8204 (tt0) REVERT: 1 25 MET cc_start: 0.7861 (mtm) cc_final: 0.7131 (ttm) REVERT: 1 46 TYR cc_start: 0.8726 (m-80) cc_final: 0.8348 (m-80) REVERT: 1 88 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8427 (mmm-85) REVERT: 1 111 LEU cc_start: 0.8960 (mt) cc_final: 0.8257 (mt) REVERT: 1 122 ILE cc_start: 0.8495 (mm) cc_final: 0.7743 (mm) REVERT: 1 173 TYR cc_start: 0.8497 (t80) cc_final: 0.7983 (t80) REVERT: 1 190 LYS cc_start: 0.7925 (ptmt) cc_final: 0.7494 (ptmm) REVERT: 2 19 CYS cc_start: 0.6824 (m) cc_final: 0.6469 (m) REVERT: 2 45 ILE cc_start: 0.8182 (tt) cc_final: 0.7775 (tt) REVERT: 2 48 ILE cc_start: 0.8769 (mm) cc_final: 0.8564 (mm) REVERT: 2 72 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8542 (mp) REVERT: 2 162 ASP cc_start: 0.6402 (m-30) cc_final: 0.6025 (m-30) REVERT: 2 190 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8567 (tttt) REVERT: 2 192 THR cc_start: 0.7479 (t) cc_final: 0.6711 (t) REVERT: 3 33 MET cc_start: 0.3133 (mtm) cc_final: 0.2565 (ptp) REVERT: 3 46 TYR cc_start: 0.6874 (m-80) cc_final: 0.6173 (m-80) REVERT: 3 90 ILE cc_start: 0.9466 (mm) cc_final: 0.8932 (tt) REVERT: 3 158 GLU cc_start: 0.7900 (pm20) cc_final: 0.7559 (mp0) REVERT: 3 197 TYR cc_start: 0.7694 (t80) cc_final: 0.7430 (t80) REVERT: 4 33 MET cc_start: 0.4543 (ttm) cc_final: 0.4043 (ttm) REVERT: 4 48 ILE cc_start: 0.9319 (mm) cc_final: 0.8689 (mm) REVERT: 4 52 MET cc_start: 0.8279 (ttm) cc_final: 0.7937 (ttm) REVERT: 4 80 ARG cc_start: 0.8788 (mtp180) cc_final: 0.7998 (mtp180) REVERT: 4 87 VAL cc_start: 0.9088 (t) cc_final: 0.8870 (t) REVERT: 4 88 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7937 (ttp-170) REVERT: 4 109 GLN cc_start: 0.6635 (mp10) cc_final: 0.6074 (mp10) REVERT: 4 123 TYR cc_start: 0.9026 (m-80) cc_final: 0.8346 (m-80) REVERT: 4 152 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8292 (mm-30) REVERT: 4 190 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8051 (ptmm) REVERT: 4 207 ILE cc_start: 0.8493 (mt) cc_final: 0.7903 (tp) REVERT: 5 33 MET cc_start: -0.1469 (mtt) cc_final: -0.1992 (ttm) REVERT: 5 46 TYR cc_start: 0.7666 (m-80) cc_final: 0.6632 (m-10) REVERT: 5 73 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7821 (mm-30) REVERT: 5 134 GLU cc_start: 0.7417 (mp0) cc_final: 0.7009 (mp0) REVERT: 6 28 GLU cc_start: 0.7907 (pm20) cc_final: 0.7705 (pm20) REVERT: 6 72 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8762 (mp) REVERT: 6 79 ILE cc_start: 0.9373 (mt) cc_final: 0.8705 (mt) REVERT: 6 81 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7955 (tpp80) REVERT: 6 122 ILE cc_start: 0.9195 (tp) cc_final: 0.8845 (tp) REVERT: 6 134 GLU cc_start: 0.8434 (mp0) cc_final: 0.8230 (mp0) REVERT: 7 44 LYS cc_start: 0.6712 (tppt) cc_final: 0.6219 (tppt) REVERT: 7 193 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7428 (tm-30) REVERT: H 396 MET cc_start: 0.7626 (ptp) cc_final: 0.7267 (ptp) outliers start: 4 outliers final: 0 residues processed: 1208 average time/residue: 0.4029 time to fit residues: 752.4553 Evaluate side-chains 1115 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1113 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 124 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 260 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** 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** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN 1 47 GLN 3 75 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 99 ASN 3 198 GLN 6 75 ASN ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.175130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.142169 restraints weight = 37091.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146375 restraints weight = 21737.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.149260 restraints weight = 14830.231| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24968 Z= 0.219 Angle : 0.740 14.679 33660 Z= 0.398 Chirality : 0.049 0.218 3881 Planarity : 0.005 0.052 4329 Dihedral : 5.621 61.838 3498 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.39 % Favored : 95.36 % Rotamer: Outliers : 0.19 % Allowed : 3.10 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3122 helix: 0.28 (0.15), residues: 1226 sheet: 0.13 (0.19), residues: 613 loop : -1.47 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 73 PHE 0.021 0.002 PHE 7 65 TYR 0.031 0.002 TYR 7 148 ARG 0.007 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1269) hydrogen bonds : angle 5.25456 ( 3699) covalent geometry : bond 0.00486 (24968) covalent geometry : angle 0.74008 (33660) *********************** 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 1248 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1243 time to evaluate : 2.701 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 31 VAL cc_start: 0.9460 (m) cc_final: 0.9227 (p) REVERT: A 44 GLU cc_start: 0.8468 (pm20) cc_final: 0.7874 (pm20) REVERT: A 51 ASP cc_start: 0.8674 (t0) cc_final: 0.8434 (t0) REVERT: A 94 ILE cc_start: 0.9298 (mt) cc_final: 0.9057 (mt) REVERT: A 98 ILE cc_start: 0.8943 (mt) cc_final: 0.8595 (mt) REVERT: A 166 MET cc_start: 0.8347 (mtp) cc_final: 0.7904 (ttt) REVERT: A 186 ASP cc_start: 0.7697 (p0) cc_final: 0.6819 (p0) REVERT: A 187 ASP cc_start: 0.7847 (m-30) cc_final: 0.7571 (m-30) REVERT: A 196 MET cc_start: 0.8991 (mmm) cc_final: 0.8752 (tpp) REVERT: A 208 ASN cc_start: 0.8897 (p0) cc_final: 0.8308 (p0) REVERT: A 211 VAL cc_start: 0.9046 (t) cc_final: 0.7671 (p) REVERT: A 222 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8318 (ttmm) REVERT: A 223 GLU cc_start: 0.8134 (tt0) cc_final: 0.7901 (tt0) REVERT: B 20 ARG cc_start: 0.8247 (ptp-110) cc_final: 0.7551 (ptp-170) REVERT: B 25 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 32 LYS cc_start: 0.8428 (mmtp) cc_final: 0.8129 (mmmm) REVERT: B 51 ASP cc_start: 0.7340 (m-30) cc_final: 0.7055 (m-30) REVERT: B 60 GLU cc_start: 0.8046 (tp30) cc_final: 0.7649 (tp30) REVERT: B 93 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8298 (mtt-85) REVERT: B 98 ILE cc_start: 0.8773 (mm) cc_final: 0.8516 (mm) REVERT: B 151 ASP cc_start: 0.9296 (t0) cc_final: 0.8869 (t0) REVERT: B 152 PRO cc_start: 0.9696 (Cg_exo) cc_final: 0.9464 (Cg_endo) REVERT: B 196 MET cc_start: 0.8543 (mmm) cc_final: 0.8105 (mmm) REVERT: B 201 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7014 (tm-30) REVERT: B 208 ASN cc_start: 0.7628 (p0) cc_final: 0.7385 (p0) REVERT: B 214 VAL cc_start: 0.9450 (t) cc_final: 0.9123 (t) REVERT: B 224 VAL cc_start: 0.8632 (t) cc_final: 0.8426 (t) REVERT: B 238 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 9 ASP cc_start: 0.7689 (p0) cc_final: 0.7368 (p0) REVERT: C 44 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6401 (tm-30) REVERT: C 95 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 123 TYR cc_start: 0.7514 (m-80) cc_final: 0.5785 (m-80) REVERT: C 148 TYR cc_start: 0.9258 (m-80) cc_final: 0.8982 (m-10) REVERT: C 160 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8543 (mtmm) REVERT: C 175 PHE cc_start: 0.9062 (m-80) cc_final: 0.8657 (m-80) REVERT: C 185 PHE cc_start: 0.8557 (t80) cc_final: 0.8335 (t80) REVERT: C 208 ASN cc_start: 0.8369 (p0) cc_final: 0.8021 (p0) REVERT: C 214 VAL cc_start: 0.9038 (t) cc_final: 0.8655 (p) REVERT: C 222 LYS cc_start: 0.8672 (tttt) cc_final: 0.8169 (ttmm) REVERT: D 24 VAL cc_start: 0.8849 (t) cc_final: 0.8599 (p) REVERT: D 41 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8458 (ttpp) REVERT: D 64 ILE cc_start: 0.7050 (pt) cc_final: 0.6679 (pt) REVERT: D 68 TYR cc_start: 0.7750 (m-80) cc_final: 0.7513 (m-80) REVERT: D 91 ARG cc_start: 0.8754 (tpt90) cc_final: 0.8512 (tpt170) REVERT: D 171 VAL cc_start: 0.9553 (t) cc_final: 0.9168 (p) REVERT: D 178 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7828 (tt0) REVERT: D 185 PHE cc_start: 0.7989 (t80) cc_final: 0.7630 (t80) REVERT: D 227 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 228 GLU cc_start: 0.7744 (tp30) cc_final: 0.7529 (tp30) REVERT: E 8 TYR cc_start: 0.8205 (m-10) cc_final: 0.7233 (m-80) REVERT: E 25 GLU cc_start: 0.8400 (tp30) cc_final: 0.7149 (tp30) REVERT: E 33 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8269 (ttt-90) REVERT: E 44 GLU cc_start: 0.7402 (pm20) cc_final: 0.6994 (pt0) REVERT: E 108 THR cc_start: 0.8963 (m) cc_final: 0.8613 (m) REVERT: E 172 THR cc_start: 0.9151 (m) cc_final: 0.8947 (t) REVERT: E 186 ASP cc_start: 0.8119 (m-30) cc_final: 0.7851 (m-30) REVERT: E 218 ASP cc_start: 0.9044 (p0) cc_final: 0.8660 (p0) REVERT: E 222 LYS cc_start: 0.8463 (mttt) cc_final: 0.8031 (tptm) REVERT: F 9 ASP cc_start: 0.8279 (p0) cc_final: 0.7781 (p0) REVERT: F 25 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7945 (mt-10) REVERT: F 26 TYR cc_start: 0.9131 (m-10) cc_final: 0.8646 (m-10) REVERT: F 158 GLU cc_start: 0.6777 (tt0) cc_final: 0.6269 (tt0) REVERT: F 173 GLU cc_start: 0.7668 (tm-30) cc_final: 0.6880 (tm-30) REVERT: F 228 GLU cc_start: 0.8430 (tp30) cc_final: 0.8041 (tp30) REVERT: F 232 TYR cc_start: 0.8971 (m-10) cc_final: 0.8682 (m-80) REVERT: G 71 ASP cc_start: 0.7927 (m-30) cc_final: 0.7580 (m-30) REVERT: G 72 GLU cc_start: 0.6376 (mp0) cc_final: 0.5601 (mp0) REVERT: G 73 HIS cc_start: 0.8432 (p-80) cc_final: 0.7653 (p90) REVERT: G 93 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8124 (mtt-85) REVERT: G 114 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8424 (ttmm) REVERT: G 171 VAL cc_start: 0.9008 (t) cc_final: 0.8631 (m) REVERT: G 172 THR cc_start: 0.8569 (p) cc_final: 0.8220 (p) REVERT: G 211 VAL cc_start: 0.9359 (t) cc_final: 0.8867 (p) REVERT: G 237 ASN cc_start: 0.7478 (m110) cc_final: 0.6640 (m110) REVERT: G 239 ARG cc_start: 0.8317 (mtp180) cc_final: 0.7949 (mtp180) REVERT: 1 17 LEU cc_start: 0.9278 (pt) cc_final: 0.8987 (pt) REVERT: 1 25 MET cc_start: 0.8065 (mtm) cc_final: 0.7346 (ttm) REVERT: 1 111 LEU cc_start: 0.8976 (mt) cc_final: 0.8355 (mt) REVERT: 1 122 ILE cc_start: 0.8780 (mm) cc_final: 0.8034 (mm) REVERT: 1 173 TYR cc_start: 0.8582 (t80) cc_final: 0.8114 (t80) REVERT: 1 190 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7816 (ptmm) REVERT: 1 208 LEU cc_start: 0.5889 (pp) cc_final: 0.5538 (pp) REVERT: 2 45 ILE cc_start: 0.8337 (tt) cc_final: 0.7923 (tt) REVERT: 2 48 ILE cc_start: 0.8960 (mm) cc_final: 0.8535 (mm) REVERT: 2 52 MET cc_start: 0.8122 (ttm) cc_final: 0.7585 (ttm) REVERT: 2 72 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8598 (mp) REVERT: 2 83 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7592 (ptt180) REVERT: 3 46 TYR cc_start: 0.7067 (m-80) cc_final: 0.6449 (m-80) REVERT: 3 158 GLU cc_start: 0.7851 (pm20) cc_final: 0.7415 (mp0) REVERT: 3 188 VAL cc_start: 0.8065 (t) cc_final: 0.7857 (t) REVERT: 3 190 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7035 (pttt) REVERT: 4 48 ILE cc_start: 0.9351 (mm) cc_final: 0.8947 (mm) REVERT: 4 52 MET cc_start: 0.8295 (ttm) cc_final: 0.8093 (ttm) REVERT: 4 80 ARG cc_start: 0.8951 (mtp180) cc_final: 0.8254 (mtp180) REVERT: 4 88 ARG cc_start: 0.8240 (ttp80) cc_final: 0.8025 (ttp-170) REVERT: 4 123 TYR cc_start: 0.9163 (m-80) cc_final: 0.8375 (m-80) REVERT: 4 135 LYS cc_start: 0.8167 (tppt) cc_final: 0.7597 (ttpt) REVERT: 4 190 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8004 (ptmm) REVERT: 5 46 TYR cc_start: 0.8243 (m-80) cc_final: 0.7805 (m-10) REVERT: 5 73 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8032 (mm-30) REVERT: 5 121 SER cc_start: 0.8472 (p) cc_final: 0.8179 (t) REVERT: 5 134 GLU cc_start: 0.7428 (mp0) cc_final: 0.7104 (mp0) REVERT: 6 28 GLU cc_start: 0.8070 (pm20) cc_final: 0.7679 (pm20) REVERT: 6 68 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7324 (ttp-110) REVERT: 6 72 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8947 (mp) REVERT: 6 81 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7843 (tpp80) REVERT: 6 163 GLU cc_start: 0.8187 (pm20) cc_final: 0.7813 (pm20) REVERT: 7 44 LYS cc_start: 0.6868 (tppt) cc_final: 0.6401 (tppt) REVERT: 7 193 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7406 (tm-30) REVERT: H 396 MET cc_start: 0.8151 (ptp) cc_final: 0.7814 (ptp) outliers start: 5 outliers final: 0 residues processed: 1246 average time/residue: 0.3675 time to fit residues: 704.9630 Evaluate side-chains 1139 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1137 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 41 optimal weight: 0.0570 chunk 236 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 226 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** F 5 GLN F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.176211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.143422 restraints weight = 36570.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.147646 restraints weight = 21158.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.150509 restraints weight = 14328.286| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24968 Z= 0.194 Angle : 0.728 14.244 33660 Z= 0.388 Chirality : 0.048 0.208 3881 Planarity : 0.005 0.079 4329 Dihedral : 5.618 68.377 3498 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.00 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3122 helix: 0.33 (0.15), residues: 1221 sheet: 0.01 (0.19), residues: 615 loop : -1.38 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 73 PHE 0.019 0.002 PHE 7 65 TYR 0.031 0.002 TYR 6 46 ARG 0.010 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1269) hydrogen bonds : angle 5.24922 ( 3699) covalent geometry : bond 0.00437 (24968) covalent geometry : angle 0.72821 (33660) *********************** 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 1227 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1227 time to evaluate : 2.673 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 31 VAL cc_start: 0.9562 (m) cc_final: 0.9257 (p) REVERT: A 44 GLU cc_start: 0.8514 (pm20) cc_final: 0.7957 (pm20) REVERT: A 51 ASP cc_start: 0.8749 (t0) cc_final: 0.8518 (t0) REVERT: A 98 ILE cc_start: 0.8935 (mt) cc_final: 0.8501 (mt) REVERT: A 166 MET cc_start: 0.8242 (mtp) cc_final: 0.7806 (ttt) REVERT: A 186 ASP cc_start: 0.7804 (p0) cc_final: 0.7127 (p0) REVERT: A 187 ASP cc_start: 0.7798 (m-30) cc_final: 0.7483 (m-30) REVERT: A 208 ASN cc_start: 0.8896 (p0) cc_final: 0.8328 (p0) REVERT: A 211 VAL cc_start: 0.9038 (t) cc_final: 0.7664 (p) REVERT: B 32 LYS cc_start: 0.8557 (mmtp) cc_final: 0.8158 (mmmm) REVERT: B 38 ILE cc_start: 0.9091 (mt) cc_final: 0.8659 (mt) REVERT: B 44 GLU cc_start: 0.8277 (tt0) cc_final: 0.7837 (tt0) REVERT: B 51 ASP cc_start: 0.7230 (m-30) cc_final: 0.7023 (m-30) REVERT: B 78 THR cc_start: 0.9124 (t) cc_final: 0.8884 (m) REVERT: B 151 ASP cc_start: 0.9282 (t0) cc_final: 0.9032 (t0) REVERT: B 176 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 186 ASP cc_start: 0.8438 (p0) cc_final: 0.8106 (p0) REVERT: B 201 GLU cc_start: 0.7893 (tm-30) cc_final: 0.6774 (tm-30) REVERT: B 208 ASN cc_start: 0.7607 (p0) cc_final: 0.7348 (p0) REVERT: B 214 VAL cc_start: 0.9474 (t) cc_final: 0.9166 (t) REVERT: B 224 VAL cc_start: 0.8474 (t) cc_final: 0.7623 (t) REVERT: B 238 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7268 (mt-10) REVERT: C 9 ASP cc_start: 0.7637 (p0) cc_final: 0.7332 (p0) REVERT: C 44 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6746 (tm-30) REVERT: C 51 ASP cc_start: 0.9152 (t0) cc_final: 0.8498 (t0) REVERT: C 57 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8533 (pttm) REVERT: C 95 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7799 (mm-30) REVERT: C 148 TYR cc_start: 0.9235 (m-80) cc_final: 0.8913 (m-10) REVERT: C 160 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8574 (mtmm) REVERT: C 172 THR cc_start: 0.9376 (m) cc_final: 0.9071 (t) REVERT: C 175 PHE cc_start: 0.9079 (m-80) cc_final: 0.8672 (m-80) REVERT: C 200 ILE cc_start: 0.9202 (mm) cc_final: 0.8916 (mm) REVERT: C 214 VAL cc_start: 0.8973 (t) cc_final: 0.8684 (t) REVERT: C 219 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7260 (mtt-85) REVERT: C 222 LYS cc_start: 0.8629 (tttt) cc_final: 0.8342 (tttp) REVERT: C 225 SER cc_start: 0.8712 (p) cc_final: 0.8253 (p) REVERT: D 18 ASP cc_start: 0.8726 (p0) cc_final: 0.8483 (p0) REVERT: D 20 ARG cc_start: 0.8546 (ptm160) cc_final: 0.8335 (ttp-110) REVERT: D 64 ILE cc_start: 0.7033 (pt) cc_final: 0.6676 (pt) REVERT: D 72 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6237 (mt-10) REVERT: D 81 LEU cc_start: 0.9252 (mp) cc_final: 0.8935 (mp) REVERT: D 91 ARG cc_start: 0.8724 (tpt90) cc_final: 0.8454 (tpt170) REVERT: D 130 ARG cc_start: 0.8576 (ptt-90) cc_final: 0.8240 (ptt-90) REVERT: D 185 PHE cc_start: 0.8036 (t80) cc_final: 0.7461 (t80) REVERT: D 196 MET cc_start: 0.8899 (mmm) cc_final: 0.8658 (mmm) REVERT: D 200 ILE cc_start: 0.8977 (pt) cc_final: 0.8620 (pt) REVERT: D 208 ASN cc_start: 0.8912 (p0) cc_final: 0.8656 (p0) REVERT: D 227 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 228 GLU cc_start: 0.7702 (tp30) cc_final: 0.7463 (tp30) REVERT: E 8 TYR cc_start: 0.8210 (m-10) cc_final: 0.7430 (m-80) REVERT: E 25 GLU cc_start: 0.8313 (tp30) cc_final: 0.7168 (tp30) REVERT: E 33 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8122 (ttt-90) REVERT: E 44 GLU cc_start: 0.7232 (pm20) cc_final: 0.6921 (pt0) REVERT: E 108 THR cc_start: 0.8958 (m) cc_final: 0.8719 (m) REVERT: E 132 PHE cc_start: 0.8894 (m-80) cc_final: 0.8692 (m-10) REVERT: E 148 TYR cc_start: 0.9228 (m-80) cc_final: 0.8994 (m-10) REVERT: E 218 ASP cc_start: 0.8963 (p0) cc_final: 0.8624 (p0) REVERT: E 222 LYS cc_start: 0.8499 (mttt) cc_final: 0.8023 (tptm) REVERT: F 9 ASP cc_start: 0.8328 (p0) cc_final: 0.7827 (p0) REVERT: F 25 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7884 (mt-10) REVERT: F 26 TYR cc_start: 0.9078 (m-10) cc_final: 0.8627 (m-10) REVERT: F 158 GLU cc_start: 0.6625 (tt0) cc_final: 0.6104 (tt0) REVERT: F 169 ASN cc_start: 0.7881 (m-40) cc_final: 0.7349 (m-40) REVERT: F 193 LEU cc_start: 0.9447 (mm) cc_final: 0.9140 (mm) REVERT: F 215 LYS cc_start: 0.7823 (mttm) cc_final: 0.7443 (tptt) REVERT: F 228 GLU cc_start: 0.8437 (tp30) cc_final: 0.8151 (tp30) REVERT: F 234 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7493 (mt-10) REVERT: G 41 LYS cc_start: 0.8449 (ttpp) cc_final: 0.7819 (ttpt) REVERT: G 71 ASP cc_start: 0.7935 (m-30) cc_final: 0.7684 (m-30) REVERT: G 73 HIS cc_start: 0.8344 (p-80) cc_final: 0.7420 (p90) REVERT: G 114 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8164 (mttp) REVERT: G 146 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8518 (mttm) REVERT: G 171 VAL cc_start: 0.9181 (t) cc_final: 0.8837 (m) REVERT: G 172 THR cc_start: 0.8584 (p) cc_final: 0.8143 (p) REVERT: G 191 LEU cc_start: 0.9117 (tp) cc_final: 0.8792 (tp) REVERT: G 234 GLU cc_start: 0.8487 (pp20) cc_final: 0.7907 (pp20) REVERT: G 237 ASN cc_start: 0.7383 (m110) cc_final: 0.6600 (m110) REVERT: G 239 ARG cc_start: 0.8392 (mtp180) cc_final: 0.7974 (mtp180) REVERT: 1 17 LEU cc_start: 0.9254 (pt) cc_final: 0.8993 (pt) REVERT: 1 25 MET cc_start: 0.8065 (mtm) cc_final: 0.7341 (ttm) REVERT: 1 87 VAL cc_start: 0.9410 (t) cc_final: 0.9132 (p) REVERT: 1 111 LEU cc_start: 0.8936 (mt) cc_final: 0.8221 (mt) REVERT: 1 122 ILE cc_start: 0.8697 (mm) cc_final: 0.7974 (mm) REVERT: 1 173 TYR cc_start: 0.8572 (t80) cc_final: 0.8061 (t80) REVERT: 1 190 LYS cc_start: 0.7928 (ptmt) cc_final: 0.7547 (ptmm) REVERT: 1 193 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7863 (tm-30) REVERT: 1 208 LEU cc_start: 0.6249 (pp) cc_final: 0.5799 (pp) REVERT: 2 45 ILE cc_start: 0.8089 (tt) cc_final: 0.7490 (tt) REVERT: 2 48 ILE cc_start: 0.8843 (mm) cc_final: 0.8168 (mm) REVERT: 2 52 MET cc_start: 0.7911 (ttm) cc_final: 0.7401 (ttm) REVERT: 2 83 ARG cc_start: 0.8186 (ptm160) cc_final: 0.7711 (ptt180) REVERT: 2 151 LEU cc_start: 0.9266 (mt) cc_final: 0.9042 (mt) REVERT: 2 190 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8433 (ttmt) REVERT: 2 203 GLU cc_start: 0.7590 (pt0) cc_final: 0.7087 (pt0) REVERT: 3 29 LYS cc_start: 0.6054 (mttt) cc_final: 0.5175 (mptt) REVERT: 3 46 TYR cc_start: 0.7054 (m-80) cc_final: 0.6441 (m-80) REVERT: 3 123 TYR cc_start: 0.8627 (m-80) cc_final: 0.8366 (m-80) REVERT: 3 190 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7260 (pttt) REVERT: 4 44 LYS cc_start: 0.6984 (tppt) cc_final: 0.6166 (tttm) REVERT: 4 52 MET cc_start: 0.8298 (ttm) cc_final: 0.8016 (ttm) REVERT: 4 80 ARG cc_start: 0.9004 (mtp180) cc_final: 0.8273 (mtp180) REVERT: 4 135 LYS cc_start: 0.8142 (tppt) cc_final: 0.7582 (ttpt) REVERT: 4 190 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7995 (ptmm) REVERT: 5 46 TYR cc_start: 0.7454 (m-80) cc_final: 0.6873 (m-10) REVERT: 5 73 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8042 (mm-30) REVERT: 5 134 GLU cc_start: 0.7461 (mp0) cc_final: 0.7133 (mp0) REVERT: 5 205 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8219 (mm-30) REVERT: 6 28 GLU cc_start: 0.8174 (pm20) cc_final: 0.7288 (pm20) REVERT: 6 68 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7344 (ttp-110) REVERT: 6 81 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7835 (tpp80) REVERT: 6 163 GLU cc_start: 0.7898 (pm20) cc_final: 0.7555 (pm20) REVERT: 6 172 ILE cc_start: 0.8709 (tt) cc_final: 0.8495 (tt) REVERT: 6 173 TYR cc_start: 0.7228 (t80) cc_final: 0.6304 (t80) REVERT: 7 193 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7215 (tm-30) REVERT: H 396 MET cc_start: 0.8104 (ptp) cc_final: 0.7881 (mtm) outliers start: 0 outliers final: 0 residues processed: 1227 average time/residue: 0.3864 time to fit residues: 735.8583 Evaluate side-chains 1138 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1138 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 34 optimal weight: 0.5980 chunk 259 optimal weight: 0.3980 chunk 247 optimal weight: 0.0000 chunk 196 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** 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 ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.177297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144558 restraints weight = 36827.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.148849 restraints weight = 21246.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151816 restraints weight = 14292.629| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24968 Z= 0.171 Angle : 0.716 13.859 33660 Z= 0.381 Chirality : 0.048 0.255 3881 Planarity : 0.005 0.088 4329 Dihedral : 5.584 76.586 3498 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3122 helix: 0.31 (0.15), residues: 1225 sheet: -0.02 (0.18), residues: 622 loop : -1.29 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.019 0.002 PHE 7 65 TYR 0.032 0.002 TYR 7 148 ARG 0.012 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1269) hydrogen bonds : angle 5.23167 ( 3699) covalent geometry : bond 0.00386 (24968) covalent geometry : angle 0.71603 (33660) *********************** 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 1222 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1222 time to evaluate : 3.805 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: 0.8207 (tt0) cc_final: 0.7185 (tt0) REVERT: A 31 VAL cc_start: 0.9589 (m) cc_final: 0.9233 (p) REVERT: A 44 GLU cc_start: 0.8480 (pm20) cc_final: 0.7979 (pm20) REVERT: A 94 ILE cc_start: 0.9284 (mt) cc_final: 0.9049 (mt) REVERT: A 98 ILE cc_start: 0.8921 (mt) cc_final: 0.8472 (mt) REVERT: A 166 MET cc_start: 0.8204 (mtp) cc_final: 0.7922 (ttt) REVERT: A 186 ASP cc_start: 0.7735 (p0) cc_final: 0.7212 (p0) REVERT: A 208 ASN cc_start: 0.9059 (p0) cc_final: 0.8337 (p0) REVERT: A 211 VAL cc_start: 0.8880 (t) cc_final: 0.7945 (p) REVERT: A 222 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8456 (ttmm) REVERT: A 235 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7716 (ttm170) REVERT: B 32 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8154 (mmmm) REVERT: B 44 GLU cc_start: 0.8271 (tt0) cc_final: 0.7864 (tt0) REVERT: B 69 LYS cc_start: 0.8944 (tttt) cc_final: 0.8726 (tttt) REVERT: B 78 THR cc_start: 0.9136 (t) cc_final: 0.8855 (m) REVERT: B 104 ASP cc_start: 0.7926 (t0) cc_final: 0.7644 (t0) REVERT: B 185 PHE cc_start: 0.8841 (t80) cc_final: 0.8590 (t80) REVERT: B 186 ASP cc_start: 0.8428 (p0) cc_final: 0.8145 (p0) REVERT: B 201 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 208 ASN cc_start: 0.7800 (p0) cc_final: 0.7545 (p0) REVERT: B 214 VAL cc_start: 0.9464 (t) cc_final: 0.9125 (t) REVERT: B 224 VAL cc_start: 0.8407 (t) cc_final: 0.8087 (t) REVERT: C 9 ASP cc_start: 0.7529 (p0) cc_final: 0.7284 (p0) REVERT: C 14 VAL cc_start: 0.9112 (t) cc_final: 0.8841 (t) REVERT: C 43 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8526 (ttmt) REVERT: C 44 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 91 ARG cc_start: 0.7615 (mmm160) cc_final: 0.6279 (tpt-90) REVERT: C 110 LYS cc_start: 0.9454 (tptp) cc_final: 0.9216 (tptt) REVERT: C 172 THR cc_start: 0.9428 (m) cc_final: 0.9150 (t) REVERT: C 175 PHE cc_start: 0.9061 (m-80) cc_final: 0.8721 (m-80) REVERT: C 208 ASN cc_start: 0.8673 (p0) cc_final: 0.8375 (p0) REVERT: C 214 VAL cc_start: 0.8958 (t) cc_final: 0.8684 (t) REVERT: C 219 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7332 (mtt90) REVERT: C 222 LYS cc_start: 0.8643 (tttt) cc_final: 0.8322 (tttp) REVERT: D 64 ILE cc_start: 0.7047 (pt) cc_final: 0.6730 (pt) REVERT: D 67 ILE cc_start: 0.9350 (mm) cc_final: 0.9145 (mm) REVERT: D 81 LEU cc_start: 0.9138 (mp) cc_final: 0.8890 (mp) REVERT: D 171 VAL cc_start: 0.9488 (t) cc_final: 0.9270 (p) REVERT: D 185 PHE cc_start: 0.7907 (t80) cc_final: 0.7160 (t80) REVERT: D 196 MET cc_start: 0.8903 (mmm) cc_final: 0.8630 (mmm) REVERT: D 208 ASN cc_start: 0.9002 (p0) cc_final: 0.8658 (p0) REVERT: D 219 ARG cc_start: 0.7724 (tpp80) cc_final: 0.7352 (tpp80) REVERT: D 227 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 234 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7469 (tm-30) REVERT: E 8 TYR cc_start: 0.8179 (m-10) cc_final: 0.7392 (m-80) REVERT: E 25 GLU cc_start: 0.8386 (tp30) cc_final: 0.7270 (tp30) REVERT: E 33 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8270 (ttt-90) REVERT: E 148 TYR cc_start: 0.9137 (m-80) cc_final: 0.8434 (m-10) REVERT: E 158 GLU cc_start: 0.7390 (tt0) cc_final: 0.7180 (tt0) REVERT: E 185 PHE cc_start: 0.8923 (t80) cc_final: 0.8440 (t80) REVERT: E 218 ASP cc_start: 0.8971 (p0) cc_final: 0.8653 (p0) REVERT: E 222 LYS cc_start: 0.8456 (mttt) cc_final: 0.7995 (tptm) REVERT: F 9 ASP cc_start: 0.8414 (p0) cc_final: 0.7834 (p0) REVERT: F 25 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7613 (mt-10) REVERT: F 26 TYR cc_start: 0.9071 (m-10) cc_final: 0.8694 (m-10) REVERT: F 158 GLU cc_start: 0.6611 (tt0) cc_final: 0.6058 (tt0) REVERT: F 169 ASN cc_start: 0.8006 (m-40) cc_final: 0.7599 (m-40) REVERT: F 200 ILE cc_start: 0.8867 (mm) cc_final: 0.8551 (mm) REVERT: F 232 TYR cc_start: 0.8954 (m-80) cc_final: 0.8721 (m-10) REVERT: F 234 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7541 (mt-10) REVERT: G 9 ASP cc_start: 0.8097 (p0) cc_final: 0.7544 (p0) REVERT: G 41 LYS cc_start: 0.8383 (ttpp) cc_final: 0.7694 (ttpt) REVERT: G 171 VAL cc_start: 0.9179 (t) cc_final: 0.8107 (p) REVERT: G 186 ASP cc_start: 0.8674 (m-30) cc_final: 0.7923 (p0) REVERT: G 187 ASP cc_start: 0.8737 (m-30) cc_final: 0.8227 (m-30) REVERT: G 191 LEU cc_start: 0.9136 (tp) cc_final: 0.8735 (tp) REVERT: G 234 GLU cc_start: 0.8467 (pp20) cc_final: 0.7879 (pp20) REVERT: G 237 ASN cc_start: 0.7422 (m110) cc_final: 0.7027 (m110) REVERT: 1 17 LEU cc_start: 0.9262 (pt) cc_final: 0.8976 (pt) REVERT: 1 25 MET cc_start: 0.8032 (mtm) cc_final: 0.7360 (ttm) REVERT: 1 27 THR cc_start: 0.8160 (m) cc_final: 0.7520 (m) REVERT: 1 79 ILE cc_start: 0.8546 (mp) cc_final: 0.8344 (mp) REVERT: 1 88 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8742 (ttm-80) REVERT: 1 111 LEU cc_start: 0.8949 (mt) cc_final: 0.8263 (mt) REVERT: 1 112 ILE cc_start: 0.9202 (mt) cc_final: 0.8967 (mt) REVERT: 1 122 ILE cc_start: 0.8569 (mm) cc_final: 0.7635 (mm) REVERT: 1 134 GLU cc_start: 0.6981 (mp0) cc_final: 0.6760 (mp0) REVERT: 1 173 TYR cc_start: 0.8591 (t80) cc_final: 0.8080 (t80) REVERT: 1 190 LYS cc_start: 0.8115 (ptmt) cc_final: 0.7758 (ptmm) REVERT: 1 193 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7748 (tm-30) REVERT: 2 45 ILE cc_start: 0.7959 (tt) cc_final: 0.7190 (tt) REVERT: 2 48 ILE cc_start: 0.8860 (mm) cc_final: 0.8417 (mm) REVERT: 2 52 MET cc_start: 0.7927 (ttm) cc_final: 0.7343 (ttm) REVERT: 2 83 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7631 (ptt180) REVERT: 2 151 LEU cc_start: 0.9216 (mt) cc_final: 0.9015 (mt) REVERT: 2 190 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8500 (ttmt) REVERT: 3 46 TYR cc_start: 0.7045 (m-80) cc_final: 0.6384 (m-80) REVERT: 3 52 MET cc_start: 0.8670 (ttt) cc_final: 0.8448 (ttt) REVERT: 3 83 ARG cc_start: 0.7066 (ptp-170) cc_final: 0.6614 (ptp-170) REVERT: 3 88 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7731 (ttm110) REVERT: 4 20 LYS cc_start: 0.8397 (tptm) cc_final: 0.7647 (pttm) REVERT: 4 28 GLU cc_start: 0.5823 (pp20) cc_final: 0.5550 (pm20) REVERT: 4 44 LYS cc_start: 0.7160 (tppt) cc_final: 0.6358 (tttm) REVERT: 4 52 MET cc_start: 0.8262 (ttm) cc_final: 0.8008 (ttm) REVERT: 4 80 ARG cc_start: 0.8942 (mtp180) cc_final: 0.8348 (mtp180) REVERT: 4 87 VAL cc_start: 0.9226 (t) cc_final: 0.8822 (t) REVERT: 4 123 TYR cc_start: 0.8962 (m-80) cc_final: 0.7628 (m-80) REVERT: 4 133 GLU cc_start: 0.7628 (tt0) cc_final: 0.7240 (tt0) REVERT: 4 134 GLU cc_start: 0.7762 (mp0) cc_final: 0.7507 (mp0) REVERT: 4 135 LYS cc_start: 0.8291 (tppt) cc_final: 0.7554 (ttpt) REVERT: 4 190 LYS cc_start: 0.8487 (ttpt) cc_final: 0.7946 (ptmm) REVERT: 5 46 TYR cc_start: 0.7418 (m-80) cc_final: 0.6966 (m-10) REVERT: 5 118 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6830 (mt-10) REVERT: 5 134 GLU cc_start: 0.7755 (mp0) cc_final: 0.7459 (mp0) REVERT: 5 146 THR cc_start: 0.9146 (p) cc_final: 0.8887 (t) REVERT: 5 193 GLU cc_start: 0.8294 (mp0) cc_final: 0.8027 (mp0) REVERT: 6 28 GLU cc_start: 0.8377 (pm20) cc_final: 0.7526 (pm20) REVERT: 6 68 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7370 (ttp-110) REVERT: 6 122 ILE cc_start: 0.8986 (tp) cc_final: 0.8615 (tp) REVERT: 6 163 GLU cc_start: 0.7827 (pm20) cc_final: 0.7535 (pm20) REVERT: 6 172 ILE cc_start: 0.8412 (tt) cc_final: 0.7938 (tt) REVERT: 6 173 TYR cc_start: 0.7124 (t80) cc_final: 0.6494 (t80) REVERT: 6 187 ASP cc_start: 0.7218 (t0) cc_final: 0.6846 (t0) REVERT: 7 44 LYS cc_start: 0.6376 (tppt) cc_final: 0.5670 (mmtp) REVERT: 7 193 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7097 (tm-30) REVERT: H 396 MET cc_start: 0.8311 (ptp) cc_final: 0.7878 (mtm) outliers start: 0 outliers final: 0 residues processed: 1222 average time/residue: 0.5323 time to fit residues: 1013.7495 Evaluate side-chains 1103 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1103 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 94 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 260 optimal weight: 0.6980 chunk 220 optimal weight: 0.0770 chunk 158 optimal weight: 0.0980 chunk 171 optimal weight: 0.7980 chunk 213 optimal weight: 0.0870 chunk 203 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 1 75 ASN 3 75 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 109 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.180272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147666 restraints weight = 36711.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.152106 restraints weight = 21133.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.155128 restraints weight = 14167.752| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24968 Z= 0.154 Angle : 0.726 13.480 33660 Z= 0.384 Chirality : 0.049 0.269 3881 Planarity : 0.004 0.046 4329 Dihedral : 5.557 81.954 3498 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3122 helix: 0.29 (0.15), residues: 1252 sheet: 0.01 (0.19), residues: 627 loop : -1.21 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 73 PHE 0.024 0.002 PHE D 185 TYR 0.035 0.002 TYR D 213 ARG 0.013 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1269) hydrogen bonds : angle 5.24124 ( 3699) covalent geometry : bond 0.00353 (24968) covalent geometry : angle 0.72642 (33660) *********************** 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 1176 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1176 time to evaluate : 2.760 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: A 31 VAL cc_start: 0.9581 (m) cc_final: 0.9254 (p) REVERT: A 44 GLU cc_start: 0.8555 (pm20) cc_final: 0.8028 (pm20) REVERT: A 100 ARG cc_start: 0.8761 (ttm170) cc_final: 0.8557 (ttm-80) REVERT: A 166 MET cc_start: 0.8167 (mtp) cc_final: 0.7833 (ttp) REVERT: A 186 ASP cc_start: 0.7439 (p0) cc_final: 0.6821 (p0) REVERT: A 208 ASN cc_start: 0.9045 (p0) cc_final: 0.8359 (p0) REVERT: A 211 VAL cc_start: 0.8893 (t) cc_final: 0.7867 (p) REVERT: A 222 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8396 (ttmm) REVERT: B 32 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8182 (mmmm) REVERT: B 44 GLU cc_start: 0.8229 (tt0) cc_final: 0.7846 (tt0) REVERT: B 60 GLU cc_start: 0.8001 (tp30) cc_final: 0.7411 (tp30) REVERT: B 78 THR cc_start: 0.9090 (t) cc_final: 0.8832 (m) REVERT: B 104 ASP cc_start: 0.7881 (t0) cc_final: 0.7612 (t0) REVERT: B 181 ASP cc_start: 0.7615 (m-30) cc_final: 0.7343 (m-30) REVERT: B 185 PHE cc_start: 0.8875 (t80) cc_final: 0.8624 (t80) REVERT: B 201 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 208 ASN cc_start: 0.7754 (p0) cc_final: 0.7483 (p0) REVERT: B 214 VAL cc_start: 0.9358 (t) cc_final: 0.9063 (t) REVERT: B 238 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7131 (mt-10) REVERT: B 239 ARG cc_start: 0.7744 (mtp-110) cc_final: 0.7454 (ttp-170) REVERT: C 9 ASP cc_start: 0.7402 (p0) cc_final: 0.7196 (p0) REVERT: C 14 VAL cc_start: 0.8987 (t) cc_final: 0.8741 (t) REVERT: C 44 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 51 ASP cc_start: 0.9193 (t0) cc_final: 0.8814 (t0) REVERT: C 95 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7527 (mm-30) REVERT: C 110 LYS cc_start: 0.9417 (tptp) cc_final: 0.9099 (tptt) REVERT: C 172 THR cc_start: 0.9435 (m) cc_final: 0.9146 (t) REVERT: C 175 PHE cc_start: 0.9036 (m-80) cc_final: 0.8738 (m-80) REVERT: C 202 SER cc_start: 0.8496 (p) cc_final: 0.8260 (p) REVERT: C 208 ASN cc_start: 0.8608 (p0) cc_final: 0.7928 (p0) REVERT: C 214 VAL cc_start: 0.8925 (t) cc_final: 0.8640 (t) REVERT: C 219 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.7385 (mtt90) REVERT: C 222 LYS cc_start: 0.8640 (tttt) cc_final: 0.8304 (tttp) REVERT: D 64 ILE cc_start: 0.6715 (pt) cc_final: 0.6338 (pt) REVERT: D 81 LEU cc_start: 0.9102 (mp) cc_final: 0.8853 (mp) REVERT: D 130 ARG cc_start: 0.8568 (ptt-90) cc_final: 0.8307 (ptt-90) REVERT: D 196 MET cc_start: 0.8906 (mmm) cc_final: 0.8646 (mmm) REVERT: D 208 ASN cc_start: 0.8853 (p0) cc_final: 0.8410 (p0) REVERT: D 227 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 234 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7428 (tm-30) REVERT: E 8 TYR cc_start: 0.8165 (m-10) cc_final: 0.7143 (m-80) REVERT: E 25 GLU cc_start: 0.8358 (tp30) cc_final: 0.7228 (tp30) REVERT: E 33 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8238 (ttt-90) REVERT: E 108 THR cc_start: 0.9030 (m) cc_final: 0.8721 (m) REVERT: E 132 PHE cc_start: 0.8942 (m-80) cc_final: 0.8694 (m-10) REVERT: E 148 TYR cc_start: 0.9059 (m-80) cc_final: 0.8175 (m-10) REVERT: E 158 GLU cc_start: 0.7076 (tt0) cc_final: 0.6830 (tt0) REVERT: E 164 ILE cc_start: 0.9119 (pt) cc_final: 0.8850 (pt) REVERT: E 183 LEU cc_start: 0.7120 (pt) cc_final: 0.6540 (pt) REVERT: E 185 PHE cc_start: 0.8782 (t80) cc_final: 0.8348 (t80) REVERT: E 186 ASP cc_start: 0.8101 (m-30) cc_final: 0.7897 (m-30) REVERT: E 222 LYS cc_start: 0.8460 (mttt) cc_final: 0.8164 (mttp) REVERT: F 9 ASP cc_start: 0.8351 (p0) cc_final: 0.7702 (p0) REVERT: F 93 ARG cc_start: 0.9118 (ttm170) cc_final: 0.8870 (tpp80) REVERT: F 95 GLU cc_start: 0.7861 (tp30) cc_final: 0.7566 (tp30) REVERT: F 99 ASN cc_start: 0.8546 (t0) cc_final: 0.8329 (t0) REVERT: F 107 ILE cc_start: 0.9102 (tt) cc_final: 0.8732 (tt) REVERT: F 112 LEU cc_start: 0.9216 (tp) cc_final: 0.8918 (tp) REVERT: F 158 GLU cc_start: 0.6479 (tt0) cc_final: 0.5857 (tt0) REVERT: F 187 ASP cc_start: 0.8753 (m-30) cc_final: 0.8523 (m-30) REVERT: F 193 LEU cc_start: 0.9471 (mm) cc_final: 0.9240 (mm) REVERT: F 201 GLU cc_start: 0.8787 (mp0) cc_final: 0.8556 (mp0) REVERT: F 213 TYR cc_start: 0.8576 (p90) cc_final: 0.8375 (p90) REVERT: F 222 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8093 (ptmm) REVERT: F 234 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7532 (mt-10) REVERT: G 9 ASP cc_start: 0.8159 (p0) cc_final: 0.7602 (p0) REVERT: G 73 HIS cc_start: 0.8447 (p-80) cc_final: 0.8120 (p90) REVERT: G 89 ILE cc_start: 0.9318 (mm) cc_final: 0.8985 (mm) REVERT: G 171 VAL cc_start: 0.9181 (t) cc_final: 0.8771 (m) REVERT: G 186 ASP cc_start: 0.8743 (m-30) cc_final: 0.7988 (p0) REVERT: G 191 LEU cc_start: 0.9007 (tp) cc_final: 0.8644 (tp) REVERT: G 234 GLU cc_start: 0.8476 (pp20) cc_final: 0.7887 (pp20) REVERT: G 237 ASN cc_start: 0.7668 (m110) cc_final: 0.7323 (m110) REVERT: 1 17 LEU cc_start: 0.9273 (pt) cc_final: 0.9015 (pt) REVERT: 1 25 MET cc_start: 0.8040 (mtm) cc_final: 0.7314 (ttm) REVERT: 1 75 ASN cc_start: 0.8799 (m-40) cc_final: 0.8581 (m110) REVERT: 1 87 VAL cc_start: 0.9411 (t) cc_final: 0.9067 (p) REVERT: 1 111 LEU cc_start: 0.8912 (mt) cc_final: 0.8244 (mt) REVERT: 1 122 ILE cc_start: 0.8483 (mm) cc_final: 0.7624 (mm) REVERT: 1 173 TYR cc_start: 0.8589 (t80) cc_final: 0.8074 (t80) REVERT: 1 187 ASP cc_start: 0.6540 (p0) cc_final: 0.6187 (p0) REVERT: 1 190 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7776 (ptmm) REVERT: 1 193 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7768 (tm-30) REVERT: 2 45 ILE cc_start: 0.8126 (tt) cc_final: 0.7153 (tt) REVERT: 2 48 ILE cc_start: 0.8873 (mm) cc_final: 0.8569 (mm) REVERT: 2 83 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7535 (ptt180) REVERT: 2 190 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8551 (ttmt) REVERT: 3 46 TYR cc_start: 0.7085 (m-80) cc_final: 0.6398 (m-80) REVERT: 3 52 MET cc_start: 0.8616 (ttt) cc_final: 0.8308 (ttt) REVERT: 3 54 MET cc_start: 0.7468 (ttp) cc_final: 0.7162 (ttp) REVERT: 3 83 ARG cc_start: 0.7018 (ptp-170) cc_final: 0.6591 (ptp-170) REVERT: 3 88 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7368 (mtp85) REVERT: 3 110 LEU cc_start: 0.9360 (mt) cc_final: 0.8993 (mt) REVERT: 3 123 TYR cc_start: 0.8432 (m-10) cc_final: 0.8078 (m-80) REVERT: 4 20 LYS cc_start: 0.8428 (tptm) cc_final: 0.7753 (pttm) REVERT: 4 52 MET cc_start: 0.8201 (ttm) cc_final: 0.7938 (ttm) REVERT: 4 80 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8357 (mtp180) REVERT: 4 135 LYS cc_start: 0.8224 (tppt) cc_final: 0.7528 (ttpt) REVERT: 4 190 LYS cc_start: 0.8437 (ttpt) cc_final: 0.7986 (ptmm) REVERT: 5 46 TYR cc_start: 0.7319 (m-80) cc_final: 0.7117 (m-10) REVERT: 5 118 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6671 (mt-10) REVERT: 5 123 TYR cc_start: 0.8680 (m-80) cc_final: 0.8384 (m-10) REVERT: 5 134 GLU cc_start: 0.7809 (mp0) cc_final: 0.7428 (mp0) REVERT: 5 146 THR cc_start: 0.9163 (p) cc_final: 0.8819 (t) REVERT: 5 191 ILE cc_start: 0.8083 (mt) cc_final: 0.7807 (mt) REVERT: 6 28 GLU cc_start: 0.8362 (pm20) cc_final: 0.7613 (pm20) REVERT: 6 68 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7423 (ttp-110) REVERT: 6 79 ILE cc_start: 0.9514 (mt) cc_final: 0.9291 (mt) REVERT: 6 122 ILE cc_start: 0.8878 (tp) cc_final: 0.8511 (tp) REVERT: 6 163 GLU cc_start: 0.8008 (pm20) cc_final: 0.7645 (pm20) REVERT: 6 172 ILE cc_start: 0.8162 (tt) cc_final: 0.7908 (tt) REVERT: 6 173 TYR cc_start: 0.7336 (t80) cc_final: 0.6688 (t80) REVERT: 7 44 LYS cc_start: 0.6405 (tppt) cc_final: 0.5790 (mmtp) REVERT: 7 193 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6962 (tm-30) REVERT: H 396 MET cc_start: 0.8304 (ptp) cc_final: 0.7905 (mtm) outliers start: 0 outliers final: 0 residues processed: 1176 average time/residue: 0.3690 time to fit residues: 671.3519 Evaluate side-chains 1092 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1092 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 306 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 275 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 284 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 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.141836 restraints weight = 36799.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.146053 restraints weight = 21460.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.148827 restraints weight = 14536.619| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24968 Z= 0.226 Angle : 0.770 13.896 33660 Z= 0.407 Chirality : 0.050 0.269 3881 Planarity : 0.004 0.042 4329 Dihedral : 5.716 83.225 3498 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3122 helix: 0.31 (0.15), residues: 1188 sheet: 0.09 (0.19), residues: 617 loop : -1.30 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.019 0.002 PHE 7 65 TYR 0.034 0.002 TYR 7 148 ARG 0.013 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 1269) hydrogen bonds : angle 5.34992 ( 3699) covalent geometry : bond 0.00510 (24968) covalent geometry : angle 0.77049 (33660) *********************** 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 1222 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1222 time to evaluate : 2.668 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 25 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 44 GLU cc_start: 0.8616 (pm20) cc_final: 0.8159 (pm20) REVERT: A 98 ILE cc_start: 0.8834 (mt) cc_final: 0.8464 (mt) REVERT: A 186 ASP cc_start: 0.7620 (p0) cc_final: 0.6907 (p0) REVERT: A 208 ASN cc_start: 0.9166 (p0) cc_final: 0.8747 (p0) REVERT: A 211 VAL cc_start: 0.8692 (t) cc_final: 0.7859 (p) REVERT: B 32 LYS cc_start: 0.8747 (mmtp) cc_final: 0.8300 (mmmm) REVERT: B 44 GLU cc_start: 0.8347 (tt0) cc_final: 0.7928 (tt0) REVERT: B 58 LEU cc_start: 0.9110 (mt) cc_final: 0.8892 (mt) REVERT: B 60 GLU cc_start: 0.8181 (tp30) cc_final: 0.7554 (tp30) REVERT: B 174 PHE cc_start: 0.8557 (t80) cc_final: 0.7604 (t80) REVERT: B 185 PHE cc_start: 0.8875 (t80) cc_final: 0.8585 (t80) REVERT: B 214 VAL cc_start: 0.9442 (t) cc_final: 0.9106 (t) REVERT: B 238 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7181 (mt-10) REVERT: C 9 ASP cc_start: 0.7464 (p0) cc_final: 0.7198 (p0) REVERT: C 14 VAL cc_start: 0.9087 (t) cc_final: 0.8818 (t) REVERT: C 44 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7397 (tm-30) REVERT: C 51 ASP cc_start: 0.9096 (t0) cc_final: 0.8790 (t0) REVERT: C 68 TYR cc_start: 0.8050 (m-80) cc_final: 0.7121 (m-80) REVERT: C 71 ASP cc_start: 0.8710 (t70) cc_final: 0.8497 (t70) REVERT: C 91 ARG cc_start: 0.7892 (mmm160) cc_final: 0.6437 (tpt170) REVERT: C 95 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 110 LYS cc_start: 0.9304 (tptp) cc_final: 0.9088 (tptt) REVERT: C 172 THR cc_start: 0.9448 (m) cc_final: 0.9238 (t) REVERT: C 175 PHE cc_start: 0.9189 (m-80) cc_final: 0.8821 (m-80) REVERT: C 196 MET cc_start: 0.8889 (tpp) cc_final: 0.8470 (mtt) REVERT: C 202 SER cc_start: 0.8591 (p) cc_final: 0.8349 (p) REVERT: C 208 ASN cc_start: 0.8769 (p0) cc_final: 0.8256 (p0) REVERT: C 214 VAL cc_start: 0.8965 (t) cc_final: 0.8685 (t) REVERT: C 217 ASP cc_start: 0.8743 (p0) cc_final: 0.8514 (p0) REVERT: C 218 ASP cc_start: 0.8174 (p0) cc_final: 0.7521 (p0) REVERT: C 220 THR cc_start: 0.8164 (p) cc_final: 0.7819 (p) REVERT: C 222 LYS cc_start: 0.8717 (tttt) cc_final: 0.8408 (tttp) REVERT: C 225 SER cc_start: 0.8944 (p) cc_final: 0.6260 (p) REVERT: D 64 ILE cc_start: 0.6915 (pt) cc_final: 0.6659 (pt) REVERT: D 234 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7609 (tm-30) REVERT: E 8 TYR cc_start: 0.8298 (m-10) cc_final: 0.7413 (m-80) REVERT: E 25 GLU cc_start: 0.8439 (tp30) cc_final: 0.7461 (tp30) REVERT: E 33 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8343 (ttt-90) REVERT: E 148 TYR cc_start: 0.9108 (m-80) cc_final: 0.8234 (m-10) REVERT: E 158 GLU cc_start: 0.7272 (tt0) cc_final: 0.6984 (tt0) REVERT: E 185 PHE cc_start: 0.8776 (t80) cc_final: 0.8490 (t80) REVERT: E 186 ASP cc_start: 0.8047 (m-30) cc_final: 0.7815 (m-30) REVERT: F 9 ASP cc_start: 0.8505 (p0) cc_final: 0.7977 (p0) REVERT: F 26 TYR cc_start: 0.8994 (m-10) cc_final: 0.8738 (m-10) REVERT: F 67 ILE cc_start: 0.9173 (mt) cc_final: 0.8968 (mt) REVERT: F 95 GLU cc_start: 0.8309 (tp30) cc_final: 0.7852 (tp30) REVERT: F 107 ILE cc_start: 0.9191 (tt) cc_final: 0.8967 (tt) REVERT: F 158 GLU cc_start: 0.6771 (tt0) cc_final: 0.6326 (tt0) REVERT: F 187 ASP cc_start: 0.8839 (m-30) cc_final: 0.8516 (m-30) REVERT: F 196 MET cc_start: 0.9130 (tpp) cc_final: 0.8618 (tpp) REVERT: F 201 GLU cc_start: 0.8783 (mp0) cc_final: 0.8567 (mp0) REVERT: F 213 TYR cc_start: 0.8650 (p90) cc_final: 0.8417 (p90) REVERT: F 215 LYS cc_start: 0.7445 (mttp) cc_final: 0.7101 (mttt) REVERT: F 222 LYS cc_start: 0.8504 (ptmt) cc_final: 0.8017 (ptmm) REVERT: G 9 ASP cc_start: 0.8178 (p0) cc_final: 0.7614 (p0) REVERT: G 41 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7798 (ttpt) REVERT: G 47 ILE cc_start: 0.9188 (mt) cc_final: 0.8356 (mt) REVERT: G 71 ASP cc_start: 0.7837 (m-30) cc_final: 0.7633 (m-30) REVERT: G 73 HIS cc_start: 0.8443 (p-80) cc_final: 0.8159 (p90) REVERT: G 171 VAL cc_start: 0.9227 (t) cc_final: 0.8188 (p) REVERT: G 186 ASP cc_start: 0.8701 (m-30) cc_final: 0.7893 (p0) REVERT: G 187 ASP cc_start: 0.8637 (m-30) cc_final: 0.8124 (m-30) REVERT: G 191 LEU cc_start: 0.9152 (tp) cc_final: 0.8750 (tp) REVERT: G 211 VAL cc_start: 0.9444 (t) cc_final: 0.8962 (p) REVERT: G 234 GLU cc_start: 0.8404 (pp20) cc_final: 0.7839 (pp20) REVERT: G 237 ASN cc_start: 0.7907 (m110) cc_final: 0.7365 (m110) REVERT: 1 17 LEU cc_start: 0.9313 (pt) cc_final: 0.9040 (pt) REVERT: 1 25 MET cc_start: 0.8050 (mtm) cc_final: 0.7308 (ttm) REVERT: 1 87 VAL cc_start: 0.9346 (t) cc_final: 0.9127 (p) REVERT: 1 111 LEU cc_start: 0.8871 (mt) cc_final: 0.8330 (mt) REVERT: 1 122 ILE cc_start: 0.8762 (mm) cc_final: 0.7932 (mm) REVERT: 1 134 GLU cc_start: 0.7081 (mp0) cc_final: 0.6823 (mp0) REVERT: 1 172 ILE cc_start: 0.8476 (mm) cc_final: 0.7930 (mm) REVERT: 1 173 TYR cc_start: 0.8657 (t80) cc_final: 0.8165 (t80) REVERT: 1 190 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7660 (ptmm) REVERT: 1 193 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7693 (tm-30) REVERT: 1 208 LEU cc_start: 0.5912 (pp) cc_final: 0.5685 (pp) REVERT: 2 45 ILE cc_start: 0.8056 (tt) cc_final: 0.7194 (tt) REVERT: 2 48 ILE cc_start: 0.8896 (mm) cc_final: 0.8646 (mm) REVERT: 2 83 ARG cc_start: 0.8197 (ptm160) cc_final: 0.7663 (ptt180) REVERT: 3 46 TYR cc_start: 0.7317 (m-80) cc_final: 0.6838 (m-80) REVERT: 3 52 MET cc_start: 0.8723 (ttt) cc_final: 0.8379 (ttt) REVERT: 3 54 MET cc_start: 0.8031 (ttp) cc_final: 0.7752 (ttp) REVERT: 3 88 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7517 (mtp85) REVERT: 3 110 LEU cc_start: 0.9431 (mt) cc_final: 0.9065 (mt) REVERT: 4 17 LEU cc_start: 0.8982 (mt) cc_final: 0.8709 (mt) REVERT: 4 20 LYS cc_start: 0.8502 (tptm) cc_final: 0.7809 (pttm) REVERT: 4 44 LYS cc_start: 0.7382 (tppt) cc_final: 0.6534 (tttt) REVERT: 4 52 MET cc_start: 0.8289 (ttm) cc_final: 0.8033 (ttm) REVERT: 4 87 VAL cc_start: 0.9371 (t) cc_final: 0.9154 (t) REVERT: 4 123 TYR cc_start: 0.9201 (m-80) cc_final: 0.8559 (m-10) REVERT: 4 134 GLU cc_start: 0.7809 (mp0) cc_final: 0.7446 (mp0) REVERT: 4 135 LYS cc_start: 0.8331 (tppt) cc_final: 0.7589 (ttpt) REVERT: 4 137 ILE cc_start: 0.8417 (mm) cc_final: 0.7843 (tt) REVERT: 4 190 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8260 (ptmm) REVERT: 4 206 GLN cc_start: 0.7513 (mt0) cc_final: 0.6491 (mm-40) REVERT: 5 46 TYR cc_start: 0.7629 (m-80) cc_final: 0.7227 (m-10) REVERT: 5 118 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6687 (mt-10) REVERT: 5 123 TYR cc_start: 0.8645 (m-80) cc_final: 0.8389 (m-10) REVERT: 5 134 GLU cc_start: 0.7899 (mp0) cc_final: 0.7583 (mp0) REVERT: 5 146 THR cc_start: 0.9216 (p) cc_final: 0.8893 (t) REVERT: 6 28 GLU cc_start: 0.8450 (pm20) cc_final: 0.7590 (pm20) REVERT: 6 68 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7697 (ttp-110) REVERT: 6 133 GLU cc_start: 0.8323 (tt0) cc_final: 0.7932 (tt0) REVERT: 6 163 GLU cc_start: 0.7926 (pm20) cc_final: 0.7531 (pm20) REVERT: 6 172 ILE cc_start: 0.8372 (tt) cc_final: 0.8153 (tt) REVERT: 6 173 TYR cc_start: 0.7498 (t80) cc_final: 0.6793 (t80) REVERT: 7 44 LYS cc_start: 0.6624 (tppt) cc_final: 0.5821 (mmtp) REVERT: 7 52 MET cc_start: 0.8390 (ttm) cc_final: 0.8112 (ttm) REVERT: 7 190 LYS cc_start: 0.8547 (pttt) cc_final: 0.8271 (pttm) REVERT: 7 193 GLU cc_start: 0.7779 (tm-30) cc_final: 0.6993 (tm-30) REVERT: H 396 MET cc_start: 0.8811 (ptp) cc_final: 0.8513 (mpp) outliers start: 0 outliers final: 0 residues processed: 1222 average time/residue: 0.3659 time to fit residues: 691.3810 Evaluate side-chains 1093 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1093 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 244 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 265 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 255 optimal weight: 0.0000 chunk 75 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 292 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.176327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.143965 restraints weight = 36518.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.148187 restraints weight = 21242.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.151025 restraints weight = 14382.092| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24968 Z= 0.197 Angle : 0.769 13.385 33660 Z= 0.407 Chirality : 0.050 0.288 3881 Planarity : 0.005 0.052 4329 Dihedral : 5.741 82.311 3498 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.39 % Favored : 95.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3122 helix: 0.25 (0.15), residues: 1187 sheet: 0.04 (0.19), residues: 626 loop : -1.24 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 73 PHE 0.021 0.002 PHE 6 36 TYR 0.039 0.002 TYR 7 148 ARG 0.016 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1269) hydrogen bonds : angle 5.40064 ( 3699) covalent geometry : bond 0.00457 (24968) covalent geometry : angle 0.76937 (33660) ********************** 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 1199 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1199 time to evaluate : 2.928 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: A 44 GLU cc_start: 0.8506 (pm20) cc_final: 0.8059 (pm20) REVERT: A 98 ILE cc_start: 0.8910 (mt) cc_final: 0.8531 (mt) REVERT: A 166 MET cc_start: 0.8197 (mtp) cc_final: 0.7857 (ttp) REVERT: A 186 ASP cc_start: 0.7427 (p0) cc_final: 0.7129 (p0) REVERT: A 208 ASN cc_start: 0.9210 (p0) cc_final: 0.8500 (p0) REVERT: A 211 VAL cc_start: 0.8881 (t) cc_final: 0.7891 (p) REVERT: B 32 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8277 (mmmm) REVERT: B 36 THR cc_start: 0.8579 (m) cc_final: 0.7933 (p) REVERT: B 44 GLU cc_start: 0.8234 (tt0) cc_final: 0.7845 (tt0) REVERT: B 60 GLU cc_start: 0.8104 (tp30) cc_final: 0.7470 (tp30) REVERT: B 66 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8435 (mtpt) REVERT: B 78 THR cc_start: 0.9186 (t) cc_final: 0.8916 (m) REVERT: B 104 ASP cc_start: 0.7939 (t70) cc_final: 0.7649 (t0) REVERT: B 174 PHE cc_start: 0.8289 (t80) cc_final: 0.7907 (t80) REVERT: B 186 ASP cc_start: 0.8390 (p0) cc_final: 0.8123 (p0) REVERT: B 214 VAL cc_start: 0.9416 (t) cc_final: 0.9116 (t) REVERT: C 9 ASP cc_start: 0.7405 (p0) cc_final: 0.6894 (p0) REVERT: C 14 VAL cc_start: 0.9003 (t) cc_final: 0.8742 (t) REVERT: C 28 ARG cc_start: 0.8740 (tpt90) cc_final: 0.8214 (mmm160) REVERT: C 44 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 91 ARG cc_start: 0.7843 (mmm160) cc_final: 0.6360 (tpt170) REVERT: C 95 GLU cc_start: 0.7958 (mm-30) cc_final: 0.6844 (mm-30) REVERT: C 110 LYS cc_start: 0.9260 (tptp) cc_final: 0.9047 (tptt) REVERT: C 175 PHE cc_start: 0.9132 (m-80) cc_final: 0.8818 (m-80) REVERT: C 196 MET cc_start: 0.8768 (tpp) cc_final: 0.8402 (mtt) REVERT: C 208 ASN cc_start: 0.8832 (p0) cc_final: 0.8282 (p0) REVERT: C 214 VAL cc_start: 0.8954 (t) cc_final: 0.8639 (t) REVERT: D 64 ILE cc_start: 0.6976 (pt) cc_final: 0.6738 (pt) REVERT: D 234 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 8 TYR cc_start: 0.8061 (m-10) cc_final: 0.7297 (m-80) REVERT: E 25 GLU cc_start: 0.8357 (tp30) cc_final: 0.7443 (tp30) REVERT: E 33 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8290 (ttt-90) REVERT: E 148 TYR cc_start: 0.9138 (m-80) cc_final: 0.8128 (m-10) REVERT: E 158 GLU cc_start: 0.7062 (tt0) cc_final: 0.6771 (tt0) REVERT: E 185 PHE cc_start: 0.8777 (t80) cc_final: 0.8566 (t80) REVERT: F 9 ASP cc_start: 0.8380 (p0) cc_final: 0.8029 (p0) REVERT: F 26 TYR cc_start: 0.8977 (m-10) cc_final: 0.8736 (m-10) REVERT: F 67 ILE cc_start: 0.9168 (mt) cc_final: 0.8954 (mt) REVERT: F 93 ARG cc_start: 0.9236 (ttm170) cc_final: 0.8784 (tpp80) REVERT: F 95 GLU cc_start: 0.8318 (tp30) cc_final: 0.7872 (tp30) REVERT: F 112 LEU cc_start: 0.9261 (tp) cc_final: 0.8930 (tp) REVERT: F 158 GLU cc_start: 0.6826 (tt0) cc_final: 0.6356 (tt0) REVERT: F 196 MET cc_start: 0.9086 (tpp) cc_final: 0.8535 (tpp) REVERT: F 200 ILE cc_start: 0.9009 (mm) cc_final: 0.8800 (mm) REVERT: F 201 GLU cc_start: 0.8766 (mp0) cc_final: 0.8477 (mp0) REVERT: F 215 LYS cc_start: 0.7484 (mttp) cc_final: 0.7102 (mttt) REVERT: F 222 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8049 (ptmm) REVERT: F 234 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7537 (mt-10) REVERT: G 9 ASP cc_start: 0.8156 (p0) cc_final: 0.7585 (p0) REVERT: G 36 THR cc_start: 0.8926 (p) cc_final: 0.8707 (p) REVERT: G 41 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7867 (ttpt) REVERT: G 47 ILE cc_start: 0.9250 (mt) cc_final: 0.8960 (mt) REVERT: G 73 HIS cc_start: 0.8102 (p-80) cc_final: 0.7801 (p90) REVERT: G 171 VAL cc_start: 0.9243 (t) cc_final: 0.8960 (m) REVERT: G 186 ASP cc_start: 0.8458 (m-30) cc_final: 0.7740 (p0) REVERT: G 191 LEU cc_start: 0.9081 (tp) cc_final: 0.8602 (tp) REVERT: G 211 VAL cc_start: 0.9351 (t) cc_final: 0.8882 (p) REVERT: G 234 GLU cc_start: 0.8389 (pp20) cc_final: 0.7828 (pp20) REVERT: G 237 ASN cc_start: 0.7908 (m110) cc_final: 0.7359 (m110) REVERT: 1 17 LEU cc_start: 0.9337 (pt) cc_final: 0.9060 (pt) REVERT: 1 25 MET cc_start: 0.8087 (mtm) cc_final: 0.7422 (ttm) REVERT: 1 87 VAL cc_start: 0.9376 (t) cc_final: 0.9159 (p) REVERT: 1 111 LEU cc_start: 0.9012 (mt) cc_final: 0.8450 (mt) REVERT: 1 122 ILE cc_start: 0.8700 (mm) cc_final: 0.7879 (mm) REVERT: 1 134 GLU cc_start: 0.7042 (mp0) cc_final: 0.6771 (mp0) REVERT: 1 172 ILE cc_start: 0.8506 (mm) cc_final: 0.7960 (mm) REVERT: 1 173 TYR cc_start: 0.8641 (t80) cc_final: 0.8127 (t80) REVERT: 1 190 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7978 (ptmm) REVERT: 1 193 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7616 (tm-30) REVERT: 1 202 GLU cc_start: 0.8139 (pm20) cc_final: 0.7913 (pt0) REVERT: 1 208 LEU cc_start: 0.6047 (pp) cc_final: 0.5822 (pp) REVERT: 2 45 ILE cc_start: 0.8289 (tt) cc_final: 0.7278 (tt) REVERT: 2 48 ILE cc_start: 0.8819 (mm) cc_final: 0.8555 (mm) REVERT: 2 83 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7644 (ptt180) REVERT: 2 162 ASP cc_start: 0.6598 (m-30) cc_final: 0.6336 (m-30) REVERT: 2 190 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8665 (ttmt) REVERT: 3 46 TYR cc_start: 0.7158 (m-80) cc_final: 0.6568 (m-80) REVERT: 3 52 MET cc_start: 0.8684 (ttt) cc_final: 0.8397 (ttt) REVERT: 3 54 MET cc_start: 0.8028 (ttp) cc_final: 0.7722 (ttp) REVERT: 3 110 LEU cc_start: 0.9393 (mt) cc_final: 0.9017 (mt) REVERT: 3 202 GLU cc_start: 0.8371 (pm20) cc_final: 0.8077 (pm20) REVERT: 3 203 GLU cc_start: 0.8039 (tp30) cc_final: 0.7813 (tp30) REVERT: 4 20 LYS cc_start: 0.8323 (tptm) cc_final: 0.7734 (pttm) REVERT: 4 28 GLU cc_start: 0.5826 (pp20) cc_final: 0.5230 (pm20) REVERT: 4 44 LYS cc_start: 0.7865 (tppt) cc_final: 0.7327 (tttt) REVERT: 4 80 ARG cc_start: 0.9030 (mtp180) cc_final: 0.8726 (mtp180) REVERT: 4 87 VAL cc_start: 0.9334 (t) cc_final: 0.9091 (t) REVERT: 4 123 TYR cc_start: 0.9180 (m-80) cc_final: 0.8604 (m-80) REVERT: 4 134 GLU cc_start: 0.7773 (mp0) cc_final: 0.7477 (mp0) REVERT: 4 135 LYS cc_start: 0.8379 (tppt) cc_final: 0.7583 (ttpt) REVERT: 4 137 ILE cc_start: 0.8477 (mm) cc_final: 0.8132 (mm) REVERT: 4 190 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8323 (ptmm) REVERT: 5 134 GLU cc_start: 0.7859 (mp0) cc_final: 0.7650 (mp0) REVERT: 5 146 THR cc_start: 0.9198 (p) cc_final: 0.8867 (t) REVERT: 6 28 GLU cc_start: 0.8473 (pm20) cc_final: 0.7610 (pm20) REVERT: 6 79 ILE cc_start: 0.9486 (mt) cc_final: 0.9216 (mt) REVERT: 6 81 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7781 (ttm110) REVERT: 6 122 ILE cc_start: 0.8958 (tp) cc_final: 0.8466 (tp) REVERT: 6 133 GLU cc_start: 0.8210 (tt0) cc_final: 0.8006 (tt0) REVERT: 6 163 GLU cc_start: 0.7914 (pm20) cc_final: 0.7481 (pm20) REVERT: 6 173 TYR cc_start: 0.7401 (t80) cc_final: 0.6713 (t80) REVERT: 7 190 LYS cc_start: 0.8575 (pttt) cc_final: 0.8362 (pttm) REVERT: 7 193 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7123 (tm-30) REVERT: H 396 MET cc_start: 0.8611 (ptp) cc_final: 0.8225 (ptp) outliers start: 0 outliers final: 0 residues processed: 1199 average time/residue: 0.3552 time to fit residues: 664.6658 Evaluate side-chains 1107 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1107 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 16 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 293 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.0010 chunk 135 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 262 optimal weight: 0.2980 chunk 220 optimal weight: 0.1980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN E 99 ASN F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN 3 64 GLN 3 75 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 64 GLN ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.178230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.145491 restraints weight = 36745.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.149868 restraints weight = 21016.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.152841 restraints weight = 14110.410| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 0.076 24968 Z= 0.169 Angle : 0.757 13.050 33660 Z= 0.401 Chirality : 0.050 0.275 3881 Planarity : 0.004 0.047 4329 Dihedral : 5.721 84.044 3498 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3122 helix: 0.23 (0.15), residues: 1189 sheet: 0.04 (0.19), residues: 615 loop : -1.22 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.037 0.002 PHE G 174 TYR 0.042 0.002 TYR 4 46 ARG 0.015 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1269) hydrogen bonds : angle 5.39403 ( 3699) covalent geometry : bond 0.00394 (24968) covalent geometry : angle 0.75725 (33660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12968.70 seconds wall clock time: 226 minutes 57.98 seconds (13617.98 seconds total)