Starting phenix.real_space_refine on Wed Mar 4 02:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykm_10828/03_2026/6ykm_10828.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykm_10828/03_2026/6ykm_10828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ykm_10828/03_2026/6ykm_10828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykm_10828/03_2026/6ykm_10828.map" model { file = "/net/cci-nas-00/data/ceres_data/6ykm_10828/03_2026/6ykm_10828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykm_10828/03_2026/6ykm_10828.cif" } resolution = 3.1 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= 0.009 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 70 5.16 5 C 6752 2.51 5 N 1688 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10434 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "E" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "F" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 328 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 328 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.24 Number of scatterers: 10434 At special positions: 0 Unit cell: (95.68, 114.816, 99.84, 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 70 16.00 O 1924 8.00 N 1688 7.00 C 6752 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: 0.79 Conformation dependent library (CDL) restraints added in 557.9 milliseconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.647A pdb=" N MET A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.919A pdb=" N ILE A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.656A pdb=" N LYS A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.662A pdb=" N ASP A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 160 removed outlier: 4.062A pdb=" N GLU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.902A pdb=" N LEU A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 174 through 199 removed outlier: 4.435A pdb=" N ALA A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.886A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'B' and resid 6 through 17 removed outlier: 3.640A pdb=" N ALA B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.532A pdb=" N VAL B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.704A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.584A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.629A pdb=" N LEU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.929A pdb=" N GLU B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 103 " --> pdb=" O THR B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 120 through 129 removed outlier: 4.031A pdb=" N GLU B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 152 removed outlier: 3.611A pdb=" N GLU B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 174 through 198 removed outlier: 3.691A pdb=" N MET B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 229 removed outlier: 4.150A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.518A pdb=" N ALA B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 removed outlier: 3.769A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.656A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.599A pdb=" N ILE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.543A pdb=" N LYS C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.554A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.646A pdb=" N GLN C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.736A pdb=" N LEU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.623A pdb=" N MET C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.883A pdb=" N GLU C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.988A pdb=" N TRP C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 174 through 199 removed outlier: 3.679A pdb=" N THR C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 229 removed outlier: 4.161A pdb=" N ASP C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'D' and resid 2 through 22 removed outlier: 3.855A pdb=" N MET D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 14 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.568A pdb=" N VAL D 30 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.597A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.631A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.624A pdb=" N THR D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 120 through 163 removed outlier: 3.784A pdb=" N GLU D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Proline residue: D 154 - end of helix removed outlier: 3.628A pdb=" N LEU D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.588A pdb=" N LYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 199 removed outlier: 3.883A pdb=" N ALA D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 231 removed outlier: 4.080A pdb=" N ASP D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 214 " --> pdb=" O ASN D 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.519A pdb=" N ILE E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 3.808A pdb=" N ILE E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.532A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.615A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 91 removed outlier: 3.781A pdb=" N GLN E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.752A pdb=" N ASN E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 120 through 133 removed outlier: 4.239A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 152 through 171 removed outlier: 3.587A pdb=" N MET E 156 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 185 through 197 Processing helix chain 'E' and resid 199 through 229 removed outlier: 3.972A pdb=" N ASP E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 216 " --> pdb=" O MET E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.850A pdb=" N TYR F 20 " --> pdb=" O TRP F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.974A pdb=" N GLU F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 37 Processing helix chain 'G' and resid 43 through 53 removed outlier: 3.833A pdb=" N ALA G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 49 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1977 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: 1.50 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2475 1.33 - 1.45: 1955 1.45 - 1.57: 6064 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 10619 Sorted by residual: bond pdb=" C MET E 40 " pdb=" N PRO E 41 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" C MET B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.336 1.372 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" C MET D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.23e-02 6.61e+03 8.79e+00 bond pdb=" CG1 ILE A 78 " pdb=" CD1 ILE A 78 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.84e+00 bond pdb=" C VAL F 18 " pdb=" N PRO F 19 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.71e+00 ... (remaining 10614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 13668 2.17 - 4.34: 559 4.34 - 6.50: 83 6.50 - 8.67: 35 8.67 - 10.84: 3 Bond angle restraints: 14348 Sorted by residual: angle pdb=" C SER G 38 " pdb=" N LYS G 39 " pdb=" CA LYS G 39 " ideal model delta sigma weight residual 122.07 127.75 -5.68 1.43e+00 4.89e-01 1.58e+01 angle pdb=" C ALA F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C SER C 253 " pdb=" N GLN C 254 " pdb=" CA GLN C 254 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C LEU E 96 " pdb=" N GLU E 97 " pdb=" CA GLU E 97 " ideal model delta sigma weight residual 120.28 124.79 -4.51 1.34e+00 5.57e-01 1.13e+01 angle pdb=" CA LEU B 115 " pdb=" CB LEU B 115 " pdb=" CG LEU B 115 " ideal model delta sigma weight residual 116.30 127.14 -10.84 3.50e+00 8.16e-02 9.59e+00 ... (remaining 14343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 5842 14.14 - 28.28: 401 28.28 - 42.42: 112 42.42 - 56.56: 18 56.56 - 70.70: 3 Dihedral angle restraints: 6376 sinusoidal: 2490 harmonic: 3886 Sorted by residual: dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N PHE B 200 " pdb=" CA PHE B 200 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LEU E 199 " pdb=" C LEU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA LEU C 199 " pdb=" C LEU C 199 " pdb=" N PHE C 200 " pdb=" CA PHE C 200 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 934 0.047 - 0.094: 550 0.094 - 0.142: 162 0.142 - 0.189: 29 0.189 - 0.236: 7 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CG LEU C 158 " pdb=" CB LEU C 158 " pdb=" CD1 LEU C 158 " pdb=" CD2 LEU C 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE E 182 " pdb=" CA ILE E 182 " pdb=" CG1 ILE E 182 " pdb=" CG2 ILE E 182 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU G 28 " pdb=" CB LEU G 28 " pdb=" CD1 LEU G 28 " pdb=" CD2 LEU G 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1679 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 149 " -0.028 2.00e-02 2.50e+03 3.07e-02 1.65e+01 pdb=" CG PHE E 149 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE E 149 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE E 149 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 149 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE E 149 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE E 149 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 149 " 0.030 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE C 149 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE C 149 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 149 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 149 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 149 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 149 " 0.029 2.00e-02 2.50e+03 2.95e-02 1.52e+01 pdb=" CG PHE B 149 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 149 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 149 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 149 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 149 " 0.011 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2487 2.78 - 3.31: 10069 3.31 - 3.84: 17573 3.84 - 4.37: 22131 4.37 - 4.90: 36677 Nonbonded interactions: 88937 Sorted by model distance: nonbonded pdb=" O ILE C 38 " pdb=" OG1 THR C 42 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU A 23 " pdb=" OG SER B 34 " model vdw 2.304 3.040 nonbonded pdb=" O HOH B 303 " pdb=" O HOH F 304 " model vdw 2.327 3.040 nonbonded pdb=" OG SER F 25 " pdb=" O HOH F 301 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU C 23 " pdb=" OG SER D 34 " model vdw 2.370 3.040 ... (remaining 88932 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.360 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.095 10619 Z= 0.367 Angle : 1.067 10.840 14348 Z= 0.565 Chirality : 0.061 0.236 1682 Planarity : 0.008 0.062 1804 Dihedral : 11.095 70.703 3862 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.17), residues: 1343 helix: -3.20 (0.11), residues: 1092 sheet: None (None), residues: 0 loop : -1.13 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 251 TYR 0.045 0.005 TYR C 197 PHE 0.068 0.005 PHE C 149 TRP 0.014 0.003 TRP F 35 HIS 0.010 0.002 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00908 (10619) covalent geometry : angle 1.06670 (14348) hydrogen bonds : bond 0.15615 ( 671) hydrogen bonds : angle 7.44956 ( 1977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.403 Fit side-chains REVERT: A 208 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7929 (tttm) REVERT: B 110 ASN cc_start: 0.8038 (p0) cc_final: 0.7680 (m110) REVERT: B 140 LYS cc_start: 0.8163 (ttmp) cc_final: 0.7759 (mtmm) REVERT: B 226 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8303 (ttmm) REVERT: C 40 MET cc_start: 0.8113 (mmt) cc_final: 0.7727 (mmt) REVERT: C 216 LYS cc_start: 0.8497 (tptm) cc_final: 0.7735 (mttt) REVERT: D 151 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7041 (mt-10) REVERT: D 223 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7763 (mm-30) REVERT: D 230 GLU cc_start: 0.7084 (mp0) cc_final: 0.6849 (mt-10) REVERT: E 28 LEU cc_start: 0.7127 (tt) cc_final: 0.6687 (mp) REVERT: E 61 LYS cc_start: 0.8339 (mttp) cc_final: 0.8068 (mtmt) REVERT: E 104 GLU cc_start: 0.7561 (mp0) cc_final: 0.7230 (mm-30) REVERT: E 140 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8012 (pttm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1115 time to fit residues: 41.0453 Evaluate side-chains 186 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 138 HIS C 52 HIS C 134 GLN D 110 ASN D 134 GLN E 134 GLN E 138 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116353 restraints weight = 11557.231| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.57 r_work: 0.3004 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10619 Z= 0.136 Angle : 0.580 6.845 14348 Z= 0.300 Chirality : 0.041 0.144 1682 Planarity : 0.005 0.047 1804 Dihedral : 5.273 22.929 1402 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.26 % Allowed : 7.94 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.21), residues: 1343 helix: -1.64 (0.14), residues: 1093 sheet: None (None), residues: 0 loop : -0.56 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 99 TYR 0.020 0.002 TYR C 197 PHE 0.023 0.002 PHE B 149 TRP 0.007 0.001 TRP F 35 HIS 0.009 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00307 (10619) covalent geometry : angle 0.58005 (14348) hydrogen bonds : bond 0.03958 ( 671) hydrogen bonds : angle 4.56181 ( 1977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.384 Fit side-chains REVERT: A 23 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7522 (tt0) REVERT: A 126 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 172 LEU cc_start: 0.5937 (pt) cc_final: 0.5711 (pt) REVERT: A 208 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8125 (tttm) REVERT: B 54 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8678 (mmmm) REVERT: B 140 LYS cc_start: 0.8535 (ttmp) cc_final: 0.8175 (mtmm) REVERT: B 226 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8445 (ttmm) REVERT: C 57 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8488 (mttp) REVERT: D 33 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8544 (tp) REVERT: D 133 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7606 (mm-30) REVERT: D 151 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7630 (mt-10) REVERT: E 3 LEU cc_start: 0.7561 (tp) cc_final: 0.7357 (tp) REVERT: E 28 LEU cc_start: 0.6397 (tt) cc_final: 0.5964 (mp) REVERT: E 61 LYS cc_start: 0.8641 (mttp) cc_final: 0.8319 (mtmt) REVERT: E 64 LYS cc_start: 0.7950 (pttm) cc_final: 0.6640 (mmmt) REVERT: E 104 GLU cc_start: 0.8265 (mp0) cc_final: 0.7572 (mm-30) REVERT: E 117 ASP cc_start: 0.8275 (m-30) cc_final: 0.8025 (m-30) REVERT: E 140 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8416 (pttm) REVERT: E 151 GLU cc_start: 0.7940 (tt0) cc_final: 0.7705 (mt-10) outliers start: 25 outliers final: 11 residues processed: 216 average time/residue: 0.1161 time to fit residues: 33.8242 Evaluate side-chains 181 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 138 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111965 restraints weight = 11681.583| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.37 r_work: 0.2990 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10619 Z= 0.148 Angle : 0.565 9.096 14348 Z= 0.288 Chirality : 0.042 0.128 1682 Planarity : 0.004 0.042 1804 Dihedral : 4.968 22.139 1402 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 10.65 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.22), residues: 1343 helix: -1.03 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -0.11 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.021 0.002 TYR C 197 PHE 0.024 0.002 PHE B 149 TRP 0.006 0.001 TRP E 146 HIS 0.017 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00350 (10619) covalent geometry : angle 0.56478 (14348) hydrogen bonds : bond 0.03811 ( 671) hydrogen bonds : angle 4.28260 ( 1977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.442 Fit side-chains REVERT: A 23 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7530 (tt0) REVERT: A 172 LEU cc_start: 0.5947 (pt) cc_final: 0.5708 (pt) REVERT: A 208 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8056 (tttm) REVERT: B 54 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8672 (mmmm) REVERT: B 113 MET cc_start: 0.8443 (ptm) cc_final: 0.8123 (ptp) REVERT: B 140 LYS cc_start: 0.8484 (ttmp) cc_final: 0.8001 (mtmm) REVERT: C 57 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8425 (mttt) REVERT: D 33 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8395 (tp) REVERT: D 133 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7515 (mm-30) REVERT: D 151 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7570 (mt-10) REVERT: E 9 MET cc_start: 0.7869 (mtp) cc_final: 0.7622 (mtm) REVERT: E 61 LYS cc_start: 0.8618 (mttp) cc_final: 0.8302 (mtmt) REVERT: E 64 LYS cc_start: 0.7969 (pttm) cc_final: 0.6590 (mmmt) REVERT: E 102 GLU cc_start: 0.7343 (pp20) cc_final: 0.7110 (pp20) REVERT: E 104 GLU cc_start: 0.8252 (mp0) cc_final: 0.7646 (mm-30) REVERT: E 117 ASP cc_start: 0.8244 (m-30) cc_final: 0.8004 (m-30) REVERT: E 140 LYS cc_start: 0.8750 (ptpt) cc_final: 0.8304 (ptmm) REVERT: E 151 GLU cc_start: 0.7895 (tt0) cc_final: 0.7624 (mt-10) REVERT: E 207 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8363 (tt) outliers start: 23 outliers final: 11 residues processed: 187 average time/residue: 0.1012 time to fit residues: 26.5787 Evaluate side-chains 182 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110046 restraints weight = 11601.596| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.37 r_work: 0.2956 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10619 Z= 0.165 Angle : 0.564 6.935 14348 Z= 0.289 Chirality : 0.042 0.123 1682 Planarity : 0.004 0.041 1804 Dihedral : 4.866 22.034 1402 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 10.65 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1343 helix: -0.67 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : 0.01 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.022 0.002 TYR C 197 PHE 0.024 0.002 PHE B 149 TRP 0.006 0.001 TRP E 146 HIS 0.006 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00400 (10619) covalent geometry : angle 0.56426 (14348) hydrogen bonds : bond 0.03844 ( 671) hydrogen bonds : angle 4.18923 ( 1977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.311 Fit side-chains REVERT: A 23 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7529 (tt0) REVERT: A 172 LEU cc_start: 0.6002 (pt) cc_final: 0.5696 (pt) REVERT: A 208 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8063 (tttm) REVERT: B 54 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8707 (mmmm) REVERT: B 140 LYS cc_start: 0.8519 (ttmp) cc_final: 0.8013 (mtmm) REVERT: C 57 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8474 (mttt) REVERT: D 33 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8536 (tp) REVERT: D 133 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7599 (mm-30) REVERT: D 151 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7664 (mt-10) REVERT: E 9 MET cc_start: 0.7942 (mtp) cc_final: 0.7702 (mtm) REVERT: E 64 LYS cc_start: 0.7997 (pttm) cc_final: 0.6629 (mmmt) REVERT: E 102 GLU cc_start: 0.7301 (pp20) cc_final: 0.7054 (pp20) REVERT: E 104 GLU cc_start: 0.8259 (mp0) cc_final: 0.7654 (mm-30) REVERT: E 117 ASP cc_start: 0.8274 (m-30) cc_final: 0.8052 (m-30) REVERT: E 140 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8319 (mtmm) REVERT: E 207 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8399 (tt) outliers start: 27 outliers final: 17 residues processed: 184 average time/residue: 0.1066 time to fit residues: 27.0023 Evaluate side-chains 184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 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 138 HIS D 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113606 restraints weight = 11572.018| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.35 r_work: 0.3004 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10619 Z= 0.114 Angle : 0.511 6.638 14348 Z= 0.263 Chirality : 0.040 0.117 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.599 21.331 1402 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.81 % Allowed : 12.27 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1343 helix: -0.26 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : 0.09 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.016 0.002 TYR C 197 PHE 0.015 0.001 PHE A 149 TRP 0.007 0.001 TRP D 203 HIS 0.009 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00256 (10619) covalent geometry : angle 0.51126 (14348) hydrogen bonds : bond 0.03379 ( 671) hydrogen bonds : angle 4.00051 ( 1977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.300 Fit side-chains REVERT: A 23 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7406 (tt0) REVERT: B 54 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8658 (mmmm) REVERT: B 113 MET cc_start: 0.8307 (ptm) cc_final: 0.8093 (ptp) REVERT: B 140 LYS cc_start: 0.8465 (ttmp) cc_final: 0.7983 (mtmm) REVERT: B 167 LEU cc_start: 0.8907 (tm) cc_final: 0.8594 (tp) REVERT: C 57 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8474 (mttt) REVERT: D 33 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8528 (tp) REVERT: D 38 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8371 (tt) REVERT: D 133 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7538 (mm-30) REVERT: D 151 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7665 (mt-10) REVERT: E 9 MET cc_start: 0.7954 (mtp) cc_final: 0.7709 (mtm) REVERT: E 64 LYS cc_start: 0.8007 (pttm) cc_final: 0.6597 (mmmt) REVERT: E 104 GLU cc_start: 0.8223 (mp0) cc_final: 0.7622 (mm-30) REVERT: E 113 MET cc_start: 0.8602 (ttm) cc_final: 0.8183 (mtp) REVERT: E 140 LYS cc_start: 0.8740 (ptpt) cc_final: 0.8283 (ptmm) REVERT: E 207 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8378 (tt) outliers start: 20 outliers final: 11 residues processed: 177 average time/residue: 0.1023 time to fit residues: 25.3965 Evaluate side-chains 172 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 20 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.138026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109557 restraints weight = 11696.947| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.39 r_work: 0.2952 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10619 Z= 0.171 Angle : 0.559 6.705 14348 Z= 0.287 Chirality : 0.043 0.185 1682 Planarity : 0.004 0.039 1804 Dihedral : 4.717 21.808 1402 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.26 % Allowed : 12.91 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1343 helix: -0.21 (0.15), residues: 1111 sheet: None (None), residues: 0 loop : 0.32 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.020 0.002 TYR C 197 PHE 0.023 0.002 PHE B 149 TRP 0.007 0.001 TRP E 146 HIS 0.009 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00419 (10619) covalent geometry : angle 0.55883 (14348) hydrogen bonds : bond 0.03781 ( 671) hydrogen bonds : angle 4.10063 ( 1977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.409 Fit side-chains REVERT: A 23 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7411 (tt0) REVERT: B 54 LYS cc_start: 0.8945 (mmtm) cc_final: 0.8683 (mmmm) REVERT: B 140 LYS cc_start: 0.8462 (ttmp) cc_final: 0.7924 (mtmm) REVERT: B 151 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7931 (mt-10) REVERT: B 167 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8562 (tp) REVERT: B 207 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8846 (tt) REVERT: D 33 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8369 (tp) REVERT: D 38 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8280 (tt) REVERT: D 133 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7540 (mm-30) REVERT: D 151 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7773 (mt-10) REVERT: E 9 MET cc_start: 0.7926 (mtp) cc_final: 0.7659 (mtm) REVERT: E 104 GLU cc_start: 0.8256 (mp0) cc_final: 0.7652 (mm-30) REVERT: E 113 MET cc_start: 0.8597 (ttm) cc_final: 0.8257 (mtp) REVERT: E 140 LYS cc_start: 0.8745 (ptpt) cc_final: 0.8266 (mtmm) REVERT: E 207 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8361 (tt) outliers start: 25 outliers final: 15 residues processed: 177 average time/residue: 0.1017 time to fit residues: 25.3271 Evaluate side-chains 183 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0670 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS C 125 HIS E 138 HIS E 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113499 restraints weight = 11495.721| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.58 r_work: 0.3025 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10619 Z= 0.105 Angle : 0.495 6.455 14348 Z= 0.255 Chirality : 0.039 0.168 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.427 20.772 1402 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.71 % Allowed : 13.90 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1343 helix: 0.28 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : 0.65 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 99 TYR 0.013 0.001 TYR C 197 PHE 0.012 0.001 PHE B 149 TRP 0.009 0.001 TRP D 203 HIS 0.002 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00230 (10619) covalent geometry : angle 0.49466 (14348) hydrogen bonds : bond 0.03169 ( 671) hydrogen bonds : angle 3.88383 ( 1977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.419 Fit side-chains REVERT: A 23 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7397 (tt0) REVERT: B 54 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8704 (mmmm) REVERT: B 140 LYS cc_start: 0.8480 (ttmp) cc_final: 0.8024 (mtmm) REVERT: B 151 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7959 (mt-10) REVERT: B 167 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8569 (tp) REVERT: D 33 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8421 (tp) REVERT: D 151 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7723 (mt-10) REVERT: E 9 MET cc_start: 0.7986 (mtp) cc_final: 0.7704 (mtm) REVERT: E 64 LYS cc_start: 0.7999 (pttm) cc_final: 0.6646 (mmmt) REVERT: E 104 GLU cc_start: 0.8232 (mp0) cc_final: 0.7660 (mm-30) REVERT: E 140 LYS cc_start: 0.8764 (ptpt) cc_final: 0.8312 (mtmm) outliers start: 19 outliers final: 11 residues processed: 184 average time/residue: 0.1086 time to fit residues: 28.0299 Evaluate side-chains 173 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain E residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 125 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 86 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113320 restraints weight = 11450.658| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.37 r_work: 0.3021 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10619 Z= 0.117 Angle : 0.512 6.395 14348 Z= 0.259 Chirality : 0.040 0.151 1682 Planarity : 0.004 0.040 1804 Dihedral : 4.397 20.667 1402 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.62 % Allowed : 14.17 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1343 helix: 0.44 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : 0.75 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 99 TYR 0.013 0.002 TYR C 197 PHE 0.015 0.001 PHE B 149 TRP 0.006 0.001 TRP C 203 HIS 0.004 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00270 (10619) covalent geometry : angle 0.51217 (14348) hydrogen bonds : bond 0.03253 ( 671) hydrogen bonds : angle 3.87780 ( 1977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.394 Fit side-chains REVERT: A 23 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7357 (tt0) REVERT: B 54 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8662 (mmmm) REVERT: B 140 LYS cc_start: 0.8429 (ttmp) cc_final: 0.7953 (mtmm) REVERT: B 151 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7938 (mt-10) REVERT: B 167 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 94 LEU cc_start: 0.8380 (mp) cc_final: 0.7904 (tp) REVERT: D 33 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8349 (tp) REVERT: D 133 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7502 (mm-30) REVERT: D 151 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7670 (mt-10) REVERT: E 9 MET cc_start: 0.7921 (mtp) cc_final: 0.7647 (mtm) REVERT: E 64 LYS cc_start: 0.7932 (pttm) cc_final: 0.6544 (mmmt) REVERT: E 104 GLU cc_start: 0.8218 (mp0) cc_final: 0.7638 (mm-30) REVERT: E 117 ASP cc_start: 0.8134 (m-30) cc_final: 0.7910 (m-30) REVERT: E 140 LYS cc_start: 0.8733 (ptpt) cc_final: 0.8322 (mtmm) outliers start: 18 outliers final: 14 residues processed: 174 average time/residue: 0.1020 time to fit residues: 25.1041 Evaluate side-chains 175 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 33 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 32 HIS E 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110143 restraints weight = 11491.805| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.36 r_work: 0.2957 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10619 Z= 0.157 Angle : 0.550 6.695 14348 Z= 0.279 Chirality : 0.042 0.145 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.548 21.194 1402 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.90 % Allowed : 14.08 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1343 helix: 0.35 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : 0.86 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 99 TYR 0.016 0.002 TYR D 197 PHE 0.019 0.002 PHE B 149 TRP 0.006 0.001 TRP E 146 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00382 (10619) covalent geometry : angle 0.55026 (14348) hydrogen bonds : bond 0.03616 ( 671) hydrogen bonds : angle 4.00374 ( 1977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.302 Fit side-chains REVERT: A 23 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7424 (tt0) REVERT: B 54 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8713 (mmmm) REVERT: B 140 LYS cc_start: 0.8528 (ttmp) cc_final: 0.8007 (mtmm) REVERT: B 151 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7995 (mt-10) REVERT: B 167 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8516 (tp) REVERT: D 33 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8440 (tp) REVERT: D 133 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7547 (mm-30) REVERT: D 151 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7753 (mt-10) REVERT: E 64 LYS cc_start: 0.7994 (pttm) cc_final: 0.6596 (mmmt) REVERT: E 104 GLU cc_start: 0.8257 (mp0) cc_final: 0.7667 (mm-30) REVERT: E 140 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8367 (mtmm) REVERT: E 207 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8444 (tt) outliers start: 21 outliers final: 14 residues processed: 180 average time/residue: 0.1023 time to fit residues: 26.0629 Evaluate side-chains 180 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 130 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111793 restraints weight = 11457.150| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.35 r_work: 0.2998 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10619 Z= 0.129 Angle : 0.530 7.131 14348 Z= 0.269 Chirality : 0.041 0.140 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.481 20.841 1402 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.62 % Allowed : 15.07 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1343 helix: 0.46 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 99 TYR 0.016 0.002 TYR D 197 PHE 0.015 0.001 PHE B 149 TRP 0.006 0.001 TRP C 203 HIS 0.008 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00306 (10619) covalent geometry : angle 0.52959 (14348) hydrogen bonds : bond 0.03435 ( 671) hydrogen bonds : angle 3.95427 ( 1977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.387 Fit side-chains REVERT: A 23 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7397 (tt0) REVERT: B 54 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8641 (mmmm) REVERT: B 140 LYS cc_start: 0.8424 (ttmp) cc_final: 0.7921 (mtmm) REVERT: B 151 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7946 (mt-10) REVERT: B 167 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8514 (tp) REVERT: C 93 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8359 (tp) REVERT: D 16 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8103 (tp) REVERT: D 33 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8449 (tp) REVERT: D 133 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7451 (mm-30) REVERT: D 151 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7703 (mt-10) REVERT: E 64 LYS cc_start: 0.7932 (pttm) cc_final: 0.6531 (mmmt) REVERT: E 104 GLU cc_start: 0.8216 (mp0) cc_final: 0.7631 (mm-30) REVERT: E 140 LYS cc_start: 0.8719 (ptpt) cc_final: 0.8312 (mtmm) REVERT: E 207 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8367 (tt) outliers start: 18 outliers final: 12 residues processed: 174 average time/residue: 0.0984 time to fit residues: 24.0475 Evaluate side-chains 179 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111537 restraints weight = 11553.264| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.35 r_work: 0.3014 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10619 Z= 0.134 Angle : 0.531 7.141 14348 Z= 0.270 Chirality : 0.041 0.134 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.481 20.926 1402 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.90 % Allowed : 14.71 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1343 helix: 0.50 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : 0.94 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 99 TYR 0.016 0.002 TYR D 197 PHE 0.016 0.001 PHE B 149 TRP 0.005 0.001 TRP E 146 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00320 (10619) covalent geometry : angle 0.53122 (14348) hydrogen bonds : bond 0.03461 ( 671) hydrogen bonds : angle 3.95307 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.26 seconds wall clock time: 44 minutes 19.69 seconds (2659.69 seconds total)