Starting phenix.real_space_refine on Fri Sep 19 07:25:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6he5_0210/09_2025/6he5_0210.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he5_0210/09_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_0210/09_2025/6he5_0210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he5_0210/09_2025/6he5_0210.map" model { file = "/net/cci-nas-00/data/ceres_data/6he5_0210/09_2025/6he5_0210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he5_0210/09_2025/6he5_0210.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 15633 2.51 5 N 4127 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 412 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24633 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "C" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "D" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "F" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "G" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "1" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'TRANS': 6} Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'TRANS': 7} Time building chain proxies: 5.73, per 1000 atoms: 0.23 Number of scatterers: 24633 At special positions: 0 Unit cell: (131.32, 134, 108.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 4776 8.00 N 4127 7.00 C 15633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 33 sheets defined 40.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.806A pdb=" N LYS A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 34' Processing helix chain 'A' and resid 81 through 103 removed outlier: 3.844A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.561A pdb=" N LYS A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.801A pdb=" N GLU A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.518A pdb=" N ILE A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 225 through 244 removed outlier: 3.651A pdb=" N LYS A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.710A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.513A pdb=" N VAL B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 removed outlier: 3.790A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.631A pdb=" N TYR B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.584A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 201 Processing helix chain 'B' and resid 225 through 245 Proline residue: B 231 - end of helix removed outlier: 4.066A pdb=" N GLU B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 81 through 103 removed outlier: 3.916A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.836A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 201 Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.762A pdb=" N LYS C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Proline residue: C 231 - end of helix removed outlier: 3.638A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 81 through 103 removed outlier: 3.866A pdb=" N VAL D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.588A pdb=" N GLU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 225 through 243 Proline residue: D 231 - end of helix removed outlier: 3.659A pdb=" N ARG D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.573A pdb=" N ARG E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.578A pdb=" N ARG E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.717A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.969A pdb=" N LYS E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.627A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.877A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 104 removed outlier: 3.747A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.574A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 225 through 244 removed outlier: 3.597A pdb=" N LYS F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 4.106A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.781A pdb=" N GLU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 104 removed outlier: 3.889A pdb=" N VAL G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.758A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.843A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 229 through 246 removed outlier: 4.077A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain '1' and resid 59 through 82 removed outlier: 3.603A pdb=" N PHE 1 65 " --> pdb=" O GLY 1 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE 1 69 " --> pdb=" O PHE 1 65 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 101 removed outlier: 3.753A pdb=" N ILE 1 90 " --> pdb=" O THR 1 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER 1 95 " --> pdb=" O ALA 1 91 " (cutoff:3.500A) Processing helix chain '1' and resid 143 through 153 removed outlier: 4.660A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 179 removed outlier: 3.608A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP 1 179 " --> pdb=" O ALA 1 175 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 208 removed outlier: 4.326A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE 1 207 " --> pdb=" O GLU 1 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 1 208 " --> pdb=" O VAL 1 204 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.711A pdb=" N ARG 2 68 " --> pdb=" O GLN 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 removed outlier: 3.669A pdb=" N ILE 2 90 " --> pdb=" O THR 2 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 2 96 " --> pdb=" O THR 2 92 " (cutoff:3.500A) Processing helix chain '2' and resid 143 through 153 removed outlier: 3.596A pdb=" N ASP 2 153 " --> pdb=" O GLY 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 177 removed outlier: 3.950A pdb=" N LEU 2 167 " --> pdb=" O GLU 2 163 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS 2 177 " --> pdb=" O TYR 2 173 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 206 removed outlier: 4.225A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 removed outlier: 3.616A pdb=" N ALA 3 63 " --> pdb=" O SER 3 59 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE 3 69 " --> pdb=" O PHE 3 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 3 70 " --> pdb=" O LEU 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 101 Processing helix chain '3' and resid 143 through 154 removed outlier: 4.111A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 3 150 " --> pdb=" O THR 3 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP 3 153 " --> pdb=" O GLY 3 149 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 176 removed outlier: 3.560A pdb=" N GLU 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA 3 175 " --> pdb=" O ALA 3 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET 3 176 " --> pdb=" O ILE 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 200 through 206 Processing helix chain '4' and resid 59 through 82 removed outlier: 3.709A pdb=" N ILE 4 69 " --> pdb=" O PHE 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 Processing helix chain '4' and resid 143 through 154 removed outlier: 3.790A pdb=" N VAL 4 150 " --> pdb=" O THR 4 146 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP 4 153 " --> pdb=" O GLY 4 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 4 154 " --> pdb=" O VAL 4 150 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 removed outlier: 3.885A pdb=" N GLU 4 166 " --> pdb=" O ASP 4 162 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 4 175 " --> pdb=" O ALA 4 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 209 removed outlier: 3.924A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE 4 207 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 82 removed outlier: 3.605A pdb=" N ALA 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE 5 65 " --> pdb=" O GLY 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 152 removed outlier: 3.559A pdb=" N GLU 5 152 " --> pdb=" O TYR 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.908A pdb=" N GLU 5 166 " --> pdb=" O ASP 5 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER 5 174 " --> pdb=" O ARG 5 170 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET 5 176 " --> pdb=" O ILE 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 179 through 184 removed outlier: 3.781A pdb=" N SER 5 182 " --> pdb=" O ASP 5 179 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP 5 184 " --> pdb=" O ALA 5 181 " (cutoff:3.500A) Processing helix chain '5' and resid 199 through 206 removed outlier: 4.443A pdb=" N GLU 5 203 " --> pdb=" O TYR 5 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL 5 204 " --> pdb=" O SER 5 200 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.732A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.511A pdb=" N ILE 6 90 " --> pdb=" O THR 6 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 6 100 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR 6 101 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 155 removed outlier: 3.630A pdb=" N GLY 6 149 " --> pdb=" O LEU 6 145 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.506A pdb=" N ALA 6 164 " --> pdb=" O GLY 6 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 6 166 " --> pdb=" O ASP 6 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE 6 172 " --> pdb=" O ALA 6 168 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.122A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 6 204 " --> pdb=" O SER 6 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN 6 206 " --> pdb=" O GLU 6 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 6 207 " --> pdb=" O GLU 6 203 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 82 Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 154 removed outlier: 3.800A pdb=" N GLY 7 149 " --> pdb=" O LEU 7 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 7 150 " --> pdb=" O THR 7 146 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 163 through 177 removed outlier: 3.837A pdb=" N LEU 7 167 " --> pdb=" O GLU 7 163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG 7 170 " --> pdb=" O GLU 7 166 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS 7 177 " --> pdb=" O TYR 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 205 removed outlier: 4.392A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.659A pdb=" N VAL A 211 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.698A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 147 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.575A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.219A pdb=" N ILE B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 147 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.836A pdb=" N GLY C 45 " --> pdb=" O CYS C 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 4.152A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 147 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.150A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.522A pdb=" N GLY E 45 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL E 211 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.553A pdb=" N ALA E 77 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.524A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL F 211 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.565A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 147 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 69 removed outlier: 4.857A pdb=" N GLY F 80 " --> pdb=" O VAL M 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.521A pdb=" N ALA G 37 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AB7, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.508A pdb=" N VAL L 398 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain '1' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain '1' and resid 45 through 49 removed outlier: 6.700A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 125 " --> pdb=" O LEU 1 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY 1 114 " --> pdb=" O SER 1 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER 1 121 " --> pdb=" O GLY 1 114 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 137 through 138 removed outlier: 3.651A pdb=" N ASP 2 187 " --> pdb=" O THR 2 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '2' and resid 32 through 33 Processing sheet with id=AC4, first strand: chain '2' and resid 45 through 49 removed outlier: 6.609A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 2 110 " --> pdb=" O ILE 2 125 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE 2 122 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 14 through 18 removed outlier: 3.540A pdb=" N ALA 3 26 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET 3 25 " --> pdb=" O VAL 3 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP 3 187 " --> pdb=" O THR 3 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 46 through 49 removed outlier: 6.667A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 137 through 138 removed outlier: 4.020A pdb=" N VAL 4 138 " --> pdb=" O GLY 4 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY 4 16 " --> pdb=" O VAL 4 138 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL 4 15 " --> pdb=" O ALA 4 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 46 through 49 removed outlier: 6.555A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 137 through 140 removed outlier: 3.637A pdb=" N ILE 5 191 " --> pdb=" O VAL 5 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 45 through 49 removed outlier: 6.742A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 5 121 " --> pdb=" O GLY 5 114 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 5 132 " --> pdb=" O SER 5 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 14 through 18 removed outlier: 3.722A pdb=" N TYR 6 197 " --> pdb=" O LYS 6 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 31 through 33 removed outlier: 6.738A pdb=" N ALA 6 31 " --> pdb=" O ALA 6 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 45 through 49 removed outlier: 6.824A pdb=" N ILE 6 45 " --> pdb=" O THR 6 56 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR 6 56 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN 6 47 " --> pdb=" O MET 6 54 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET 6 54 " --> pdb=" O GLN 6 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY 6 113 " --> pdb=" O ALA 6 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 6 110 " --> pdb=" O ILE 6 125 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 137 through 141 removed outlier: 5.394A pdb=" N THR 7 13 " --> pdb=" O GLU 7 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU 7 28 " --> pdb=" O THR 7 13 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 7 22 " --> pdb=" O CYS 7 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 7 23 " --> pdb=" O ILE 7 191 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE 7 122 " --> pdb=" O GLU 7 134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.23: 1776 1.23 - 1.46: 10918 1.46 - 1.69: 12100 1.69 - 1.92: 167 1.92 - 2.15: 7 Bond restraints: 24968 Sorted by residual: bond pdb=" CZ ARG 5 170 " pdb=" NH2 ARG 5 170 " ideal model delta sigma weight residual 1.330 2.147 -0.817 1.30e-02 5.92e+03 3.95e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.104 -0.720 2.10e-02 2.27e+03 1.17e+03 bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.041 -0.657 2.10e-02 2.27e+03 9.80e+02 bond pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 1.330 1.710 -0.380 1.23e-02 6.61e+03 9.52e+02 bond pdb=" N GLN E 5 " pdb=" CA GLN E 5 " ideal model delta sigma weight residual 1.458 1.000 0.458 1.90e-02 2.77e+03 5.80e+02 ... (remaining 24963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 26571 4.27 - 8.54: 6410 8.54 - 12.81: 642 12.81 - 17.07: 33 17.07 - 21.34: 4 Bond angle restraints: 33660 Sorted by residual: angle pdb=" NE ARG 5 170 " pdb=" CZ ARG 5 170 " pdb=" NH1 ARG 5 170 " ideal model delta sigma weight residual 121.50 101.39 20.11 1.00e+00 1.00e+00 4.05e+02 angle pdb=" N LYS 2 40 " pdb=" CA LYS 2 40 " pdb=" C LYS 2 40 " ideal model delta sigma weight residual 114.62 95.87 18.75 1.14e+00 7.69e-01 2.71e+02 angle pdb=" C GLU E 65 " pdb=" N LYS E 66 " pdb=" CA LYS E 66 " ideal model delta sigma weight residual 120.38 141.72 -21.34 1.37e+00 5.33e-01 2.43e+02 angle pdb=" CA LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 117.22 101.99 15.23 1.17e+00 7.31e-01 1.69e+02 angle pdb=" O LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 122.12 135.88 -13.76 1.06e+00 8.90e-01 1.69e+02 ... (remaining 33655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14375 25.08 - 50.16: 682 50.16 - 75.23: 224 75.23 - 100.31: 60 100.31 - 125.39: 2 Dihedral angle restraints: 15343 sinusoidal: 6204 harmonic: 9139 Sorted by residual: dihedral pdb=" CA GLU A 65 " pdb=" C GLU A 65 " pdb=" N LYS A 66 " pdb=" CA LYS A 66 " ideal model delta harmonic sigma weight residual -180.00 -54.61 -125.39 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA GLY H 394 " pdb=" C GLY H 394 " pdb=" N VAL H 395 " pdb=" CA VAL H 395 " ideal model delta harmonic sigma weight residual -180.00 -70.34 -109.66 0 5.00e+00 4.00e-02 4.81e+02 dihedral pdb=" CA ALA 2 139 " pdb=" C ALA 2 139 " pdb=" N THR 2 140 " pdb=" CA THR 2 140 " ideal model delta harmonic sigma weight residual 180.00 110.18 69.82 0 5.00e+00 4.00e-02 1.95e+02 ... (remaining 15340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 2874 0.225 - 0.450: 890 0.450 - 0.674: 107 0.674 - 0.899: 9 0.899 - 1.124: 1 Chirality restraints: 3881 Sorted by residual: chirality pdb=" CA THR 3 140 " pdb=" N THR 3 140 " pdb=" C THR 3 140 " pdb=" CB THR 3 140 " both_signs ideal model delta sigma weight residual False 2.53 1.40 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASP B 217 " pdb=" N ASP B 217 " pdb=" C ASP B 217 " pdb=" CB ASP B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA GLU D 65 " pdb=" N GLU D 65 " pdb=" C GLU D 65 " pdb=" CB GLU D 65 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3878 not shown) Planarity restraints: 4329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 5 199 " 0.225 2.00e-02 2.50e+03 1.45e-01 4.21e+02 pdb=" CG TYR 5 199 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR 5 199 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR 5 199 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 TYR 5 199 " -0.166 2.00e-02 2.50e+03 pdb=" CE2 TYR 5 199 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR 5 199 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR 5 199 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 123 " 0.214 2.00e-02 2.50e+03 1.28e-01 3.30e+02 pdb=" CG TYR G 123 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 123 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 TYR G 123 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR G 123 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR G 123 " -0.121 2.00e-02 2.50e+03 pdb=" CZ TYR G 123 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR G 123 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 101 " -0.196 2.00e-02 2.50e+03 1.26e-01 3.20e+02 pdb=" CG TYR 3 101 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 101 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 101 " 0.142 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 101 " 0.139 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 101 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR 3 101 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR 3 101 " -0.209 2.00e-02 2.50e+03 ... (remaining 4326 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3223 2.77 - 3.30: 22758 3.30 - 3.83: 39960 3.83 - 4.37: 53183 4.37 - 4.90: 84967 Nonbonded interactions: 204091 Sorted by model distance: nonbonded pdb=" NH2 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.236 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.237 3.340 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE1 PHE 5 211 " model vdw 2.242 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.250 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CZ PHE 5 211 " model vdw 2.251 3.420 ... (remaining 204086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 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: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.817 24968 Z= 2.308 Angle : 3.508 21.343 33660 Z= 2.349 Chirality : 0.204 1.124 3881 Planarity : 0.030 0.297 4329 Dihedral : 17.648 125.386 9493 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 2.18 % Allowed : 5.32 % Favored : 92.50 % Rotamer: Outliers : 4.51 % Allowed : 9.74 % Favored : 85.75 % Cbeta Deviations : 6.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 1.10 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.13), residues: 3122 helix: -1.29 (0.13), residues: 1197 sheet: -0.43 (0.20), residues: 563 loop : -2.82 (0.13), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.012 ARG 1 83 TYR 0.243 0.049 TYR F 8 PHE 0.189 0.040 PHE A 221 HIS 0.032 0.015 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.03648 (24968) covalent geometry : angle 3.50752 (33660) hydrogen bonds : bond 0.28205 ( 1269) hydrogen bonds : angle 9.34882 ( 3699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1303 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6473 (mm-30) REVERT: A 208 ASN cc_start: 0.7788 (p0) cc_final: 0.7357 (p0) REVERT: A 211 VAL cc_start: 0.7891 (t) cc_final: 0.7530 (p) REVERT: A 220 THR cc_start: 0.8239 (m) cc_final: 0.7978 (m) REVERT: B 24 VAL cc_start: 0.8283 (t) cc_final: 0.7918 (t) REVERT: B 152 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8589 (Cg_endo) REVERT: B 208 ASN cc_start: 0.6638 (p0) cc_final: 0.6184 (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: 0.8079 (ttpt) REVERT: C 47 ILE cc_start: 0.8472 (mt) cc_final: 0.8255 (mt) REVERT: C 144 VAL cc_start: 0.8745 (m) cc_final: 0.8484 (m) REVERT: C 160 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7659 (mtpt) REVERT: D 82 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8638 (t) REVERT: D 115 LYS cc_start: 0.8472 (mttm) cc_final: 0.7810 (mttt) REVERT: D 121 GLN cc_start: 0.8060 (tm130) cc_final: 0.7740 (tm130) REVERT: D 174 PHE cc_start: 0.7339 (t80) cc_final: 0.6544 (t80) REVERT: D 211 VAL cc_start: 0.8980 (t) cc_final: 0.8744 (t) REVERT: E 25 GLU cc_start: 0.6352 (tp30) cc_final: 0.5639 (tp30) REVERT: E 41 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7074 (ptmt) REVERT: E 49 ILE cc_start: 0.6840 (tt) cc_final: 0.6596 (tt) REVERT: E 68 TYR cc_start: 0.8023 (m-80) cc_final: 0.7697 (m-80) REVERT: E 116 ILE cc_start: 0.8525 (mt) cc_final: 0.8321 (mt) REVERT: E 120 LYS cc_start: 0.7119 (mttt) cc_final: 0.6914 (mttm) REVERT: E 186 ASP cc_start: 0.6779 (m-30) cc_final: 0.6126 (m-30) REVERT: E 235 ARG cc_start: 0.6204 (ttp-170) cc_final: 0.5557 (ttp80) REVERT: F 22 PHE cc_start: 0.6992 (m-80) cc_final: 0.6424 (m-80) REVERT: F 99 ASN cc_start: 0.7781 (t0) cc_final: 0.7489 (t0) REVERT: F 106 PRO cc_start: 0.9192 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: G 5 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.3616 (pm20) REVERT: G 16 SER cc_start: 0.7584 (p) cc_final: 0.7166 (p) REVERT: G 23 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7964 (tp40) REVERT: G 47 ILE cc_start: 0.8519 (mt) cc_final: 0.7840 (mt) REVERT: G 157 LEU cc_start: 0.7984 (mt) cc_final: 0.7600 (mt) REVERT: G 171 VAL cc_start: 0.5969 (t) cc_final: 0.4307 (t) REVERT: G 200 ILE cc_start: 0.7751 (pt) cc_final: 0.7382 (pt) REVERT: G 224 VAL cc_start: 0.6674 (t) cc_final: 0.6381 (t) REVERT: 1 107 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0699 (pt) REVERT: 2 44 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3394 (mptm) REVERT: 2 162 ASP cc_start: 0.4157 (m-30) cc_final: 0.3664 (m-30) REVERT: 3 24 VAL cc_start: 0.8584 (t) cc_final: 0.8350 (t) REVERT: 3 46 TYR cc_start: 0.7226 (m-80) cc_final: 0.6541 (m-80) REVERT: 3 93 LEU cc_start: 0.8152 (tp) cc_final: 0.7541 (tt) REVERT: 4 70 ILE cc_start: 0.9169 (mt) cc_final: 0.8898 (mt) REVERT: 5 146 THR cc_start: 0.6265 (p) cc_final: 0.5918 (p) REVERT: 6 155 PHE cc_start: 0.3192 (t80) cc_final: 0.2984 (t80) outliers start: 118 outliers final: 19 residues processed: 1361 average time/residue: 0.1819 time to fit residues: 367.2477 Evaluate side-chains 1111 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1088 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 237 ASN G 97 GLN G 99 ASN 1 64 GLN 3 96 ASN 4 99 ASN 7 109 GLN 7 198 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.186175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153757 restraints weight = 36901.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.158305 restraints weight = 21437.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.161391 restraints weight = 14380.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.163370 restraints weight = 10774.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.164808 restraints weight = 8857.416| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24968 Z= 0.258 Angle : 0.881 14.202 33660 Z= 0.482 Chirality : 0.052 0.213 3881 Planarity : 0.006 0.088 4329 Dihedral : 6.552 56.473 3498 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.62 % Favored : 96.06 % Rotamer: Outliers : 0.19 % Allowed : 4.66 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3122 helix: -0.06 (0.14), residues: 1242 sheet: 0.12 (0.19), residues: 593 loop : -2.09 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 5 170 TYR 0.039 0.002 TYR 6 46 PHE 0.030 0.003 PHE 4 155 HIS 0.008 0.003 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00561 (24968) covalent geometry : angle 0.88084 (33660) hydrogen bonds : bond 0.05041 ( 1269) hydrogen bonds : angle 5.78466 ( 3699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1299 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 CYS cc_start: 0.8476 (m) cc_final: 0.8276 (m) REVERT: A 121 GLN cc_start: 0.8625 (tp40) cc_final: 0.7661 (tm-30) REVERT: A 172 THR cc_start: 0.8552 (p) cc_final: 0.7797 (p) REVERT: A 186 ASP cc_start: 0.7703 (p0) cc_final: 0.7063 (p0) REVERT: A 208 ASN cc_start: 0.8716 (p0) cc_final: 0.8152 (p0) REVERT: A 211 VAL cc_start: 0.8728 (t) cc_final: 0.7128 (p) REVERT: A 222 LYS cc_start: 0.8500 (tttm) cc_final: 0.8204 (ttmm) REVERT: B 104 ASP cc_start: 0.7156 (m-30) cc_final: 0.6564 (m-30) REVERT: B 176 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 181 ASP cc_start: 0.7762 (m-30) cc_final: 0.7497 (m-30) REVERT: B 186 ASP cc_start: 0.8486 (p0) cc_final: 0.8284 (p0) REVERT: B 201 GLU cc_start: 0.7924 (tm-30) cc_final: 0.6928 (tm-30) REVERT: B 208 ASN cc_start: 0.7419 (p0) cc_final: 0.7120 (p0) REVERT: B 214 VAL cc_start: 0.9423 (t) cc_final: 0.9202 (p) REVERT: B 238 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6727 (mt-10) REVERT: C 57 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8465 (pttm) REVERT: C 123 TYR cc_start: 0.7866 (m-80) cc_final: 0.7487 (m-80) REVERT: C 137 LEU cc_start: 0.9358 (mt) cc_final: 0.8787 (mt) REVERT: C 149 GLU cc_start: 0.8733 (tt0) cc_final: 0.8533 (tt0) REVERT: C 160 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8239 (mtmm) REVERT: C 164 ILE cc_start: 0.9546 (pt) cc_final: 0.9329 (pt) REVERT: C 185 PHE cc_start: 0.8829 (t80) cc_final: 0.8465 (t80) REVERT: C 189 MET cc_start: 0.9141 (ttm) cc_final: 0.8807 (ttm) REVERT: C 202 SER cc_start: 0.8522 (p) cc_final: 0.8093 (p) REVERT: C 208 ASN cc_start: 0.8541 (p0) cc_final: 0.8041 (p0) REVERT: C 209 ILE cc_start: 0.9099 (pt) cc_final: 0.8740 (pt) REVERT: C 214 VAL cc_start: 0.8939 (t) cc_final: 0.8583 (t) REVERT: C 225 SER cc_start: 0.8905 (p) cc_final: 0.7956 (p) REVERT: D 33 ARG cc_start: 0.8539 (ptm160) cc_final: 0.8188 (mtp-110) REVERT: D 60 GLU cc_start: 0.7797 (pp20) cc_final: 0.7540 (pp20) REVERT: D 64 ILE cc_start: 0.6738 (pt) cc_final: 0.6455 (pt) REVERT: D 91 ARG cc_start: 0.8681 (tpt170) cc_final: 0.8204 (tpt90) REVERT: D 95 GLU cc_start: 0.8059 (tt0) cc_final: 0.6848 (tt0) REVERT: D 115 LYS cc_start: 0.8571 (mttm) cc_final: 0.7979 (mtpt) REVERT: D 121 GLN cc_start: 0.7958 (tp40) cc_final: 0.7612 (tm-30) REVERT: D 174 PHE cc_start: 0.8543 (t80) cc_final: 0.8280 (t80) REVERT: D 185 PHE cc_start: 0.7864 (t80) cc_final: 0.7410 (t80) REVERT: D 228 GLU cc_start: 0.7986 (tp30) cc_final: 0.7745 (tp30) REVERT: E 25 GLU cc_start: 0.8074 (tp30) cc_final: 0.6780 (tp30) REVERT: E 65 GLU cc_start: 0.5289 (tt0) cc_final: 0.4639 (tt0) REVERT: E 68 TYR cc_start: 0.8848 (m-80) cc_final: 0.8228 (m-80) REVERT: E 72 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6951 (mt-10) REVERT: E 75 CYS cc_start: 0.9044 (p) cc_final: 0.8819 (p) REVERT: E 88 LEU cc_start: 0.9154 (tp) cc_final: 0.8914 (tt) REVERT: E 93 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8607 (mtp85) REVERT: E 172 THR cc_start: 0.8999 (m) cc_final: 0.8678 (t) REVERT: E 221 PHE cc_start: 0.8443 (t80) cc_final: 0.8021 (t80) REVERT: F 9 ASP cc_start: 0.8620 (p0) cc_final: 0.8345 (p0) REVERT: F 26 TYR cc_start: 0.9231 (m-10) cc_final: 0.8710 (m-10) REVERT: F 99 ASN cc_start: 0.9044 (t0) cc_final: 0.8814 (t0) REVERT: F 150 THR cc_start: 0.8562 (p) cc_final: 0.8251 (p) REVERT: F 151 ASP cc_start: 0.7869 (m-30) cc_final: 0.7662 (m-30) REVERT: F 187 ASP cc_start: 0.8543 (m-30) cc_final: 0.7964 (m-30) REVERT: F 196 MET cc_start: 0.9127 (tpp) cc_final: 0.8778 (tpp) REVERT: F 210 GLU cc_start: 0.7922 (tt0) cc_final: 0.7027 (tt0) REVERT: F 228 GLU cc_start: 0.8413 (tp30) cc_final: 0.8102 (tp30) REVERT: G 23 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8410 (tp40) REVERT: G 33 ARG cc_start: 0.7198 (ptp-170) cc_final: 0.6845 (mtm180) REVERT: G 44 GLU cc_start: 0.7826 (mp0) cc_final: 0.7570 (mp0) REVERT: G 47 ILE cc_start: 0.9298 (mt) cc_final: 0.9029 (mt) REVERT: G 89 ILE cc_start: 0.9334 (mm) cc_final: 0.9076 (mm) REVERT: G 93 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8421 (mtt-85) REVERT: G 104 ASP cc_start: 0.7929 (t70) cc_final: 0.7335 (t0) REVERT: G 171 VAL cc_start: 0.8673 (t) cc_final: 0.7361 (p) REVERT: G 187 ASP cc_start: 0.8190 (m-30) cc_final: 0.7988 (m-30) REVERT: G 209 ILE cc_start: 0.9158 (pt) cc_final: 0.8902 (pt) REVERT: 1 44 LYS cc_start: 0.8124 (tttt) cc_final: 0.7908 (tptt) REVERT: 1 111 LEU cc_start: 0.9013 (mt) cc_final: 0.8672 (mt) REVERT: 1 116 ASP cc_start: 0.8818 (p0) cc_final: 0.8574 (p0) REVERT: 1 122 ILE cc_start: 0.8377 (mm) cc_final: 0.7768 (mm) REVERT: 1 135 LYS cc_start: 0.7779 (mppt) cc_final: 0.7477 (mppt) REVERT: 1 173 TYR cc_start: 0.8482 (t80) cc_final: 0.7968 (t80) REVERT: 1 190 LYS cc_start: 0.8562 (ptpp) cc_final: 0.7982 (ptpp) REVERT: 1 208 LEU cc_start: 0.4755 (pp) cc_final: 0.4217 (pp) REVERT: 2 19 CYS cc_start: 0.6861 (m) cc_final: 0.6390 (m) REVERT: 2 72 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8714 (mp) REVERT: 2 159 ILE cc_start: 0.8296 (tt) cc_final: 0.7862 (tt) REVERT: 2 162 ASP cc_start: 0.5839 (m-30) cc_final: 0.5474 (m-30) REVERT: 2 163 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7029 (mp0) REVERT: 2 190 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8704 (tttt) REVERT: 2 203 GLU cc_start: 0.7393 (pt0) cc_final: 0.6959 (pt0) REVERT: 3 46 TYR cc_start: 0.7336 (m-80) cc_final: 0.6498 (m-10) REVERT: 3 48 ILE cc_start: 0.8949 (mm) cc_final: 0.8725 (tp) REVERT: 3 84 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7661 (mptt) REVERT: 3 90 ILE cc_start: 0.9477 (mm) cc_final: 0.8998 (tt) REVERT: 3 188 VAL cc_start: 0.7533 (t) cc_final: 0.7293 (t) REVERT: 4 48 ILE cc_start: 0.9307 (mm) cc_final: 0.8591 (mm) REVERT: 4 80 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8336 (mtp180) REVERT: 4 87 VAL cc_start: 0.9376 (t) cc_final: 0.9008 (t) REVERT: 4 88 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7973 (ttp-170) REVERT: 4 132 ILE cc_start: 0.8878 (mt) cc_final: 0.8661 (mt) REVERT: 4 190 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7868 (ptmm) REVERT: 5 79 ILE cc_start: 0.8899 (mt) cc_final: 0.8507 (mt) REVERT: 5 92 THR cc_start: 0.8796 (p) cc_final: 0.8576 (p) REVERT: 5 122 ILE cc_start: 0.8985 (mt) cc_final: 0.8354 (mt) REVERT: 5 132 ILE cc_start: 0.8491 (mt) cc_final: 0.8136 (mt) REVERT: 5 134 GLU cc_start: 0.7043 (mp0) cc_final: 0.6729 (mp0) REVERT: 6 33 MET cc_start: 0.1424 (pmm) cc_final: 0.1210 (pmm) REVERT: 6 68 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.7056 (mtm-85) REVERT: 6 72 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8505 (mp) REVERT: 6 81 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8097 (tpp80) REVERT: 6 137 ILE cc_start: 0.8282 (mm) cc_final: 0.7632 (mp) REVERT: 7 44 LYS cc_start: 0.6346 (tppt) cc_final: 0.5917 (tppt) REVERT: 7 75 ASN cc_start: 0.8920 (m-40) cc_final: 0.8644 (m-40) REVERT: 7 120 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8233 (mtmm) REVERT: 7 152 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6923 (mt-10) outliers start: 5 outliers final: 0 residues processed: 1301 average time/residue: 0.1831 time to fit residues: 359.5955 Evaluate side-chains 1116 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1114 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 179 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 148 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN 3 75 ASN 6 96 ASN 6 198 GLN 7 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.181324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.148735 restraints weight = 36807.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.153241 restraints weight = 21206.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156263 restraints weight = 14168.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.158227 restraints weight = 10641.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.159752 restraints weight = 8723.118| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24968 Z= 0.187 Angle : 0.744 14.328 33660 Z= 0.405 Chirality : 0.049 0.222 3881 Planarity : 0.005 0.068 4329 Dihedral : 5.883 58.921 3498 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.94 % Favored : 95.74 % Rotamer: Outliers : 0.27 % Allowed : 3.63 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3122 helix: 0.13 (0.14), residues: 1239 sheet: 0.26 (0.19), residues: 599 loop : -1.73 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 81 TYR 0.031 0.002 TYR 6 148 PHE 0.024 0.002 PHE 5 155 HIS 0.005 0.002 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00412 (24968) covalent geometry : angle 0.74386 (33660) hydrogen bonds : bond 0.04244 ( 1269) hydrogen bonds : angle 5.36405 ( 3699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1260 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8266 (pm20) cc_final: 0.7977 (pm20) REVERT: A 117 CYS cc_start: 0.8398 (m) cc_final: 0.8170 (m) REVERT: A 121 GLN cc_start: 0.8159 (tp40) cc_final: 0.7670 (tm-30) REVERT: A 172 THR cc_start: 0.8793 (p) cc_final: 0.8571 (p) REVERT: A 182 ASP cc_start: 0.7235 (p0) cc_final: 0.7031 (p0) REVERT: A 186 ASP cc_start: 0.7568 (p0) cc_final: 0.6810 (p0) REVERT: A 208 ASN cc_start: 0.8765 (p0) cc_final: 0.8258 (p0) REVERT: A 211 VAL cc_start: 0.8942 (t) cc_final: 0.7453 (p) REVERT: A 222 LYS cc_start: 0.8558 (tttm) cc_final: 0.8350 (ttmm) REVERT: B 38 ILE cc_start: 0.8966 (mt) cc_final: 0.8515 (mt) REVERT: B 47 ILE cc_start: 0.8912 (mt) cc_final: 0.8216 (mt) REVERT: B 93 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8059 (mtt-85) REVERT: B 116 ILE cc_start: 0.9378 (tt) cc_final: 0.9079 (tt) REVERT: B 151 ASP cc_start: 0.9159 (t0) cc_final: 0.8683 (t0) REVERT: B 152 PRO cc_start: 0.9636 (Cg_exo) cc_final: 0.9313 (Cg_endo) REVERT: B 174 PHE cc_start: 0.7995 (t80) cc_final: 0.7453 (t80) REVERT: B 176 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 187 ASP cc_start: 0.7729 (m-30) cc_final: 0.7288 (m-30) REVERT: B 189 MET cc_start: 0.8305 (tpt) cc_final: 0.7892 (tpt) REVERT: B 196 MET cc_start: 0.8589 (mmm) cc_final: 0.8123 (mmm) REVERT: B 201 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 207 GLU cc_start: 0.7316 (mp0) cc_final: 0.6933 (mp0) REVERT: B 208 ASN cc_start: 0.7492 (p0) cc_final: 0.7257 (p0) REVERT: C 26 TYR cc_start: 0.8713 (m-10) cc_final: 0.8007 (m-10) REVERT: C 44 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5856 (tm-30) REVERT: C 52 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8440 (ttpt) REVERT: C 57 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8466 (pttm) REVERT: C 103 TYR cc_start: 0.8437 (m-80) cc_final: 0.8057 (m-10) REVERT: C 123 TYR cc_start: 0.7368 (m-80) cc_final: 0.7015 (m-80) REVERT: C 160 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8275 (mtmm) REVERT: C 175 PHE cc_start: 0.9038 (m-80) cc_final: 0.8826 (m-80) REVERT: C 185 PHE cc_start: 0.8444 (t80) cc_final: 0.8216 (t80) REVERT: C 189 MET cc_start: 0.8972 (ttm) cc_final: 0.8760 (ttm) REVERT: C 202 SER cc_start: 0.8649 (p) cc_final: 0.8386 (p) REVERT: C 203 GLU cc_start: 0.6004 (pm20) cc_final: 0.5735 (pm20) REVERT: C 208 ASN cc_start: 0.8497 (p0) cc_final: 0.7838 (p0) REVERT: C 222 LYS cc_start: 0.8355 (tttt) cc_final: 0.8106 (ttmm) REVERT: D 18 ASP cc_start: 0.8409 (p0) cc_final: 0.7694 (p0) REVERT: D 33 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8176 (mtp-110) REVERT: D 38 ILE cc_start: 0.9144 (mt) cc_final: 0.8771 (mt) REVERT: D 57 LYS cc_start: 0.8682 (pttm) cc_final: 0.7983 (mppt) REVERT: D 64 ILE cc_start: 0.6761 (pt) cc_final: 0.6424 (pt) REVERT: D 67 ILE cc_start: 0.9233 (mm) cc_final: 0.9002 (mm) REVERT: D 68 TYR cc_start: 0.7708 (m-80) cc_final: 0.7505 (m-80) REVERT: D 91 ARG cc_start: 0.8729 (tpt170) cc_final: 0.8471 (tpt90) REVERT: D 95 GLU cc_start: 0.8230 (tt0) cc_final: 0.7953 (tt0) REVERT: D 104 ASP cc_start: 0.7986 (t0) cc_final: 0.7746 (t0) REVERT: D 115 LYS cc_start: 0.8727 (mttm) cc_final: 0.8137 (mtmt) REVERT: D 174 PHE cc_start: 0.8702 (t80) cc_final: 0.8312 (t80) REVERT: D 178 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7444 (mt-10) REVERT: E 25 GLU cc_start: 0.8178 (tp30) cc_final: 0.6810 (tp30) REVERT: E 28 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7936 (mmm160) REVERT: E 68 TYR cc_start: 0.8765 (m-80) cc_final: 0.8192 (m-80) REVERT: E 159 TYR cc_start: 0.9015 (m-80) cc_final: 0.8695 (m-80) REVERT: E 172 THR cc_start: 0.9115 (m) cc_final: 0.8840 (t) REVERT: E 218 ASP cc_start: 0.8934 (p0) cc_final: 0.8284 (p0) REVERT: E 222 LYS cc_start: 0.8414 (mttt) cc_final: 0.8108 (mttp) REVERT: F 9 ASP cc_start: 0.8518 (p0) cc_final: 0.8000 (p0) REVERT: F 26 TYR cc_start: 0.9202 (m-10) cc_final: 0.8758 (m-10) REVERT: F 99 ASN cc_start: 0.9120 (t0) cc_final: 0.8875 (t0) REVERT: F 120 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8281 (ttmm) REVERT: F 142 ASP cc_start: 0.7096 (p0) cc_final: 0.6451 (p0) REVERT: F 150 THR cc_start: 0.8630 (p) cc_final: 0.8257 (p) REVERT: F 173 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7627 (tm-30) REVERT: F 193 LEU cc_start: 0.9267 (mm) cc_final: 0.9054 (mm) REVERT: F 210 GLU cc_start: 0.7005 (tt0) cc_final: 0.6613 (tt0) REVERT: F 213 TYR cc_start: 0.8661 (p90) cc_final: 0.8125 (p90) REVERT: F 223 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8013 (mm-30) REVERT: G 33 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6878 (mtm180) REVERT: G 51 ASP cc_start: 0.8683 (t0) cc_final: 0.8399 (t70) REVERT: G 66 LYS cc_start: 0.8560 (tptt) cc_final: 0.7445 (mptt) REVERT: G 68 TYR cc_start: 0.8399 (m-80) cc_final: 0.8184 (m-80) REVERT: G 73 HIS cc_start: 0.8069 (p-80) cc_final: 0.7621 (p-80) REVERT: G 104 ASP cc_start: 0.7645 (t70) cc_final: 0.6899 (t0) REVERT: G 114 LYS cc_start: 0.8349 (mttp) cc_final: 0.8048 (ttmm) REVERT: G 171 VAL cc_start: 0.8741 (t) cc_final: 0.7469 (p) REVERT: G 187 ASP cc_start: 0.8285 (m-30) cc_final: 0.7990 (m-30) REVERT: G 211 VAL cc_start: 0.9273 (t) cc_final: 0.9059 (t) REVERT: G 234 GLU cc_start: 0.8523 (pp20) cc_final: 0.8207 (pp20) REVERT: G 237 ASN cc_start: 0.7401 (m110) cc_final: 0.6794 (m110) REVERT: 1 80 ARG cc_start: 0.8922 (mtm180) cc_final: 0.8523 (mtt180) REVERT: 1 88 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8578 (mmm-85) REVERT: 1 111 LEU cc_start: 0.9003 (mt) cc_final: 0.8583 (mt) REVERT: 1 122 ILE cc_start: 0.8520 (mm) cc_final: 0.7920 (mm) REVERT: 1 123 TYR cc_start: 0.8438 (m-80) cc_final: 0.8126 (m-80) REVERT: 1 135 LYS cc_start: 0.7847 (mppt) cc_final: 0.7577 (mppt) REVERT: 1 173 TYR cc_start: 0.8506 (t80) cc_final: 0.7905 (t80) REVERT: 1 208 LEU cc_start: 0.5217 (pp) cc_final: 0.4702 (pp) REVERT: 2 19 CYS cc_start: 0.7066 (m) cc_final: 0.6750 (m) REVERT: 2 72 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8594 (mp) REVERT: 2 93 LEU cc_start: 0.9031 (tt) cc_final: 0.8752 (tt) REVERT: 2 116 ASP cc_start: 0.4616 (p0) cc_final: 0.4056 (p0) REVERT: 2 159 ILE cc_start: 0.8148 (tt) cc_final: 0.7779 (mt) REVERT: 2 190 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8832 (tttt) REVERT: 3 46 TYR cc_start: 0.7245 (m-80) cc_final: 0.6306 (m-80) REVERT: 3 78 GLU cc_start: 0.8039 (tt0) cc_final: 0.7834 (tt0) REVERT: 3 84 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7828 (mptt) REVERT: 3 90 ILE cc_start: 0.9401 (mm) cc_final: 0.8895 (tt) REVERT: 3 202 GLU cc_start: 0.8345 (pm20) cc_final: 0.8055 (pm20) REVERT: 4 48 ILE cc_start: 0.9364 (mm) cc_final: 0.8835 (mm) REVERT: 4 52 MET cc_start: 0.8349 (ttm) cc_final: 0.7902 (ttm) REVERT: 4 80 ARG cc_start: 0.8747 (mtp180) cc_final: 0.7926 (mtp180) REVERT: 4 83 ARG cc_start: 0.8560 (ptm160) cc_final: 0.7735 (ptm160) REVERT: 4 87 VAL cc_start: 0.9135 (t) cc_final: 0.8934 (t) REVERT: 4 88 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7913 (ttp-170) REVERT: 4 109 GLN cc_start: 0.6823 (mp10) cc_final: 0.6557 (mp10) REVERT: 4 123 TYR cc_start: 0.9080 (m-80) cc_final: 0.8649 (m-80) REVERT: 4 135 LYS cc_start: 0.8091 (tppt) cc_final: 0.7457 (ttpt) REVERT: 4 152 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8341 (mm-30) REVERT: 4 190 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7983 (ptmm) REVERT: 5 33 MET cc_start: -0.1087 (mtt) cc_final: -0.1893 (ttm) REVERT: 5 46 TYR cc_start: 0.7635 (m-80) cc_final: 0.6601 (m-10) REVERT: 5 73 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8062 (mm-30) REVERT: 5 87 VAL cc_start: 0.9425 (t) cc_final: 0.9062 (m) REVERT: 5 92 THR cc_start: 0.8815 (p) cc_final: 0.8607 (p) REVERT: 5 115 ILE cc_start: 0.7248 (pt) cc_final: 0.6806 (pt) REVERT: 5 134 GLU cc_start: 0.7381 (mp0) cc_final: 0.7028 (mp0) REVERT: 5 165 VAL cc_start: 0.8907 (m) cc_final: 0.8529 (m) REVERT: 6 72 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8585 (mp) REVERT: 6 79 ILE cc_start: 0.9597 (mt) cc_final: 0.9274 (mt) REVERT: 6 81 ARG cc_start: 0.8525 (ttm110) cc_final: 0.8213 (tpp80) REVERT: 6 122 ILE cc_start: 0.9216 (tp) cc_final: 0.8852 (tp) REVERT: 6 163 GLU cc_start: 0.7916 (mp0) cc_final: 0.7376 (pm20) REVERT: 6 170 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8195 (mmm-85) REVERT: 7 44 LYS cc_start: 0.6622 (tppt) cc_final: 0.6153 (tppt) REVERT: 7 75 ASN cc_start: 0.8777 (m-40) cc_final: 0.8381 (m-40) REVERT: 7 77 TYR cc_start: 0.8059 (t80) cc_final: 0.7827 (t80) REVERT: 7 120 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8103 (mtmm) REVERT: 7 122 ILE cc_start: 0.8994 (tp) cc_final: 0.8747 (tp) REVERT: 7 193 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 7 outliers final: 1 residues processed: 1264 average time/residue: 0.1808 time to fit residues: 349.7118 Evaluate side-chains 1132 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1129 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 190 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 211 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 125 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 5 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN 3 75 ASN 3 198 GLN 4 75 ASN 4 96 ASN 6 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.178468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.146093 restraints weight = 36845.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.150468 restraints weight = 21150.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.153326 restraints weight = 14162.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.155428 restraints weight = 10677.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156760 restraints weight = 8713.586| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24968 Z= 0.191 Angle : 0.722 14.500 33660 Z= 0.390 Chirality : 0.048 0.222 3881 Planarity : 0.005 0.170 4329 Dihedral : 5.707 58.122 3498 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.00 % Favored : 95.68 % Rotamer: Outliers : 0.27 % Allowed : 3.40 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3122 helix: 0.32 (0.15), residues: 1226 sheet: 0.08 (0.19), residues: 629 loop : -1.52 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 88 TYR 0.034 0.002 TYR 3 123 PHE 0.026 0.002 PHE 5 196 HIS 0.006 0.002 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00426 (24968) covalent geometry : angle 0.72173 (33660) hydrogen bonds : bond 0.04009 ( 1269) hydrogen bonds : angle 5.21233 ( 3699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1263 time to evaluate : 1.019 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 98 ILE cc_start: 0.8867 (mt) cc_final: 0.8442 (mt) REVERT: A 121 GLN cc_start: 0.8483 (tp40) cc_final: 0.7761 (tm-30) REVERT: A 166 MET cc_start: 0.8305 (mtp) cc_final: 0.8044 (ttt) REVERT: A 186 ASP cc_start: 0.7582 (p0) cc_final: 0.6771 (p0) REVERT: A 187 ASP cc_start: 0.7920 (m-30) cc_final: 0.7699 (m-30) REVERT: A 208 ASN cc_start: 0.8859 (p0) cc_final: 0.8350 (p0) REVERT: A 211 VAL cc_start: 0.8980 (t) cc_final: 0.7448 (p) REVERT: A 213 TYR cc_start: 0.8804 (p90) cc_final: 0.8375 (p90) REVERT: A 222 LYS cc_start: 0.8712 (tttm) cc_final: 0.8383 (ttmm) REVERT: B 32 LYS cc_start: 0.8337 (mmtp) cc_final: 0.8085 (mmmm) REVERT: B 43 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8256 (ttmt) REVERT: B 51 ASP cc_start: 0.7485 (m-30) cc_final: 0.6850 (m-30) REVERT: B 60 GLU cc_start: 0.7962 (tp30) cc_final: 0.7705 (tp30) REVERT: B 69 LYS cc_start: 0.8927 (tttt) cc_final: 0.8627 (mtpt) REVERT: B 201 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7045 (tm-30) REVERT: B 207 GLU cc_start: 0.7490 (mp0) cc_final: 0.7215 (mp0) REVERT: B 214 VAL cc_start: 0.9401 (t) cc_final: 0.9131 (t) REVERT: C 9 ASP cc_start: 0.7803 (p0) cc_final: 0.7478 (p0) REVERT: C 44 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6117 (tm-30) REVERT: C 123 TYR cc_start: 0.7311 (m-80) cc_final: 0.6887 (m-80) REVERT: C 148 TYR cc_start: 0.9314 (m-80) cc_final: 0.9083 (m-10) REVERT: C 175 PHE cc_start: 0.9027 (m-80) cc_final: 0.8772 (m-80) REVERT: C 185 PHE cc_start: 0.8527 (t80) cc_final: 0.8282 (t80) REVERT: C 189 MET cc_start: 0.9018 (ttm) cc_final: 0.8648 (ttm) REVERT: C 202 SER cc_start: 0.8679 (p) cc_final: 0.8301 (p) REVERT: C 203 GLU cc_start: 0.6375 (pm20) cc_final: 0.6099 (pm20) REVERT: C 208 ASN cc_start: 0.8481 (p0) cc_final: 0.7956 (p0) REVERT: C 211 VAL cc_start: 0.9087 (t) cc_final: 0.8884 (p) REVERT: C 214 VAL cc_start: 0.8890 (t) cc_final: 0.8634 (t) REVERT: C 222 LYS cc_start: 0.8628 (tttt) cc_final: 0.8282 (ttmm) REVERT: C 225 SER cc_start: 0.8868 (p) cc_final: 0.7977 (t) REVERT: D 33 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8322 (mtp-110) REVERT: D 38 ILE cc_start: 0.9341 (mt) cc_final: 0.9134 (mt) REVERT: D 57 LYS cc_start: 0.8621 (pttm) cc_final: 0.7996 (mppt) REVERT: D 64 ILE cc_start: 0.6787 (pt) cc_final: 0.6434 (pt) REVERT: D 67 ILE cc_start: 0.9383 (mm) cc_final: 0.9161 (mm) REVERT: D 104 ASP cc_start: 0.7996 (t0) cc_final: 0.7666 (t0) REVERT: D 108 THR cc_start: 0.8690 (p) cc_final: 0.8484 (m) REVERT: D 171 VAL cc_start: 0.9630 (t) cc_final: 0.9282 (p) REVERT: D 174 PHE cc_start: 0.8631 (t80) cc_final: 0.8076 (t80) REVERT: D 196 MET cc_start: 0.8894 (mmm) cc_final: 0.8431 (tpp) REVERT: D 240 ILE cc_start: 0.8680 (pt) cc_final: 0.8407 (pt) REVERT: E 8 TYR cc_start: 0.7808 (m-10) cc_final: 0.6916 (m-80) REVERT: E 21 LEU cc_start: 0.7932 (mt) cc_final: 0.7658 (mp) REVERT: E 25 GLU cc_start: 0.8202 (tp30) cc_final: 0.6849 (tp30) REVERT: E 28 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8135 (mmm-85) REVERT: E 33 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8608 (mtp-110) REVERT: E 52 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8918 (ttpp) REVERT: E 68 TYR cc_start: 0.8766 (m-80) cc_final: 0.8301 (m-10) REVERT: E 108 THR cc_start: 0.9066 (m) cc_final: 0.8706 (m) REVERT: E 112 LEU cc_start: 0.9472 (tp) cc_final: 0.9258 (tp) REVERT: E 148 TYR cc_start: 0.9018 (m-80) cc_final: 0.8506 (m-10) REVERT: E 164 ILE cc_start: 0.9370 (pt) cc_final: 0.8760 (pt) REVERT: E 172 THR cc_start: 0.9145 (m) cc_final: 0.8905 (t) REVERT: E 186 ASP cc_start: 0.8188 (m-30) cc_final: 0.7953 (m-30) REVERT: E 218 ASP cc_start: 0.8983 (p0) cc_final: 0.8212 (p0) REVERT: E 222 LYS cc_start: 0.8498 (mttt) cc_final: 0.8260 (mttp) REVERT: E 234 GLU cc_start: 0.8330 (tp30) cc_final: 0.8115 (tp30) REVERT: F 9 ASP cc_start: 0.8367 (p0) cc_final: 0.7858 (p0) REVERT: F 26 TYR cc_start: 0.9087 (m-10) cc_final: 0.8676 (m-10) REVERT: F 51 ASP cc_start: 0.8909 (t70) cc_final: 0.8585 (t70) REVERT: F 71 ASP cc_start: 0.8249 (t70) cc_final: 0.8026 (t70) REVERT: F 99 ASN cc_start: 0.9166 (t0) cc_final: 0.8723 (t0) REVERT: F 150 THR cc_start: 0.8828 (p) cc_final: 0.8600 (p) REVERT: F 158 GLU cc_start: 0.6656 (tt0) cc_final: 0.6036 (tt0) REVERT: F 173 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7445 (tm-30) REVERT: F 229 LEU cc_start: 0.9099 (tt) cc_final: 0.8861 (tt) REVERT: F 241 ARG cc_start: 0.7495 (ptp-110) cc_final: 0.6846 (mtm110) REVERT: G 16 SER cc_start: 0.8833 (p) cc_final: 0.8583 (t) REVERT: G 33 ARG cc_start: 0.7353 (ptp-170) cc_final: 0.6921 (mtp180) REVERT: G 47 ILE cc_start: 0.9257 (mt) cc_final: 0.8984 (mt) REVERT: G 51 ASP cc_start: 0.8906 (t0) cc_final: 0.8448 (t0) REVERT: G 66 LYS cc_start: 0.8935 (tppp) cc_final: 0.8186 (mptt) REVERT: G 73 HIS cc_start: 0.8422 (p-80) cc_final: 0.7767 (p-80) REVERT: G 104 ASP cc_start: 0.7649 (t70) cc_final: 0.6600 (t0) REVERT: G 171 VAL cc_start: 0.8993 (t) cc_final: 0.7804 (p) REVERT: G 172 THR cc_start: 0.8516 (p) cc_final: 0.8106 (p) REVERT: G 187 ASP cc_start: 0.8421 (m-30) cc_final: 0.8126 (m-30) REVERT: G 211 VAL cc_start: 0.9267 (t) cc_final: 0.8692 (t) REVERT: G 234 GLU cc_start: 0.8560 (pp20) cc_final: 0.8126 (pp20) REVERT: G 237 ASN cc_start: 0.7739 (m110) cc_final: 0.7163 (m110) REVERT: 1 25 MET cc_start: 0.7860 (mtm) cc_final: 0.7184 (ttm) REVERT: 1 88 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: 1 111 LEU cc_start: 0.8963 (mt) cc_final: 0.8325 (mt) REVERT: 1 122 ILE cc_start: 0.8672 (mm) cc_final: 0.7962 (mm) REVERT: 1 135 LYS cc_start: 0.7834 (mppt) cc_final: 0.7592 (mppt) REVERT: 1 173 TYR cc_start: 0.8483 (t80) cc_final: 0.7962 (t80) REVERT: 1 176 MET cc_start: 0.7271 (mtm) cc_final: 0.7061 (mtm) REVERT: 1 190 LYS cc_start: 0.8277 (ptmt) cc_final: 0.8061 (ptmm) REVERT: 1 208 LEU cc_start: 0.5048 (pp) cc_final: 0.4523 (pp) REVERT: 2 45 ILE cc_start: 0.8306 (tt) cc_final: 0.7963 (tt) REVERT: 2 48 ILE cc_start: 0.8875 (mm) cc_final: 0.8592 (mm) REVERT: 2 68 ARG cc_start: 0.8517 (ttm110) cc_final: 0.8244 (ttm110) REVERT: 2 72 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8443 (mp) REVERT: 2 116 ASP cc_start: 0.5539 (p0) cc_final: 0.5244 (p0) REVERT: 2 162 ASP cc_start: 0.6235 (m-30) cc_final: 0.5507 (m-30) REVERT: 2 190 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8631 (tttt) REVERT: 2 192 THR cc_start: 0.7596 (t) cc_final: 0.6927 (t) REVERT: 3 46 TYR cc_start: 0.7156 (m-80) cc_final: 0.6641 (m-80) REVERT: 3 48 ILE cc_start: 0.8900 (tp) cc_final: 0.8624 (tp) REVERT: 3 84 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7804 (mptt) REVERT: 3 86 THR cc_start: 0.9157 (m) cc_final: 0.8610 (p) REVERT: 3 88 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7666 (ttm110) REVERT: 3 138 VAL cc_start: 0.8354 (p) cc_final: 0.8088 (p) REVERT: 3 188 VAL cc_start: 0.7992 (t) cc_final: 0.7762 (t) REVERT: 3 190 LYS cc_start: 0.7522 (ttmm) cc_final: 0.7060 (ptmm) REVERT: 4 33 MET cc_start: 0.4896 (ttm) cc_final: 0.4375 (ttm) REVERT: 4 48 ILE cc_start: 0.9330 (mm) cc_final: 0.8728 (mm) REVERT: 4 52 MET cc_start: 0.8236 (ttm) cc_final: 0.7908 (ttm) REVERT: 4 80 ARG cc_start: 0.8950 (mtp180) cc_final: 0.8314 (mtp180) REVERT: 4 87 VAL cc_start: 0.9132 (t) cc_final: 0.8870 (t) REVERT: 4 88 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7990 (ttp-170) REVERT: 4 109 GLN cc_start: 0.6594 (mp10) cc_final: 0.6091 (mp10) REVERT: 4 116 ASP cc_start: 0.7626 (p0) cc_final: 0.7401 (p0) REVERT: 4 123 TYR cc_start: 0.9066 (m-80) cc_final: 0.8402 (m-80) REVERT: 4 134 GLU cc_start: 0.7455 (mp0) cc_final: 0.7052 (mp0) REVERT: 4 135 LYS cc_start: 0.8120 (tppt) cc_final: 0.7512 (ttpt) REVERT: 4 152 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8275 (mm-30) REVERT: 4 190 LYS cc_start: 0.8399 (ttpt) cc_final: 0.7989 (ptmm) REVERT: 5 33 MET cc_start: -0.0723 (mtt) cc_final: -0.1478 (ttm) REVERT: 5 43 LYS cc_start: 0.7641 (tptt) cc_final: 0.7411 (tptt) REVERT: 5 46 TYR cc_start: 0.7934 (m-80) cc_final: 0.7129 (m-10) REVERT: 5 73 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8000 (mm-30) REVERT: 5 134 GLU cc_start: 0.7273 (mp0) cc_final: 0.6871 (mp0) REVERT: 5 152 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7776 (tm-30) REVERT: 5 165 VAL cc_start: 0.8593 (m) cc_final: 0.8312 (m) REVERT: 5 193 GLU cc_start: 0.8523 (mp0) cc_final: 0.8253 (mp0) REVERT: 6 28 GLU cc_start: 0.7926 (pm20) cc_final: 0.7713 (pm20) REVERT: 6 72 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8759 (mp) REVERT: 6 79 ILE cc_start: 0.9423 (mt) cc_final: 0.8813 (mt) REVERT: 6 81 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8003 (tpp80) REVERT: 6 122 ILE cc_start: 0.9227 (tp) cc_final: 0.8934 (tp) REVERT: 6 163 GLU cc_start: 0.7939 (mp0) cc_final: 0.7384 (pm20) REVERT: 6 173 TYR cc_start: 0.7281 (t80) cc_final: 0.6946 (t80) REVERT: 7 44 LYS cc_start: 0.6659 (tppt) cc_final: 0.6229 (tppt) REVERT: 7 75 ASN cc_start: 0.8763 (m-40) cc_final: 0.8515 (m-40) REVERT: 7 193 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7390 (tm-30) outliers start: 7 outliers final: 0 residues processed: 1265 average time/residue: 0.1789 time to fit residues: 348.4713 Evaluate side-chains 1155 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1153 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 164 optimal weight: 0.4980 chunk 243 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 chunk 280 optimal weight: 0.6980 chunk 285 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN 3 75 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 99 ASN 3 198 GLN 4 75 ASN ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 75 ASN ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.177699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.145201 restraints weight = 36636.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.149522 restraints weight = 20916.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152454 restraints weight = 13973.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.154365 restraints weight = 10511.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.155678 restraints weight = 8638.435| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24968 Z= 0.173 Angle : 0.698 14.257 33660 Z= 0.374 Chirality : 0.048 0.195 3881 Planarity : 0.004 0.052 4329 Dihedral : 5.553 55.047 3498 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.97 % Favored : 95.80 % Rotamer: Outliers : 0.23 % Allowed : 2.14 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3122 helix: 0.39 (0.15), residues: 1226 sheet: 0.18 (0.19), residues: 616 loop : -1.52 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 91 TYR 0.031 0.002 TYR 7 148 PHE 0.025 0.002 PHE A 175 HIS 0.005 0.002 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00389 (24968) covalent geometry : angle 0.69768 (33660) hydrogen bonds : bond 0.03801 ( 1269) hydrogen bonds : angle 5.12368 ( 3699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1232 time to evaluate : 0.638 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 186 ASP cc_start: 0.7710 (p0) cc_final: 0.7031 (p0) REVERT: A 208 ASN cc_start: 0.8928 (p0) cc_final: 0.8186 (p0) REVERT: A 211 VAL cc_start: 0.8998 (t) cc_final: 0.7518 (p) REVERT: B 20 ARG cc_start: 0.8135 (ptp-110) cc_final: 0.7587 (ptp-170) REVERT: B 25 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 93 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8553 (mtt-85) REVERT: B 98 ILE cc_start: 0.8613 (mm) cc_final: 0.8399 (mm) REVERT: B 104 ASP cc_start: 0.7680 (t0) cc_final: 0.7419 (t70) REVERT: B 174 PHE cc_start: 0.8087 (t80) cc_final: 0.7505 (t80) REVERT: B 201 GLU cc_start: 0.7867 (tm-30) cc_final: 0.6825 (tm-30) REVERT: B 208 ASN cc_start: 0.7716 (p0) cc_final: 0.7381 (p0) REVERT: B 214 VAL cc_start: 0.9427 (t) cc_final: 0.9146 (t) REVERT: B 234 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 238 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7012 (mt-10) REVERT: C 9 ASP cc_start: 0.7709 (p0) cc_final: 0.7457 (p0) REVERT: C 44 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6385 (tm-30) REVERT: C 68 TYR cc_start: 0.8334 (m-80) cc_final: 0.8125 (m-80) REVERT: C 110 LYS cc_start: 0.9479 (tptp) cc_final: 0.9150 (tptt) REVERT: C 148 TYR cc_start: 0.9269 (m-80) cc_final: 0.8926 (m-10) REVERT: C 175 PHE cc_start: 0.9035 (m-80) cc_final: 0.8692 (m-80) REVERT: C 185 PHE cc_start: 0.8499 (t80) cc_final: 0.8265 (t80) REVERT: C 189 MET cc_start: 0.8966 (ttm) cc_final: 0.8670 (ttm) REVERT: C 202 SER cc_start: 0.8819 (p) cc_final: 0.8470 (p) REVERT: C 203 GLU cc_start: 0.6380 (pm20) cc_final: 0.6060 (pm20) REVERT: C 208 ASN cc_start: 0.8421 (p0) cc_final: 0.7924 (p0) REVERT: C 214 VAL cc_start: 0.8961 (t) cc_final: 0.8531 (p) REVERT: C 222 LYS cc_start: 0.8675 (tttt) cc_final: 0.8387 (tttp) REVERT: D 33 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8489 (ptm-80) REVERT: D 41 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8486 (ttpp) REVERT: D 57 LYS cc_start: 0.8628 (pttm) cc_final: 0.7831 (mppt) REVERT: D 60 GLU cc_start: 0.7520 (pp20) cc_final: 0.6360 (pm20) REVERT: D 64 ILE cc_start: 0.6896 (pt) cc_final: 0.6693 (pt) REVERT: D 91 ARG cc_start: 0.8825 (tpt90) cc_final: 0.8450 (tpt170) REVERT: D 104 ASP cc_start: 0.8045 (t0) cc_final: 0.7760 (t0) REVERT: D 115 LYS cc_start: 0.8307 (mttm) cc_final: 0.7193 (mtpt) REVERT: D 171 VAL cc_start: 0.9638 (t) cc_final: 0.9380 (p) REVERT: D 228 GLU cc_start: 0.7775 (tp30) cc_final: 0.7501 (tp30) REVERT: E 25 GLU cc_start: 0.8323 (tp30) cc_final: 0.7031 (tp30) REVERT: E 28 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8221 (mmm-85) REVERT: E 44 GLU cc_start: 0.7844 (pm20) cc_final: 0.6781 (pt0) REVERT: E 52 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8785 (ttpp) REVERT: E 86 ARG cc_start: 0.7757 (mmt180) cc_final: 0.7525 (mmt180) REVERT: E 108 THR cc_start: 0.8991 (m) cc_final: 0.8681 (m) REVERT: E 112 LEU cc_start: 0.9446 (tp) cc_final: 0.9238 (tp) REVERT: E 148 TYR cc_start: 0.8888 (m-80) cc_final: 0.8496 (m-10) REVERT: E 186 ASP cc_start: 0.8091 (m-30) cc_final: 0.7883 (m-30) REVERT: E 218 ASP cc_start: 0.9048 (p0) cc_final: 0.8511 (p0) REVERT: E 234 GLU cc_start: 0.8408 (tp30) cc_final: 0.8143 (tp30) REVERT: F 22 PHE cc_start: 0.8657 (m-80) cc_final: 0.8451 (m-80) REVERT: F 25 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8475 (mm-30) REVERT: F 26 TYR cc_start: 0.8966 (m-10) cc_final: 0.8727 (m-10) REVERT: F 33 ARG cc_start: 0.7903 (tpt170) cc_final: 0.7687 (tpt90) REVERT: F 104 ASP cc_start: 0.7727 (t70) cc_final: 0.7370 (t0) REVERT: F 158 GLU cc_start: 0.6495 (tt0) cc_final: 0.5865 (tt0) REVERT: F 173 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7361 (tm-30) REVERT: F 193 LEU cc_start: 0.9423 (mm) cc_final: 0.9179 (mm) REVERT: F 219 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8126 (tpp80) REVERT: F 228 GLU cc_start: 0.8336 (tp30) cc_final: 0.8091 (tp30) REVERT: F 229 LEU cc_start: 0.9175 (tt) cc_final: 0.8972 (tt) REVERT: F 234 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7528 (mt-10) REVERT: G 33 ARG cc_start: 0.7389 (ptp-170) cc_final: 0.7082 (mtp180) REVERT: G 47 ILE cc_start: 0.9259 (mt) cc_final: 0.9051 (mt) REVERT: G 51 ASP cc_start: 0.8737 (t0) cc_final: 0.8367 (t0) REVERT: G 66 LYS cc_start: 0.8896 (tppp) cc_final: 0.8361 (mptt) REVERT: G 71 ASP cc_start: 0.7726 (m-30) cc_final: 0.7397 (m-30) REVERT: G 72 GLU cc_start: 0.6236 (mp0) cc_final: 0.5677 (mp0) REVERT: G 73 HIS cc_start: 0.8349 (p-80) cc_final: 0.7828 (p-80) REVERT: G 93 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8375 (mtt-85) REVERT: G 143 GLU cc_start: 0.7116 (pm20) cc_final: 0.6776 (pm20) REVERT: G 171 VAL cc_start: 0.9019 (t) cc_final: 0.7798 (p) REVERT: G 187 ASP cc_start: 0.8451 (m-30) cc_final: 0.8085 (m-30) REVERT: G 234 GLU cc_start: 0.8521 (pp20) cc_final: 0.7990 (pp20) REVERT: 1 17 LEU cc_start: 0.9214 (pt) cc_final: 0.8958 (pt) REVERT: 1 25 MET cc_start: 0.7846 (mtm) cc_final: 0.7203 (ttm) REVERT: 1 111 LEU cc_start: 0.8980 (mt) cc_final: 0.8297 (mt) REVERT: 1 122 ILE cc_start: 0.8644 (mm) cc_final: 0.7870 (mm) REVERT: 1 123 TYR cc_start: 0.8735 (m-80) cc_final: 0.8507 (m-80) REVERT: 1 173 TYR cc_start: 0.8584 (t80) cc_final: 0.7860 (t80) REVERT: 1 190 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7732 (ptmm) REVERT: 1 208 LEU cc_start: 0.5877 (pp) cc_final: 0.5454 (pp) REVERT: 2 19 CYS cc_start: 0.6474 (m) cc_final: 0.6157 (m) REVERT: 2 45 ILE cc_start: 0.7874 (tt) cc_final: 0.7281 (tt) REVERT: 2 48 ILE cc_start: 0.8911 (mm) cc_final: 0.8575 (mm) REVERT: 2 72 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (mp) REVERT: 2 162 ASP cc_start: 0.6494 (m-30) cc_final: 0.6047 (m-30) REVERT: 3 46 TYR cc_start: 0.6938 (m-80) cc_final: 0.6577 (m-80) REVERT: 3 48 ILE cc_start: 0.9032 (tp) cc_final: 0.8826 (tp) REVERT: 3 190 LYS cc_start: 0.7676 (ttmm) cc_final: 0.7248 (ptmm) REVERT: 3 202 GLU cc_start: 0.8173 (pm20) cc_final: 0.7799 (pm20) REVERT: 4 44 LYS cc_start: 0.6610 (tppt) cc_final: 0.5966 (tttt) REVERT: 4 48 ILE cc_start: 0.9285 (mm) cc_final: 0.8741 (mm) REVERT: 4 52 MET cc_start: 0.8302 (ttm) cc_final: 0.7889 (ttm) REVERT: 4 80 ARG cc_start: 0.9035 (mtp180) cc_final: 0.8417 (mtp180) REVERT: 4 88 ARG cc_start: 0.8243 (ttp80) cc_final: 0.8020 (ttp-170) REVERT: 4 123 TYR cc_start: 0.9133 (m-80) cc_final: 0.8795 (m-80) REVERT: 4 135 LYS cc_start: 0.8121 (tppt) cc_final: 0.7566 (ttpt) REVERT: 4 190 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8005 (ptmm) REVERT: 5 46 TYR cc_start: 0.8087 (m-80) cc_final: 0.7510 (m-10) REVERT: 5 73 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8005 (mm-30) REVERT: 5 76 LEU cc_start: 0.9266 (tt) cc_final: 0.9038 (tt) REVERT: 5 134 GLU cc_start: 0.7271 (mp0) cc_final: 0.6966 (mp0) REVERT: 6 28 GLU cc_start: 0.8052 (pm20) cc_final: 0.7701 (pm20) REVERT: 6 68 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.6813 (ttp-110) REVERT: 6 72 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8818 (mp) REVERT: 6 163 GLU cc_start: 0.8033 (mp0) cc_final: 0.7473 (pm20) REVERT: 7 122 ILE cc_start: 0.9048 (tp) cc_final: 0.8717 (tp) REVERT: 7 193 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7186 (tm-30) REVERT: H 396 MET cc_start: 0.7679 (ptp) cc_final: 0.7366 (mtm) outliers start: 6 outliers final: 0 residues processed: 1235 average time/residue: 0.1676 time to fit residues: 321.6979 Evaluate side-chains 1120 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1118 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 22 optimal weight: 0.0970 chunk 137 optimal weight: 1.9990 chunk 214 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 274 optimal weight: 0.4980 chunk 129 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 198 GLN 4 75 ASN ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.177707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144630 restraints weight = 36642.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.148941 restraints weight = 21168.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.151871 restraints weight = 14272.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.153676 restraints weight = 10804.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.155172 restraints weight = 8966.301| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.7005 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 : 0.695 14.054 33660 Z= 0.371 Chirality : 0.048 0.208 3881 Planarity : 0.004 0.046 4329 Dihedral : 5.539 51.962 3498 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3122 helix: 0.36 (0.14), residues: 1254 sheet: 0.27 (0.19), residues: 600 loop : -1.34 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 88 TYR 0.038 0.002 TYR 5 197 PHE 0.021 0.002 PHE D 174 HIS 0.005 0.002 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00382 (24968) covalent geometry : angle 0.69520 (33660) hydrogen bonds : bond 0.03808 ( 1269) hydrogen bonds : angle 5.11978 ( 3699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1216 time to evaluate : 0.615 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: A 44 GLU cc_start: 0.8500 (pm20) cc_final: 0.8195 (pm20) REVERT: A 68 TYR cc_start: 0.8295 (m-10) cc_final: 0.7922 (m-10) REVERT: A 98 ILE cc_start: 0.8815 (mt) cc_final: 0.8449 (mt) REVERT: A 100 ARG cc_start: 0.8722 (ttm170) cc_final: 0.8514 (ttm-80) REVERT: A 132 PHE cc_start: 0.8511 (m-10) cc_final: 0.8280 (m-10) REVERT: A 166 MET cc_start: 0.8239 (mtp) cc_final: 0.7899 (ttp) REVERT: A 186 ASP cc_start: 0.7608 (p0) cc_final: 0.7257 (p0) REVERT: A 208 ASN cc_start: 0.8984 (p0) cc_final: 0.8326 (p0) REVERT: A 211 VAL cc_start: 0.8755 (t) cc_final: 0.7764 (p) REVERT: B 20 ARG cc_start: 0.7958 (ptp-110) cc_final: 0.7504 (ptp-170) REVERT: B 25 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 44 GLU cc_start: 0.8308 (tt0) cc_final: 0.7995 (tt0) REVERT: B 60 GLU cc_start: 0.8071 (tp30) cc_final: 0.7473 (tp30) REVERT: B 93 ARG cc_start: 0.8797 (mtt-85) cc_final: 0.8443 (mtt-85) REVERT: B 104 ASP cc_start: 0.7696 (t0) cc_final: 0.7452 (t70) REVERT: B 151 ASP cc_start: 0.8964 (t70) cc_final: 0.8532 (t0) REVERT: B 174 PHE cc_start: 0.8025 (t80) cc_final: 0.7208 (t80) REVERT: B 186 ASP cc_start: 0.8278 (p0) cc_final: 0.7973 (p0) REVERT: B 201 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 208 ASN cc_start: 0.7639 (p0) cc_final: 0.7399 (p0) REVERT: B 214 VAL cc_start: 0.9443 (t) cc_final: 0.9141 (t) REVERT: B 234 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 238 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7034 (mt-10) REVERT: C 9 ASP cc_start: 0.7588 (p0) cc_final: 0.7345 (p0) REVERT: C 44 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6899 (tm-30) REVERT: C 52 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8091 (ttmm) REVERT: C 110 LYS cc_start: 0.9477 (tptp) cc_final: 0.9139 (tptt) REVERT: C 172 THR cc_start: 0.9353 (m) cc_final: 0.9020 (t) REVERT: C 175 PHE cc_start: 0.9080 (m-80) cc_final: 0.8729 (m-80) REVERT: C 189 MET cc_start: 0.8987 (ttm) cc_final: 0.8614 (ttm) REVERT: C 202 SER cc_start: 0.8834 (p) cc_final: 0.8497 (p) REVERT: C 203 GLU cc_start: 0.6583 (pm20) cc_final: 0.6283 (pm20) REVERT: C 208 ASN cc_start: 0.8486 (p0) cc_final: 0.8066 (p0) REVERT: C 214 VAL cc_start: 0.8950 (t) cc_final: 0.8654 (p) REVERT: C 222 LYS cc_start: 0.8694 (tttt) cc_final: 0.8384 (tttp) REVERT: D 57 LYS cc_start: 0.8618 (pttm) cc_final: 0.7812 (mppt) REVERT: D 67 ILE cc_start: 0.9390 (mm) cc_final: 0.9188 (mm) REVERT: D 81 LEU cc_start: 0.9138 (mp) cc_final: 0.8865 (mp) REVERT: D 91 ARG cc_start: 0.8872 (tpt90) cc_final: 0.8429 (tpt170) REVERT: D 104 ASP cc_start: 0.8106 (t0) cc_final: 0.7898 (t0) REVERT: D 115 LYS cc_start: 0.8242 (mttm) cc_final: 0.7221 (mtpt) REVERT: D 151 ASP cc_start: 0.8650 (t0) cc_final: 0.8178 (t0) REVERT: D 171 VAL cc_start: 0.9536 (t) cc_final: 0.9284 (p) REVERT: D 185 PHE cc_start: 0.7864 (t80) cc_final: 0.7620 (t80) REVERT: D 196 MET cc_start: 0.8917 (mmm) cc_final: 0.8667 (mmm) REVERT: D 208 ASN cc_start: 0.8722 (p0) cc_final: 0.8251 (p0) REVERT: E 8 TYR cc_start: 0.8041 (m-80) cc_final: 0.7085 (m-80) REVERT: E 25 GLU cc_start: 0.8301 (tp30) cc_final: 0.6994 (tp30) REVERT: E 28 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.8159 (mmm-85) REVERT: E 44 GLU cc_start: 0.7607 (pm20) cc_final: 0.6947 (pt0) REVERT: E 52 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8031 (ttpp) REVERT: E 86 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7595 (mmt180) REVERT: E 108 THR cc_start: 0.9117 (m) cc_final: 0.8894 (m) REVERT: E 148 TYR cc_start: 0.9109 (m-80) cc_final: 0.8345 (m-10) REVERT: E 186 ASP cc_start: 0.8007 (m-30) cc_final: 0.7733 (m-30) REVERT: E 210 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7132 (mm-30) REVERT: E 218 ASP cc_start: 0.8912 (p0) cc_final: 0.8527 (p0) REVERT: E 222 LYS cc_start: 0.8188 (mttp) cc_final: 0.7815 (tptm) REVERT: F 9 ASP cc_start: 0.8384 (p0) cc_final: 0.7926 (p0) REVERT: F 25 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8448 (mm-30) REVERT: F 26 TYR cc_start: 0.9054 (m-10) cc_final: 0.8765 (m-10) REVERT: F 33 ARG cc_start: 0.7984 (tpt170) cc_final: 0.7723 (tpt90) REVERT: F 158 GLU cc_start: 0.6623 (tt0) cc_final: 0.6095 (tt0) REVERT: F 173 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 187 ASP cc_start: 0.9007 (m-30) cc_final: 0.8740 (m-30) REVERT: F 193 LEU cc_start: 0.9396 (mm) cc_final: 0.9174 (mm) REVERT: F 200 ILE cc_start: 0.8827 (mm) cc_final: 0.8576 (mm) REVERT: G 33 ARG cc_start: 0.7524 (ptp-170) cc_final: 0.7164 (mtp180) REVERT: G 51 ASP cc_start: 0.8819 (t0) cc_final: 0.8322 (t0) REVERT: G 66 LYS cc_start: 0.8825 (tppp) cc_final: 0.8370 (mptt) REVERT: G 71 ASP cc_start: 0.7736 (m-30) cc_final: 0.7519 (m-30) REVERT: G 73 HIS cc_start: 0.8232 (p-80) cc_final: 0.7383 (p90) REVERT: G 93 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8342 (mtt-85) REVERT: G 104 ASP cc_start: 0.7826 (t70) cc_final: 0.7624 (t0) REVERT: G 143 GLU cc_start: 0.7822 (pm20) cc_final: 0.7555 (pm20) REVERT: G 171 VAL cc_start: 0.9128 (t) cc_final: 0.7949 (p) REVERT: G 187 ASP cc_start: 0.8599 (m-30) cc_final: 0.8057 (m-30) REVERT: G 191 LEU cc_start: 0.9296 (tp) cc_final: 0.8873 (tp) REVERT: G 234 GLU cc_start: 0.8436 (pp20) cc_final: 0.7859 (pp20) REVERT: G 237 ASN cc_start: 0.7660 (m110) cc_final: 0.7325 (m110) REVERT: 1 17 LEU cc_start: 0.9224 (pt) cc_final: 0.8997 (pt) REVERT: 1 25 MET cc_start: 0.8039 (mtm) cc_final: 0.7331 (ttm) REVERT: 1 52 MET cc_start: 0.7875 (ttm) cc_final: 0.7661 (ttp) REVERT: 1 111 LEU cc_start: 0.8998 (mt) cc_final: 0.8320 (mt) REVERT: 1 112 ILE cc_start: 0.9294 (mt) cc_final: 0.9064 (mt) REVERT: 1 122 ILE cc_start: 0.8691 (mm) cc_final: 0.7875 (mm) REVERT: 1 173 TYR cc_start: 0.8542 (t80) cc_final: 0.7862 (t80) REVERT: 1 190 LYS cc_start: 0.7800 (ptmt) cc_final: 0.7324 (ptmm) REVERT: 1 193 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7663 (tm-30) REVERT: 1 208 LEU cc_start: 0.6006 (pp) cc_final: 0.5607 (pp) REVERT: 2 45 ILE cc_start: 0.7979 (tt) cc_final: 0.7452 (tt) REVERT: 2 48 ILE cc_start: 0.8844 (mm) cc_final: 0.8483 (mm) REVERT: 2 83 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7619 (ptt180) REVERT: 2 151 LEU cc_start: 0.9208 (mt) cc_final: 0.8906 (mt) REVERT: 2 159 ILE cc_start: 0.8183 (tt) cc_final: 0.7899 (tt) REVERT: 3 46 TYR cc_start: 0.6997 (m-80) cc_final: 0.6774 (m-80) REVERT: 3 88 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7309 (mtp85) REVERT: 3 123 TYR cc_start: 0.8184 (m-80) cc_final: 0.7843 (m-10) REVERT: 3 190 LYS cc_start: 0.7626 (ttmm) cc_final: 0.7270 (ptmm) REVERT: 4 44 LYS cc_start: 0.7068 (tppt) cc_final: 0.6380 (tttt) REVERT: 4 52 MET cc_start: 0.8260 (ttm) cc_final: 0.7985 (ttm) REVERT: 4 80 ARG cc_start: 0.8988 (mtp180) cc_final: 0.8390 (mtp180) REVERT: 4 87 VAL cc_start: 0.9264 (t) cc_final: 0.9022 (t) REVERT: 4 123 TYR cc_start: 0.9052 (m-80) cc_final: 0.8197 (m-80) REVERT: 4 135 LYS cc_start: 0.8132 (tppt) cc_final: 0.7564 (ttpt) REVERT: 4 148 TYR cc_start: 0.7310 (t80) cc_final: 0.6912 (t80) REVERT: 4 190 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8146 (ptmm) REVERT: 5 46 TYR cc_start: 0.8122 (m-80) cc_final: 0.7628 (m-10) REVERT: 5 73 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8249 (mm-30) REVERT: 5 76 LEU cc_start: 0.9324 (tt) cc_final: 0.8991 (tt) REVERT: 5 134 GLU cc_start: 0.7537 (mp0) cc_final: 0.7250 (mp0) REVERT: 5 195 GLU cc_start: 0.6506 (tt0) cc_final: 0.6214 (tt0) REVERT: 6 28 GLU cc_start: 0.8145 (pm20) cc_final: 0.7259 (pm20) REVERT: 6 79 ILE cc_start: 0.9599 (mt) cc_final: 0.9347 (mt) REVERT: 6 172 ILE cc_start: 0.8644 (tt) cc_final: 0.8443 (tt) REVERT: 6 173 TYR cc_start: 0.7157 (t80) cc_final: 0.6309 (t80) REVERT: 7 120 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8296 (mtmt) REVERT: 7 193 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7258 (tm-30) REVERT: H 396 MET cc_start: 0.7874 (ptp) cc_final: 0.7298 (mtm) outliers start: 0 outliers final: 0 residues processed: 1216 average time/residue: 0.1775 time to fit residues: 335.5893 Evaluate side-chains 1140 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1140 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 113 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 97 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 96 ASN 3 198 GLN ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 109 GLN 7 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.175998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.143348 restraints weight = 36653.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.147544 restraints weight = 21240.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.150469 restraints weight = 14426.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.152357 restraints weight = 10875.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.153694 restraints weight = 8978.051| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24968 Z= 0.186 Angle : 0.716 14.080 33660 Z= 0.381 Chirality : 0.048 0.263 3881 Planarity : 0.004 0.042 4329 Dihedral : 5.534 50.794 3498 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3122 helix: 0.31 (0.15), residues: 1244 sheet: 0.12 (0.19), residues: 611 loop : -1.39 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 88 TYR 0.032 0.002 TYR 7 148 PHE 0.025 0.002 PHE A 119 HIS 0.006 0.002 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00421 (24968) covalent geometry : angle 0.71575 (33660) hydrogen bonds : bond 0.03836 ( 1269) hydrogen bonds : angle 5.17299 ( 3699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1220 time to evaluate : 0.868 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: 0.9599 (m) cc_final: 0.9219 (p) REVERT: A 86 ARG cc_start: 0.7899 (mmt180) cc_final: 0.7689 (mmt180) REVERT: A 98 ILE cc_start: 0.8811 (mt) cc_final: 0.8417 (mt) REVERT: A 100 ARG cc_start: 0.8750 (ttm170) cc_final: 0.8457 (ttm-80) REVERT: A 130 ARG cc_start: 0.8426 (ptt90) cc_final: 0.8091 (ptt-90) REVERT: A 166 MET cc_start: 0.8153 (mtp) cc_final: 0.7765 (ttp) REVERT: A 186 ASP cc_start: 0.7149 (p0) cc_final: 0.6817 (p0) REVERT: A 208 ASN cc_start: 0.9042 (p0) cc_final: 0.8316 (p0) REVERT: A 211 VAL cc_start: 0.8955 (t) cc_final: 0.7779 (p) REVERT: B 38 ILE cc_start: 0.8923 (mt) cc_final: 0.8685 (mt) REVERT: B 44 GLU cc_start: 0.8256 (tt0) cc_final: 0.8045 (tt0) REVERT: B 60 GLU cc_start: 0.8097 (tp30) cc_final: 0.7498 (tp30) REVERT: B 72 GLU cc_start: 0.7545 (tt0) cc_final: 0.7335 (tt0) REVERT: B 93 ARG cc_start: 0.8746 (mtt-85) cc_final: 0.8474 (mtt-85) REVERT: B 104 ASP cc_start: 0.7624 (t0) cc_final: 0.7307 (t70) REVERT: B 151 ASP cc_start: 0.8992 (t70) cc_final: 0.8704 (t0) REVERT: B 186 ASP cc_start: 0.8381 (p0) cc_final: 0.8083 (p0) REVERT: B 196 MET cc_start: 0.8573 (mmm) cc_final: 0.8266 (mmm) REVERT: B 201 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 214 VAL cc_start: 0.9461 (t) cc_final: 0.9099 (t) REVERT: B 234 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8115 (mt-10) REVERT: C 9 ASP cc_start: 0.7616 (p0) cc_final: 0.7185 (p0) REVERT: C 36 THR cc_start: 0.8462 (p) cc_final: 0.8248 (p) REVERT: C 44 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 110 LYS cc_start: 0.9436 (tptp) cc_final: 0.9085 (tptt) REVERT: C 172 THR cc_start: 0.9359 (m) cc_final: 0.9083 (t) REVERT: C 175 PHE cc_start: 0.9123 (m-80) cc_final: 0.8799 (m-80) REVERT: C 189 MET cc_start: 0.8980 (ttm) cc_final: 0.8555 (ttm) REVERT: C 202 SER cc_start: 0.8864 (p) cc_final: 0.8532 (p) REVERT: C 203 GLU cc_start: 0.6661 (pm20) cc_final: 0.6416 (pm20) REVERT: C 208 ASN cc_start: 0.8537 (p0) cc_final: 0.8172 (p0) REVERT: C 214 VAL cc_start: 0.8877 (t) cc_final: 0.8472 (p) REVERT: C 219 ARG cc_start: 0.7484 (mtt90) cc_final: 0.7273 (mtt90) REVERT: C 222 LYS cc_start: 0.8654 (tttt) cc_final: 0.8391 (tttp) REVERT: D 24 VAL cc_start: 0.9134 (t) cc_final: 0.8737 (p) REVERT: D 42 CYS cc_start: 0.8531 (p) cc_final: 0.8251 (p) REVERT: D 57 LYS cc_start: 0.8622 (pttm) cc_final: 0.7793 (mppt) REVERT: D 60 GLU cc_start: 0.7172 (pp20) cc_final: 0.5926 (pm20) REVERT: D 64 ILE cc_start: 0.7099 (pt) cc_final: 0.6841 (pt) REVERT: D 72 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6784 (mt-10) REVERT: D 81 LEU cc_start: 0.9023 (mp) cc_final: 0.8813 (mp) REVERT: D 91 ARG cc_start: 0.8837 (tpt90) cc_final: 0.8313 (tpt170) REVERT: D 115 LYS cc_start: 0.8236 (mttm) cc_final: 0.7249 (mtpt) REVERT: D 196 MET cc_start: 0.8791 (mmm) cc_final: 0.8471 (mmm) REVERT: D 213 TYR cc_start: 0.8916 (p90) cc_final: 0.8688 (p90) REVERT: D 234 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 25 GLU cc_start: 0.8282 (tp30) cc_final: 0.6979 (tp30) REVERT: E 28 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: E 44 GLU cc_start: 0.7646 (pm20) cc_final: 0.7079 (pt0) REVERT: E 52 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8137 (ttpp) REVERT: E 86 ARG cc_start: 0.8013 (mmt180) cc_final: 0.7718 (mmt180) REVERT: E 148 TYR cc_start: 0.9028 (m-80) cc_final: 0.8141 (m-10) REVERT: E 158 GLU cc_start: 0.7038 (tt0) cc_final: 0.6662 (tt0) REVERT: E 210 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7120 (mm-30) REVERT: E 218 ASP cc_start: 0.8939 (p0) cc_final: 0.8635 (p0) REVERT: E 222 LYS cc_start: 0.8337 (mttp) cc_final: 0.8119 (mmtp) REVERT: E 234 GLU cc_start: 0.8217 (tp30) cc_final: 0.8014 (tp30) REVERT: F 9 ASP cc_start: 0.8618 (p0) cc_final: 0.8133 (p0) REVERT: F 25 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8895 (mm-30) REVERT: F 26 TYR cc_start: 0.9025 (m-10) cc_final: 0.8778 (m-10) REVERT: F 33 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7834 (tpt90) REVERT: F 158 GLU cc_start: 0.6640 (tt0) cc_final: 0.6037 (tt0) REVERT: F 173 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7467 (tm-30) REVERT: F 234 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7492 (mt-10) REVERT: G 33 ARG cc_start: 0.7675 (ptp-170) cc_final: 0.7317 (mtp180) REVERT: G 51 ASP cc_start: 0.9056 (t0) cc_final: 0.8503 (t0) REVERT: G 66 LYS cc_start: 0.8986 (tppp) cc_final: 0.8409 (mptt) REVERT: G 71 ASP cc_start: 0.7637 (m-30) cc_final: 0.7410 (m-30) REVERT: G 73 HIS cc_start: 0.8272 (p-80) cc_final: 0.7584 (p-80) REVERT: G 89 ILE cc_start: 0.9367 (mm) cc_final: 0.9165 (mm) REVERT: G 93 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8278 (mtt-85) REVERT: G 171 VAL cc_start: 0.9189 (t) cc_final: 0.8047 (p) REVERT: G 191 LEU cc_start: 0.9154 (tp) cc_final: 0.8654 (tp) REVERT: G 234 GLU cc_start: 0.8424 (pp20) cc_final: 0.7683 (pp20) REVERT: G 237 ASN cc_start: 0.7755 (m110) cc_final: 0.7223 (m110) REVERT: 1 17 LEU cc_start: 0.9252 (pt) cc_final: 0.9019 (pt) REVERT: 1 25 MET cc_start: 0.8017 (mtm) cc_final: 0.7289 (ttm) REVERT: 1 111 LEU cc_start: 0.8895 (mt) cc_final: 0.8232 (mt) REVERT: 1 122 ILE cc_start: 0.8739 (mm) cc_final: 0.7982 (mm) REVERT: 1 134 GLU cc_start: 0.7172 (mp0) cc_final: 0.6899 (mp0) REVERT: 1 173 TYR cc_start: 0.8636 (t80) cc_final: 0.7974 (t80) REVERT: 1 190 LYS cc_start: 0.7972 (ptmt) cc_final: 0.7548 (ptmm) REVERT: 1 193 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7640 (tm-30) REVERT: 2 45 ILE cc_start: 0.8039 (tt) cc_final: 0.7537 (tt) REVERT: 2 48 ILE cc_start: 0.8831 (mm) cc_final: 0.8359 (mm) REVERT: 2 52 MET cc_start: 0.8134 (ttm) cc_final: 0.7636 (ttm) REVERT: 2 83 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7616 (ptt180) REVERT: 2 133 GLU cc_start: 0.7633 (tt0) cc_final: 0.7122 (tt0) REVERT: 2 151 LEU cc_start: 0.9211 (mt) cc_final: 0.8901 (mt) REVERT: 2 159 ILE cc_start: 0.8107 (tt) cc_final: 0.7878 (tt) REVERT: 3 46 TYR cc_start: 0.7143 (m-80) cc_final: 0.6719 (m-80) REVERT: 3 48 ILE cc_start: 0.8887 (tp) cc_final: 0.8647 (tp) REVERT: 3 88 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7499 (mtp85) REVERT: 3 123 TYR cc_start: 0.8486 (m-80) cc_final: 0.8111 (m-10) REVERT: 3 190 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7413 (ptmm) REVERT: 4 44 LYS cc_start: 0.7203 (tppt) cc_final: 0.6500 (tttt) REVERT: 4 52 MET cc_start: 0.8225 (ttm) cc_final: 0.7973 (ttm) REVERT: 4 80 ARG cc_start: 0.9064 (mtp180) cc_final: 0.8801 (mtp180) REVERT: 4 87 VAL cc_start: 0.9257 (t) cc_final: 0.9034 (t) REVERT: 4 123 TYR cc_start: 0.9032 (m-80) cc_final: 0.8455 (m-80) REVERT: 4 134 GLU cc_start: 0.7699 (mp0) cc_final: 0.7455 (mp0) REVERT: 4 135 LYS cc_start: 0.8351 (tppt) cc_final: 0.7596 (ttpt) REVERT: 4 190 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8193 (ptmm) REVERT: 5 44 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6897 (mmtt) REVERT: 5 115 ILE cc_start: 0.8129 (pt) cc_final: 0.7714 (tp) REVERT: 5 134 GLU cc_start: 0.7832 (mp0) cc_final: 0.7441 (mp0) REVERT: 5 193 GLU cc_start: 0.8440 (mp0) cc_final: 0.8221 (mp0) REVERT: 6 28 GLU cc_start: 0.8259 (pm20) cc_final: 0.7433 (pm20) REVERT: 6 79 ILE cc_start: 0.9465 (mt) cc_final: 0.9256 (mt) REVERT: 6 133 GLU cc_start: 0.8344 (tt0) cc_final: 0.8091 (tt0) REVERT: 6 172 ILE cc_start: 0.8425 (tt) cc_final: 0.8051 (tt) REVERT: 6 173 TYR cc_start: 0.7057 (t80) cc_final: 0.6471 (t80) REVERT: 7 120 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8327 (mtmt) REVERT: 7 122 ILE cc_start: 0.9117 (tp) cc_final: 0.8698 (tp) REVERT: 7 193 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7254 (tm-30) REVERT: H 396 MET cc_start: 0.7999 (ptp) cc_final: 0.7117 (mtm) outliers start: 0 outliers final: 0 residues processed: 1220 average time/residue: 0.1606 time to fit residues: 304.8050 Evaluate side-chains 1115 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1115 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 213 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 64 GLN ** 3 75 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.170304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137217 restraints weight = 37043.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.141306 restraints weight = 21562.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.144003 restraints weight = 14682.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.145744 restraints weight = 11294.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.147037 restraints weight = 9448.058| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.7665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24968 Z= 0.247 Angle : 0.776 14.247 33660 Z= 0.411 Chirality : 0.050 0.260 3881 Planarity : 0.005 0.063 4329 Dihedral : 5.743 51.441 3498 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.14), residues: 3122 helix: 0.15 (0.14), residues: 1233 sheet: 0.03 (0.19), residues: 614 loop : -1.45 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 88 TYR 0.037 0.003 TYR 6 46 PHE 0.034 0.002 PHE 2 196 HIS 0.006 0.002 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00558 (24968) covalent geometry : angle 0.77627 (33660) hydrogen bonds : bond 0.04097 ( 1269) hydrogen bonds : angle 5.36890 ( 3699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1241 time to evaluate : 0.995 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 98 ILE cc_start: 0.8862 (mt) cc_final: 0.8406 (mt) REVERT: A 100 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8629 (ttm-80) REVERT: A 130 ARG cc_start: 0.8587 (ptt90) cc_final: 0.8137 (ptt-90) REVERT: A 166 MET cc_start: 0.8199 (mtp) cc_final: 0.7941 (ttt) REVERT: A 186 ASP cc_start: 0.7615 (p0) cc_final: 0.6962 (p0) REVERT: A 208 ASN cc_start: 0.9072 (p0) cc_final: 0.8486 (p0) REVERT: A 211 VAL cc_start: 0.8945 (t) cc_final: 0.7811 (p) REVERT: A 222 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8515 (ttmm) REVERT: B 44 GLU cc_start: 0.8319 (tt0) cc_final: 0.8091 (tt0) REVERT: B 58 LEU cc_start: 0.9122 (mt) cc_final: 0.8891 (mt) REVERT: B 60 GLU cc_start: 0.8248 (tp30) cc_final: 0.7668 (tp30) REVERT: B 93 ARG cc_start: 0.8775 (mtt-85) cc_final: 0.8488 (mtt-85) REVERT: B 104 ASP cc_start: 0.7769 (t0) cc_final: 0.7387 (t70) REVERT: B 151 ASP cc_start: 0.9020 (t70) cc_final: 0.8727 (t0) REVERT: B 186 ASP cc_start: 0.8572 (p0) cc_final: 0.8332 (p0) REVERT: B 201 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7094 (tm-30) REVERT: B 214 VAL cc_start: 0.9402 (t) cc_final: 0.9025 (t) REVERT: B 232 TYR cc_start: 0.8659 (m-80) cc_final: 0.8321 (m-80) REVERT: C 9 ASP cc_start: 0.7535 (p0) cc_final: 0.7308 (p0) REVERT: C 14 VAL cc_start: 0.8995 (t) cc_final: 0.8685 (t) REVERT: C 44 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 68 TYR cc_start: 0.8537 (m-10) cc_final: 0.8227 (m-10) REVERT: C 172 THR cc_start: 0.9370 (m) cc_final: 0.9168 (t) REVERT: C 175 PHE cc_start: 0.9221 (m-80) cc_final: 0.8937 (m-80) REVERT: C 189 MET cc_start: 0.9024 (ttm) cc_final: 0.8642 (ttm) REVERT: C 202 SER cc_start: 0.8933 (p) cc_final: 0.8583 (p) REVERT: C 203 GLU cc_start: 0.6737 (pm20) cc_final: 0.6465 (pm20) REVERT: C 208 ASN cc_start: 0.8537 (p0) cc_final: 0.8203 (p0) REVERT: C 214 VAL cc_start: 0.8933 (t) cc_final: 0.8476 (p) REVERT: C 222 LYS cc_start: 0.8713 (tttt) cc_final: 0.8409 (ttmm) REVERT: C 232 TYR cc_start: 0.8260 (m-80) cc_final: 0.7957 (m-80) REVERT: D 18 ASP cc_start: 0.9094 (p0) cc_final: 0.8852 (p0) REVERT: D 64 ILE cc_start: 0.7260 (pt) cc_final: 0.7033 (pt) REVERT: D 81 LEU cc_start: 0.9178 (mp) cc_final: 0.8935 (mp) REVERT: D 91 ARG cc_start: 0.8796 (tpt90) cc_final: 0.8201 (tpt170) REVERT: D 112 LEU cc_start: 0.9203 (tp) cc_final: 0.8909 (tp) REVERT: D 115 LYS cc_start: 0.8306 (mttm) cc_final: 0.7345 (mtpt) REVERT: D 213 TYR cc_start: 0.8885 (p90) cc_final: 0.8594 (p90) REVERT: D 234 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7533 (tm-30) REVERT: E 9 ASP cc_start: 0.7503 (p0) cc_final: 0.6652 (p0) REVERT: E 25 GLU cc_start: 0.8306 (tp30) cc_final: 0.7069 (tp30) REVERT: E 28 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: E 33 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8492 (ttm-80) REVERT: E 44 GLU cc_start: 0.7994 (pm20) cc_final: 0.7565 (pt0) REVERT: E 86 ARG cc_start: 0.7991 (mmt180) cc_final: 0.7751 (mmt180) REVERT: E 148 TYR cc_start: 0.9012 (m-80) cc_final: 0.8186 (m-10) REVERT: E 158 GLU cc_start: 0.7276 (tt0) cc_final: 0.7028 (tt0) REVERT: E 210 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6863 (mm-30) REVERT: E 218 ASP cc_start: 0.8995 (p0) cc_final: 0.8669 (p0) REVERT: E 222 LYS cc_start: 0.8402 (mttp) cc_final: 0.7870 (tptm) REVERT: F 9 ASP cc_start: 0.8753 (p0) cc_final: 0.8316 (p0) REVERT: F 25 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8826 (mm-30) REVERT: F 26 TYR cc_start: 0.9039 (m-10) cc_final: 0.8756 (m-10) REVERT: F 33 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7896 (tpt90) REVERT: F 95 GLU cc_start: 0.8308 (tp30) cc_final: 0.7912 (tp30) REVERT: F 99 ASN cc_start: 0.8810 (t0) cc_final: 0.8382 (t0) REVERT: F 173 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7650 (tm-30) REVERT: F 186 ASP cc_start: 0.8109 (p0) cc_final: 0.7785 (p0) REVERT: G 33 ARG cc_start: 0.7792 (ptp-170) cc_final: 0.7134 (mtp180) REVERT: G 51 ASP cc_start: 0.8987 (t0) cc_final: 0.8602 (t0) REVERT: G 73 HIS cc_start: 0.8383 (p-80) cc_final: 0.7992 (p90) REVERT: G 105 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8411 (mm-30) REVERT: G 186 ASP cc_start: 0.8499 (m-30) cc_final: 0.7938 (p0) REVERT: G 191 LEU cc_start: 0.9316 (tp) cc_final: 0.8906 (tp) REVERT: G 213 TYR cc_start: 0.8317 (p90) cc_final: 0.7798 (p90) REVERT: G 234 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7598 (tm-30) REVERT: G 237 ASN cc_start: 0.7439 (m110) cc_final: 0.7023 (m110) REVERT: 1 17 LEU cc_start: 0.9263 (pt) cc_final: 0.8741 (pt) REVERT: 1 25 MET cc_start: 0.8016 (mtm) cc_final: 0.7271 (ttm) REVERT: 1 111 LEU cc_start: 0.8922 (mt) cc_final: 0.8271 (mt) REVERT: 1 112 ILE cc_start: 0.9293 (mt) cc_final: 0.9072 (mt) REVERT: 1 121 SER cc_start: 0.7895 (p) cc_final: 0.7596 (p) REVERT: 1 122 ILE cc_start: 0.8937 (mm) cc_final: 0.8349 (mm) REVERT: 1 134 GLU cc_start: 0.7193 (mp0) cc_final: 0.6930 (mp0) REVERT: 1 172 ILE cc_start: 0.8542 (mm) cc_final: 0.7787 (mm) REVERT: 1 173 TYR cc_start: 0.8761 (t80) cc_final: 0.8065 (t80) REVERT: 1 193 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7613 (tm-30) REVERT: 2 45 ILE cc_start: 0.8106 (tt) cc_final: 0.7531 (tt) REVERT: 2 83 ARG cc_start: 0.8338 (ptm160) cc_final: 0.8074 (ptm160) REVERT: 3 40 LYS cc_start: 0.4903 (mttt) cc_final: 0.4173 (mttt) REVERT: 3 46 TYR cc_start: 0.7157 (m-80) cc_final: 0.6634 (m-80) REVERT: 3 88 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7486 (mtp85) REVERT: 3 110 LEU cc_start: 0.9513 (mt) cc_final: 0.9223 (mt) REVERT: 3 120 LYS cc_start: 0.9034 (mttm) cc_final: 0.8547 (mttp) REVERT: 3 123 TYR cc_start: 0.8502 (m-80) cc_final: 0.7594 (m-10) REVERT: 3 154 ARG cc_start: 0.5580 (ptp-170) cc_final: 0.5376 (ptm160) REVERT: 3 194 ASP cc_start: 0.6750 (m-30) cc_final: 0.6425 (t0) REVERT: 4 17 LEU cc_start: 0.9064 (mt) cc_final: 0.8835 (mt) REVERT: 4 20 LYS cc_start: 0.8439 (tptm) cc_final: 0.7711 (pttm) REVERT: 4 44 LYS cc_start: 0.7309 (tppt) cc_final: 0.6565 (tttt) REVERT: 4 68 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8037 (ttp-110) REVERT: 4 75 ASN cc_start: 0.9053 (m110) cc_final: 0.8819 (m110) REVERT: 4 80 ARG cc_start: 0.9184 (mtp180) cc_final: 0.8405 (mtp180) REVERT: 4 87 VAL cc_start: 0.9303 (t) cc_final: 0.9064 (t) REVERT: 4 123 TYR cc_start: 0.9040 (m-80) cc_final: 0.8431 (m-80) REVERT: 4 134 GLU cc_start: 0.7670 (mp0) cc_final: 0.7463 (mp0) REVERT: 4 135 LYS cc_start: 0.8405 (tppt) cc_final: 0.7661 (ttpt) REVERT: 4 137 ILE cc_start: 0.8553 (mm) cc_final: 0.7693 (tt) REVERT: 4 190 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8170 (ptmm) REVERT: 5 46 TYR cc_start: 0.8244 (m-80) cc_final: 0.7805 (m-80) REVERT: 5 92 THR cc_start: 0.8753 (p) cc_final: 0.8360 (p) REVERT: 5 116 ASP cc_start: 0.8663 (m-30) cc_final: 0.8462 (m-30) REVERT: 5 123 TYR cc_start: 0.8676 (m-80) cc_final: 0.8152 (m-10) REVERT: 5 134 GLU cc_start: 0.7865 (mp0) cc_final: 0.7517 (mp0) REVERT: 5 148 TYR cc_start: 0.8434 (t80) cc_final: 0.8211 (t80) REVERT: 5 195 GLU cc_start: 0.6469 (tt0) cc_final: 0.6217 (tt0) REVERT: 6 28 GLU cc_start: 0.8458 (pm20) cc_final: 0.7583 (pm20) REVERT: 6 79 ILE cc_start: 0.9427 (mt) cc_final: 0.8796 (mt) REVERT: 6 80 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8548 (ttm110) REVERT: 6 122 ILE cc_start: 0.8988 (tp) cc_final: 0.8657 (tp) REVERT: 6 133 GLU cc_start: 0.8315 (tt0) cc_final: 0.8019 (tt0) REVERT: 6 172 ILE cc_start: 0.8194 (tt) cc_final: 0.7988 (tt) REVERT: 6 173 TYR cc_start: 0.7393 (t80) cc_final: 0.6751 (t80) REVERT: 7 81 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6647 (ttp-170) REVERT: 7 120 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8255 (mtmt) REVERT: 7 190 LYS cc_start: 0.8349 (pttt) cc_final: 0.8143 (pttm) REVERT: 7 193 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7043 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1241 average time/residue: 0.1766 time to fit residues: 342.2158 Evaluate side-chains 1141 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1141 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 180 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 182 optimal weight: 0.3980 chunk 228 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 chunk 194 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.176069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.143288 restraints weight = 36594.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147640 restraints weight = 21028.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.150588 restraints weight = 14160.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.152449 restraints weight = 10724.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153804 restraints weight = 8889.014| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24968 Z= 0.170 Angle : 0.734 13.627 33660 Z= 0.389 Chirality : 0.049 0.271 3881 Planarity : 0.004 0.045 4329 Dihedral : 5.630 43.242 3498 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 3122 helix: 0.16 (0.14), residues: 1248 sheet: 0.05 (0.19), residues: 613 loop : -1.35 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 88 TYR 0.032 0.002 TYR 7 148 PHE 0.035 0.002 PHE 2 196 HIS 0.005 0.002 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00392 (24968) covalent geometry : angle 0.73390 (33660) hydrogen bonds : bond 0.03873 ( 1269) hydrogen bonds : angle 5.28730 ( 3699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1221 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 THR cc_start: 0.9191 (m) cc_final: 0.8986 (m) REVERT: A 44 GLU cc_start: 0.8335 (pm20) cc_final: 0.8059 (pm20) REVERT: A 86 ARG cc_start: 0.7726 (mmt180) cc_final: 0.7504 (mmt180) REVERT: A 91 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7052 (tpp-160) REVERT: A 98 ILE cc_start: 0.8799 (mt) cc_final: 0.8238 (mt) REVERT: A 130 ARG cc_start: 0.8259 (ptt90) cc_final: 0.7731 (ptt-90) REVERT: A 166 MET cc_start: 0.8166 (mtp) cc_final: 0.7810 (ttp) REVERT: A 168 ARG cc_start: 0.8610 (tpt-90) cc_final: 0.8393 (tpt-90) REVERT: A 186 ASP cc_start: 0.7643 (p0) cc_final: 0.6793 (p0) REVERT: A 208 ASN cc_start: 0.8989 (p0) cc_final: 0.8353 (p0) REVERT: A 211 VAL cc_start: 0.8942 (t) cc_final: 0.7884 (p) REVERT: B 44 GLU cc_start: 0.8259 (tt0) cc_final: 0.7959 (tt0) REVERT: B 58 LEU cc_start: 0.9105 (mt) cc_final: 0.8839 (mt) REVERT: B 104 ASP cc_start: 0.7766 (t0) cc_final: 0.7433 (t0) REVERT: B 174 PHE cc_start: 0.7998 (t80) cc_final: 0.7174 (t80) REVERT: B 186 ASP cc_start: 0.8406 (p0) cc_final: 0.8155 (p0) REVERT: B 201 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 203 GLU cc_start: 0.7828 (tp30) cc_final: 0.7462 (tp30) REVERT: B 214 VAL cc_start: 0.9368 (t) cc_final: 0.9045 (t) REVERT: B 232 TYR cc_start: 0.8563 (m-80) cc_final: 0.8231 (m-80) REVERT: B 234 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8729 (mt-10) REVERT: C 9 ASP cc_start: 0.7700 (p0) cc_final: 0.7213 (p0) REVERT: C 29 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 68 TYR cc_start: 0.8312 (m-10) cc_final: 0.8049 (m-10) REVERT: C 110 LYS cc_start: 0.9355 (tmtt) cc_final: 0.8865 (tptt) REVERT: C 172 THR cc_start: 0.9358 (m) cc_final: 0.9140 (t) REVERT: C 189 MET cc_start: 0.9040 (ttm) cc_final: 0.8649 (ttm) REVERT: C 202 SER cc_start: 0.8935 (p) cc_final: 0.8592 (p) REVERT: C 203 GLU cc_start: 0.6787 (pm20) cc_final: 0.6531 (pm20) REVERT: C 208 ASN cc_start: 0.8510 (p0) cc_final: 0.8228 (p0) REVERT: C 214 VAL cc_start: 0.8932 (t) cc_final: 0.8472 (p) REVERT: C 222 LYS cc_start: 0.8695 (tttt) cc_final: 0.8386 (ttmm) REVERT: C 232 TYR cc_start: 0.8180 (m-80) cc_final: 0.7916 (m-80) REVERT: D 18 ASP cc_start: 0.9158 (p0) cc_final: 0.8792 (p0) REVERT: D 42 CYS cc_start: 0.8708 (p) cc_final: 0.8274 (p) REVERT: D 64 ILE cc_start: 0.7150 (pt) cc_final: 0.6930 (pt) REVERT: D 75 CYS cc_start: 0.8312 (p) cc_final: 0.7954 (p) REVERT: D 81 LEU cc_start: 0.9162 (mp) cc_final: 0.8842 (mp) REVERT: D 91 ARG cc_start: 0.9010 (tpt90) cc_final: 0.8263 (tpt170) REVERT: D 148 TYR cc_start: 0.9079 (m-10) cc_final: 0.8188 (m-10) REVERT: D 185 PHE cc_start: 0.7804 (t80) cc_final: 0.7266 (t80) REVERT: D 213 TYR cc_start: 0.8851 (p90) cc_final: 0.7942 (p90) REVERT: D 234 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7576 (tm-30) REVERT: E 9 ASP cc_start: 0.7557 (p0) cc_final: 0.6781 (p0) REVERT: E 25 GLU cc_start: 0.8279 (tp30) cc_final: 0.6984 (tp30) REVERT: E 28 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8138 (mmm-85) REVERT: E 44 GLU cc_start: 0.7708 (pm20) cc_final: 0.7139 (mp0) REVERT: E 52 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8036 (ttpp) REVERT: E 86 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7694 (mmt180) REVERT: E 210 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6970 (mm-30) REVERT: E 218 ASP cc_start: 0.8892 (p0) cc_final: 0.8550 (p0) REVERT: E 222 LYS cc_start: 0.8266 (mttp) cc_final: 0.7843 (tptm) REVERT: F 8 TYR cc_start: 0.7821 (m-80) cc_final: 0.7529 (m-80) REVERT: F 9 ASP cc_start: 0.8781 (p0) cc_final: 0.8250 (p0) REVERT: F 26 TYR cc_start: 0.9026 (m-10) cc_final: 0.8716 (m-10) REVERT: F 33 ARG cc_start: 0.8085 (tpt170) cc_final: 0.7857 (tpt90) REVERT: F 95 GLU cc_start: 0.8413 (tp30) cc_final: 0.7906 (tp30) REVERT: F 158 GLU cc_start: 0.6906 (tt0) cc_final: 0.6300 (tt0) REVERT: F 173 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7592 (tm-30) REVERT: F 234 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7491 (mt-10) REVERT: G 51 ASP cc_start: 0.9004 (t0) cc_final: 0.8740 (t0) REVERT: G 73 HIS cc_start: 0.8182 (p-80) cc_final: 0.7823 (p90) REVERT: G 105 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8387 (mm-30) REVERT: G 187 ASP cc_start: 0.8487 (m-30) cc_final: 0.8276 (m-30) REVERT: G 234 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7574 (tm-30) REVERT: G 237 ASN cc_start: 0.7577 (m110) cc_final: 0.7141 (m110) REVERT: 1 17 LEU cc_start: 0.9284 (pt) cc_final: 0.9050 (pt) REVERT: 1 25 MET cc_start: 0.7938 (mtm) cc_final: 0.7304 (ttm) REVERT: 1 27 THR cc_start: 0.8085 (m) cc_final: 0.7649 (m) REVERT: 1 43 LYS cc_start: 0.8025 (tppp) cc_final: 0.7657 (tttm) REVERT: 1 84 LYS cc_start: 0.8600 (tptt) cc_final: 0.8219 (mmmt) REVERT: 1 87 VAL cc_start: 0.9286 (t) cc_final: 0.8960 (p) REVERT: 1 111 LEU cc_start: 0.8886 (mt) cc_final: 0.8232 (mt) REVERT: 1 122 ILE cc_start: 0.8720 (mm) cc_final: 0.7985 (mm) REVERT: 1 123 TYR cc_start: 0.8564 (m-80) cc_final: 0.8234 (m-80) REVERT: 1 172 ILE cc_start: 0.8432 (mm) cc_final: 0.7713 (mm) REVERT: 1 173 TYR cc_start: 0.8720 (t80) cc_final: 0.8012 (t80) REVERT: 1 190 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7416 (ptpt) REVERT: 1 193 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7509 (tm-30) REVERT: 2 45 ILE cc_start: 0.8150 (tt) cc_final: 0.7909 (tt) REVERT: 2 52 MET cc_start: 0.7855 (ttm) cc_final: 0.7231 (ttm) REVERT: 2 83 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7992 (ptm160) REVERT: 3 88 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7279 (mtp85) REVERT: 3 110 LEU cc_start: 0.9390 (mt) cc_final: 0.8957 (mt) REVERT: 3 120 LYS cc_start: 0.8972 (mttm) cc_final: 0.8504 (mttp) REVERT: 3 123 TYR cc_start: 0.8421 (m-80) cc_final: 0.7443 (m-10) REVERT: 3 133 GLU cc_start: 0.7750 (tt0) cc_final: 0.7482 (tt0) REVERT: 3 154 ARG cc_start: 0.5529 (ptp-170) cc_final: 0.5295 (ptm160) REVERT: 4 20 LYS cc_start: 0.8214 (tptm) cc_final: 0.7602 (pttm) REVERT: 4 28 GLU cc_start: 0.5876 (pp20) cc_final: 0.5581 (pm20) REVERT: 4 44 LYS cc_start: 0.7221 (tppt) cc_final: 0.6246 (tttm) REVERT: 4 48 ILE cc_start: 0.9283 (mm) cc_final: 0.8768 (mm) REVERT: 4 52 MET cc_start: 0.8215 (ttm) cc_final: 0.7916 (ttm) REVERT: 4 87 VAL cc_start: 0.9187 (t) cc_final: 0.8940 (t) REVERT: 4 123 TYR cc_start: 0.8951 (m-80) cc_final: 0.8443 (m-80) REVERT: 4 135 LYS cc_start: 0.8259 (tppt) cc_final: 0.7616 (ttpt) REVERT: 4 137 ILE cc_start: 0.8385 (mm) cc_final: 0.7897 (mm) REVERT: 4 190 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8268 (ptmm) REVERT: 5 116 ASP cc_start: 0.8442 (m-30) cc_final: 0.8198 (m-30) REVERT: 5 123 TYR cc_start: 0.8490 (m-80) cc_final: 0.8250 (m-10) REVERT: 5 134 GLU cc_start: 0.7740 (mp0) cc_final: 0.7497 (mp0) REVERT: 5 163 GLU cc_start: 0.7924 (pm20) cc_final: 0.7134 (tp30) REVERT: 5 193 GLU cc_start: 0.8142 (mp0) cc_final: 0.7907 (mp0) REVERT: 6 28 GLU cc_start: 0.8521 (pm20) cc_final: 0.7748 (pm20) REVERT: 6 79 ILE cc_start: 0.9626 (mt) cc_final: 0.8560 (mt) REVERT: 6 80 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8593 (ttm110) REVERT: 6 122 ILE cc_start: 0.8907 (tp) cc_final: 0.8532 (tp) REVERT: 6 172 ILE cc_start: 0.8260 (tt) cc_final: 0.8057 (tt) REVERT: 6 173 TYR cc_start: 0.7365 (t80) cc_final: 0.6736 (t80) REVERT: 7 81 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.6840 (ttp-170) REVERT: 7 190 LYS cc_start: 0.8424 (pttt) cc_final: 0.8181 (pttm) REVERT: 7 193 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6954 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1221 average time/residue: 0.1758 time to fit residues: 336.3273 Evaluate side-chains 1124 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1124 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 189 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 196 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN 1 47 GLN 3 64 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 198 GLN 6 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.173505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.140520 restraints weight = 36802.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.144773 restraints weight = 21152.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.147636 restraints weight = 14289.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149553 restraints weight = 10861.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.150826 restraints weight = 8973.285| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24968 Z= 0.218 Angle : 0.776 13.862 33660 Z= 0.410 Chirality : 0.050 0.284 3881 Planarity : 0.005 0.049 4329 Dihedral : 5.733 40.675 3498 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.14), residues: 3122 helix: 0.15 (0.15), residues: 1186 sheet: 0.03 (0.19), residues: 598 loop : -1.49 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 80 TYR 0.037 0.002 TYR 6 46 PHE 0.034 0.002 PHE G 174 HIS 0.006 0.002 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00496 (24968) covalent geometry : angle 0.77582 (33660) hydrogen bonds : bond 0.04039 ( 1269) hydrogen bonds : angle 5.42791 ( 3699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1213 time to evaluate : 0.997 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 25 GLU cc_start: 0.7982 (tt0) cc_final: 0.7775 (mt-10) REVERT: A 86 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7544 (mmt180) REVERT: A 100 ARG cc_start: 0.9115 (ttm-80) cc_final: 0.8623 (mtt-85) REVERT: A 130 ARG cc_start: 0.8273 (ptt90) cc_final: 0.7762 (ptt-90) REVERT: A 166 MET cc_start: 0.8201 (mtp) cc_final: 0.7856 (ttp) REVERT: A 186 ASP cc_start: 0.7606 (p0) cc_final: 0.6904 (p0) REVERT: A 208 ASN cc_start: 0.9074 (p0) cc_final: 0.8469 (p0) REVERT: A 211 VAL cc_start: 0.8993 (t) cc_final: 0.7919 (p) REVERT: A 222 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8524 (ttmt) REVERT: B 44 GLU cc_start: 0.8275 (tt0) cc_final: 0.7939 (tt0) REVERT: B 58 LEU cc_start: 0.9061 (mt) cc_final: 0.8798 (mt) REVERT: B 104 ASP cc_start: 0.7850 (t0) cc_final: 0.7478 (t0) REVERT: B 186 ASP cc_start: 0.8438 (p0) cc_final: 0.8196 (p0) REVERT: B 201 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 214 VAL cc_start: 0.9380 (t) cc_final: 0.9064 (t) REVERT: B 227 GLU cc_start: 0.7733 (mp0) cc_final: 0.7475 (mp0) REVERT: B 232 TYR cc_start: 0.8610 (m-80) cc_final: 0.8220 (m-80) REVERT: B 234 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8695 (mt-10) REVERT: C 9 ASP cc_start: 0.7410 (p0) cc_final: 0.7096 (p0) REVERT: C 14 VAL cc_start: 0.8957 (t) cc_final: 0.8653 (t) REVERT: C 28 ARG cc_start: 0.8802 (tpt90) cc_final: 0.8234 (mmm160) REVERT: C 68 TYR cc_start: 0.8447 (m-10) cc_final: 0.8214 (m-10) REVERT: C 110 LYS cc_start: 0.9434 (tmtt) cc_final: 0.9088 (tptt) REVERT: C 171 VAL cc_start: 0.8773 (t) cc_final: 0.8525 (t) REVERT: C 175 PHE cc_start: 0.9278 (m-80) cc_final: 0.8410 (m-80) REVERT: C 189 MET cc_start: 0.9070 (ttm) cc_final: 0.8724 (ttm) REVERT: C 202 SER cc_start: 0.8988 (p) cc_final: 0.8609 (p) REVERT: C 203 GLU cc_start: 0.6925 (pm20) cc_final: 0.6605 (pm20) REVERT: C 208 ASN cc_start: 0.8477 (p0) cc_final: 0.8162 (p0) REVERT: C 214 VAL cc_start: 0.8874 (t) cc_final: 0.8581 (m) REVERT: C 222 LYS cc_start: 0.8718 (tttt) cc_final: 0.8390 (ttmm) REVERT: C 232 TYR cc_start: 0.8298 (m-80) cc_final: 0.8085 (m-80) REVERT: D 42 CYS cc_start: 0.8813 (p) cc_final: 0.8325 (p) REVERT: D 46 VAL cc_start: 0.8804 (t) cc_final: 0.8456 (p) REVERT: D 75 CYS cc_start: 0.8369 (p) cc_final: 0.7962 (p) REVERT: D 185 PHE cc_start: 0.8031 (t80) cc_final: 0.7806 (t80) REVERT: D 234 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 242 GLU cc_start: 0.8514 (pm20) cc_final: 0.8236 (pm20) REVERT: E 9 ASP cc_start: 0.7579 (p0) cc_final: 0.6711 (p0) REVERT: E 25 GLU cc_start: 0.8286 (tp30) cc_final: 0.7085 (tp30) REVERT: E 28 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8065 (mmm-85) REVERT: E 52 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8118 (ttpp) REVERT: E 86 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7679 (mmt180) REVERT: E 186 ASP cc_start: 0.8219 (m-30) cc_final: 0.7980 (m-30) REVERT: E 210 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6900 (mm-30) REVERT: E 222 LYS cc_start: 0.8325 (mttp) cc_final: 0.7835 (tptm) REVERT: F 8 TYR cc_start: 0.7739 (m-80) cc_final: 0.7418 (m-80) REVERT: F 9 ASP cc_start: 0.8873 (p0) cc_final: 0.8044 (p0) REVERT: F 26 TYR cc_start: 0.9012 (m-10) cc_final: 0.8669 (m-10) REVERT: F 33 ARG cc_start: 0.8101 (tpt170) cc_final: 0.7889 (tpt90) REVERT: F 95 GLU cc_start: 0.8587 (tp30) cc_final: 0.8032 (tp30) REVERT: F 99 ASN cc_start: 0.8769 (t0) cc_final: 0.8499 (t0) REVERT: F 173 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7535 (tm-30) REVERT: F 185 PHE cc_start: 0.8064 (t80) cc_final: 0.7792 (t80) REVERT: F 196 MET cc_start: 0.9045 (tpp) cc_final: 0.8443 (tpp) REVERT: F 211 VAL cc_start: 0.8971 (t) cc_final: 0.8599 (t) REVERT: G 51 ASP cc_start: 0.9212 (t0) cc_final: 0.8766 (t0) REVERT: G 73 HIS cc_start: 0.8315 (p-80) cc_final: 0.7999 (p90) REVERT: G 105 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8390 (mm-30) REVERT: G 186 ASP cc_start: 0.8499 (m-30) cc_final: 0.8123 (p0) REVERT: G 234 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 237 ASN cc_start: 0.7725 (m110) cc_final: 0.7490 (m110) REVERT: 1 17 LEU cc_start: 0.9329 (pt) cc_final: 0.8966 (pt) REVERT: 1 25 MET cc_start: 0.8152 (mtm) cc_final: 0.7455 (ttm) REVERT: 1 111 LEU cc_start: 0.8900 (mt) cc_final: 0.8336 (mt) REVERT: 1 121 SER cc_start: 0.8108 (p) cc_final: 0.7443 (p) REVERT: 1 122 ILE cc_start: 0.8859 (mm) cc_final: 0.8138 (mm) REVERT: 1 134 GLU cc_start: 0.7157 (mp0) cc_final: 0.6849 (mp0) REVERT: 1 172 ILE cc_start: 0.8445 (mm) cc_final: 0.7932 (mm) REVERT: 1 173 TYR cc_start: 0.8714 (t80) cc_final: 0.8042 (t80) REVERT: 1 190 LYS cc_start: 0.8241 (ptmt) cc_final: 0.8029 (ptmm) REVERT: 1 193 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7486 (tm-30) REVERT: 2 45 ILE cc_start: 0.8157 (tt) cc_final: 0.7507 (tt) REVERT: 2 52 MET cc_start: 0.7785 (ttm) cc_final: 0.7183 (ttm) REVERT: 2 83 ARG cc_start: 0.8256 (ptm160) cc_final: 0.7722 (ptm160) REVERT: 3 88 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7474 (mtp85) REVERT: 3 110 LEU cc_start: 0.9389 (mt) cc_final: 0.9038 (mt) REVERT: 3 120 LYS cc_start: 0.8960 (mttm) cc_final: 0.8520 (mttp) REVERT: 3 123 TYR cc_start: 0.8402 (m-80) cc_final: 0.8112 (m-10) REVERT: 3 154 ARG cc_start: 0.5615 (ptp-170) cc_final: 0.5291 (ptm160) REVERT: 4 17 LEU cc_start: 0.9026 (mt) cc_final: 0.8721 (mt) REVERT: 4 20 LYS cc_start: 0.8162 (tptm) cc_final: 0.7584 (pttm) REVERT: 4 44 LYS cc_start: 0.7456 (tppt) cc_final: 0.6616 (ttpt) REVERT: 4 52 MET cc_start: 0.8303 (ttm) cc_final: 0.8095 (ttm) REVERT: 4 87 VAL cc_start: 0.9289 (t) cc_final: 0.9043 (t) REVERT: 4 123 TYR cc_start: 0.8913 (m-80) cc_final: 0.8437 (m-80) REVERT: 4 134 GLU cc_start: 0.7729 (mp0) cc_final: 0.7457 (mp0) REVERT: 4 135 LYS cc_start: 0.8462 (tppt) cc_final: 0.7763 (ttpt) REVERT: 4 137 ILE cc_start: 0.8486 (mm) cc_final: 0.7835 (tt) REVERT: 4 190 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8272 (ptmm) REVERT: 5 46 TYR cc_start: 0.7535 (m-10) cc_final: 0.7280 (m-10) REVERT: 5 134 GLU cc_start: 0.7902 (mp0) cc_final: 0.7635 (mp0) REVERT: 6 28 GLU cc_start: 0.8598 (pm20) cc_final: 0.7901 (pm20) REVERT: 6 79 ILE cc_start: 0.9660 (mt) cc_final: 0.8688 (mt) REVERT: 6 80 ARG cc_start: 0.9090 (ttm-80) cc_final: 0.8609 (ttm110) REVERT: 6 122 ILE cc_start: 0.8922 (tp) cc_final: 0.8582 (tp) REVERT: 6 163 GLU cc_start: 0.8186 (pm20) cc_final: 0.7627 (pm20) REVERT: 7 81 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.6957 (tmm-80) REVERT: 7 86 THR cc_start: 0.9513 (p) cc_final: 0.9128 (p) REVERT: 7 120 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8119 (mtmt) REVERT: 7 190 LYS cc_start: 0.8341 (pttt) cc_final: 0.8060 (pttm) REVERT: 7 193 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7164 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1213 average time/residue: 0.1770 time to fit residues: 335.5368 Evaluate side-chains 1108 residues out of total 2617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1108 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 298 optimal weight: 0.9980 chunk 197 optimal weight: 0.4980 chunk 264 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 280 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 296 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN 3 75 ASN ** 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 = 0.3851 r_free = 0.3851 target = 0.173123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.140469 restraints weight = 36624.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.144648 restraints weight = 21117.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147429 restraints weight = 14242.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149291 restraints weight = 10873.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.150576 restraints weight = 8999.816| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24968 Z= 0.199 Angle : 0.770 13.609 33660 Z= 0.406 Chirality : 0.050 0.291 3881 Planarity : 0.005 0.055 4329 Dihedral : 5.750 39.162 3498 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.32 % Favored : 95.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.14), residues: 3122 helix: 0.15 (0.15), residues: 1191 sheet: 0.06 (0.19), residues: 600 loop : -1.40 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 180 TYR 0.036 0.002 TYR 7 148 PHE 0.024 0.002 PHE 2 196 HIS 0.006 0.002 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00461 (24968) covalent geometry : angle 0.76992 (33660) hydrogen bonds : bond 0.03952 ( 1269) hydrogen bonds : angle 5.39152 ( 3699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6150.05 seconds wall clock time: 106 minutes 17.22 seconds (6377.22 seconds total)