Starting phenix.real_space_refine on Fri Sep 11 21:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wig_65993/09_2026/9wig_65993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wig_65993/09_2026/9wig_65993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wig_65993/09_2026/9wig_65993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wig_65993/09_2026/9wig_65993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wig_65993/09_2026/9wig_65993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wig_65993/09_2026/9wig_65993.map" } resolution = 3.93 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= 0.001 sd= 0.018 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 44 5.16 5 C 7236 2.51 5 N 1912 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11469 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1667 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 2 Chain: "B" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1561 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1589 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 9, 'TRANS': 205} Chain breaks: 1 Chain: "D" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1582 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 3 Chain: "E" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1402 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 4 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1357 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 14, 'TRANS': 166} Chain breaks: 3 Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2241 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 15, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.53, per 1000 atoms: 0.22 Number of scatterers: 11469 At special positions: 0 Unit cell: (79.21, 163.76, 184.23, 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 44 16.00 O 2277 8.00 N 1912 7.00 C 7236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 211 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 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 Links applied NAG-ASN " NAG G 401 " - " ASN G 61 " " NAG G 402 " - " ASN G 122 " " NAG G 403 " - " ASN G 165 " " NAG G 404 " - " ASN G 234 " " NAG G 405 " - " ASN G 282 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 558.5 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 36 sheets defined 4.5% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.840A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.010A pdb=" N GLU B 84 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.791A pdb=" N THR C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 182 through 189 removed outlier: 3.513A pdb=" N TYR D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 124 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 5.909A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 98 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 113 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 removed outlier: 5.909A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 73 removed outlier: 3.929A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 106 removed outlier: 9.239A pdb=" N LEU G 223 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS G 207 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS G 187 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE G 194 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL G 90 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA G 27 " --> pdb=" O TRP G 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.441A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 147 through 152 removed outlier: 3.670A pdb=" N VAL A 195 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.527A pdb=" N CYS A 207 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.924A pdb=" N THR B 108 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.924A pdb=" N THR B 108 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AB3, first strand: chain 'B' and resid 118 through 122 removed outlier: 3.582A pdb=" N VAL B 137 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.648A pdb=" N ALA B 151 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN B 198 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR B 195 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 210 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 197 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 208 " --> pdb=" O CYS B 197 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 199 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 206 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS B 201 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.604A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.737A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.676A pdb=" N GLY C 154 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR C 191 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER C 192 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA C 183 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 194 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.593A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.593A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 90 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.764A pdb=" N CYS D 23 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 118 removed outlier: 4.009A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER D 131 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 181 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 173 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER D 176 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER D 162 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.076A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.559A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 124 through 125 removed outlier: 5.744A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 155 through 157 removed outlier: 3.565A pdb=" N VAL E 202 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'F' and resid 44 through 48 removed outlier: 5.632A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 114 through 117 removed outlier: 4.044A pdb=" N SER F 114 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER F 137 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 116 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 135 " --> pdb=" O THR F 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'F' and resid 144 through 145 removed outlier: 3.655A pdb=" N THR F 145 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 196 " --> pdb=" O THR F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 165 through 166 removed outlier: 3.598A pdb=" N ALA F 173 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 48 through 55 removed outlier: 4.536A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.533A pdb=" N PHE G 238 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU G 241 " --> pdb=" O GLY G 103 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 172 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL G 130 " --> pdb=" O PHE G 168 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE G 168 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 143 through 146 Processing sheet with id=AD9, first strand: chain 'G' and resid 245 through 246 340 hydrogen bonds defined for protein. 813 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: 1.86 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 11675 1.56 - 1.89: 61 1.89 - 2.22: 0 2.22 - 2.56: 0 2.56 - 2.89: 1 Bond restraints: 11737 Sorted by residual: bond pdb=" C THR C 105 " pdb=" N GLU C 107 " ideal model delta sigma weight residual 1.332 2.888 -1.556 1.40e-02 5.10e+03 1.23e+04 bond pdb=" C GLN E 39 " pdb=" N ALA E 40 " ideal model delta sigma weight residual 1.329 1.381 -0.052 1.86e-02 2.89e+03 7.89e+00 bond pdb=" CB PRO F 58 " pdb=" CG PRO F 58 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.53e+00 bond pdb=" CA GLY E 101 " pdb=" C GLY E 101 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.22e+00 bond pdb=" C1 NAG G 404 " pdb=" O5 NAG G 404 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 11732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.63: 15969 10.63 - 21.26: 2 21.26 - 31.89: 1 31.89 - 42.51: 0 42.51 - 53.14: 1 Bond angle restraints: 15973 Sorted by residual: angle pdb=" O THR C 105 " pdb=" C THR C 105 " pdb=" N GLU C 107 " ideal model delta sigma weight residual 122.59 69.45 53.14 1.33e+00 5.65e-01 1.60e+03 angle pdb=" C THR C 105 " pdb=" N GLU C 107 " pdb=" CA GLU C 107 " ideal model delta sigma weight residual 121.54 144.25 -22.71 1.91e+00 2.74e-01 1.41e+02 angle pdb=" CA THR C 105 " pdb=" C THR C 105 " pdb=" N GLU C 107 " ideal model delta sigma weight residual 116.84 132.37 -15.53 1.71e+00 3.42e-01 8.24e+01 angle pdb=" CA LYS D 39 " pdb=" CB LYS D 39 " pdb=" CG LYS D 39 " ideal model delta sigma weight residual 114.10 122.44 -8.34 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CB LYS E 43 " pdb=" CG LYS E 43 " pdb=" CD LYS E 43 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 ... (remaining 15968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 6154 22.23 - 44.47: 747 44.47 - 66.70: 92 66.70 - 88.93: 21 88.93 - 111.16: 1 Dihedral angle restraints: 7015 sinusoidal: 2712 harmonic: 4303 Sorted by residual: dihedral pdb=" CA THR C 105 " pdb=" C THR C 105 " pdb=" N GLU C 107 " pdb=" CA GLU C 107 " ideal model delta harmonic sigma weight residual 180.00 68.84 111.16 0 5.00e+00 4.00e-02 4.94e+02 dihedral pdb=" CB CYS G 131 " pdb=" SG CYS G 131 " pdb=" SG CYS G 166 " pdb=" CB CYS G 166 " ideal model delta sinusoidal sigma weight residual 93.00 36.76 56.24 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CB CYS G 15 " pdb=" SG CYS G 15 " pdb=" SG CYS G 136 " pdb=" CB CYS G 136 " ideal model delta sinusoidal sigma weight residual 93.00 149.14 -56.14 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 7012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1161 0.034 - 0.068: 414 0.068 - 0.102: 146 0.102 - 0.136: 79 0.136 - 0.170: 13 Chirality restraints: 1813 Sorted by residual: chirality pdb=" C2 NAG G 402 " pdb=" C1 NAG G 402 " pdb=" C3 NAG G 402 " pdb=" N2 NAG G 402 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA PRO F 141 " pdb=" N PRO F 141 " pdb=" C PRO F 141 " pdb=" CB PRO F 141 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE F 57 " pdb=" N ILE F 57 " pdb=" C ILE F 57 " pdb=" CB ILE F 57 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1810 not shown) Planarity restraints: 2033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 105 " 0.189 2.00e-02 2.50e+03 2.34e-01 5.46e+02 pdb=" C THR C 105 " -0.396 2.00e-02 2.50e+03 pdb=" O THR C 105 " 0.150 2.00e-02 2.50e+03 pdb=" N GLU C 107 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 118 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO F 119 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 119 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 119 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 140 " -0.049 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO F 141 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 141 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 141 " -0.039 5.00e-02 4.00e+02 ... (remaining 2030 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 188 2.64 - 3.21: 10169 3.21 - 3.77: 16711 3.77 - 4.34: 22117 4.34 - 4.90: 36052 Nonbonded interactions: 85237 Sorted by model distance: nonbonded pdb=" OG SER B 31 " pdb=" OD1 ASN B 32 " model vdw 2.080 3.040 nonbonded pdb=" OD2 ASP A 112 " pdb=" OH TYR B 37 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR G 37 " pdb=" NZ LYS G 195 " model vdw 2.208 3.120 nonbonded pdb=" O PRO G 85 " pdb=" OH TYR G 269 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR C 28 " pdb=" OE1 GLU C 31 " model vdw 2.221 3.040 ... (remaining 85232 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 0.015 1.556 11756 Z= 1.036 Angle : 0.907 53.143 16016 Z= 0.524 Chirality : 0.045 0.170 1813 Planarity : 0.008 0.234 2028 Dihedral : 17.719 111.164 4219 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.54 % Favored : 93.39 % Rotamer: Outliers : 0.94 % Allowed : 35.38 % Favored : 63.68 % 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: -1.08 (0.21), residues: 1452 helix: -1.79 (0.68), residues: 40 sheet: 0.19 (0.22), residues: 561 loop : -1.34 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 67 TYR 0.032 0.001 TYR F 140 PHE 0.027 0.001 PHE C 137 TRP 0.027 0.002 TRP C 169 HIS 0.013 0.002 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.01476 / 1.04 (11737) covalent geometry : angle 0.90256 / 0.52 (15973) SS BOND : bond 0.00400 / 0.22 ( 14) SS BOND : angle 1.29205 / 1.02 ( 28) hydrogen bonds : bond 0.14392 / 9.45 ( 321) hydrogen bonds : angle 8.03675 / 5.74 ( 813) link_NAG-ASN : bond 0.00312 / 0.15 ( 5) link_NAG-ASN : angle 2.90777 / 1.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 316 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6609 (tpp) cc_final: 0.6218 (tpp) REVERT: C 80 TYR cc_start: 0.6040 (m-80) cc_final: 0.5709 (m-80) REVERT: F 53 ARG cc_start: 0.6337 (mtm110) cc_final: 0.5930 (mtm110) REVERT: G 133 PHE cc_start: 0.7817 (m-80) cc_final: 0.7612 (m-10) REVERT: G 152 TRP cc_start: 0.6918 (m100) cc_final: 0.6703 (m100) REVERT: G 192 PHE cc_start: 0.7243 (m-80) cc_final: 0.6824 (m-80) outliers start: 12 outliers final: 5 residues processed: 319 average time/residue: 0.1079 time to fit residues: 48.7890 Evaluate side-chains 315 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 310 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 94 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN G 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.143372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116265 restraints weight = 25389.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119543 restraints weight = 14121.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121684 restraints weight = 9158.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123099 restraints weight = 6657.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124018 restraints weight = 5281.719| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11756 Z= 0.131 Angle : 0.670 9.285 16016 Z= 0.343 Chirality : 0.044 0.249 1813 Planarity : 0.006 0.073 2028 Dihedral : 5.748 57.909 1708 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 5.35 % Allowed : 30.97 % Favored : 63.68 % 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: -1.07 (0.21), residues: 1454 helix: -1.64 (0.63), residues: 47 sheet: 0.22 (0.22), residues: 541 loop : -1.31 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.017 0.001 TYR F 140 PHE 0.019 0.001 PHE C 137 TRP 0.016 0.001 TRP C 169 HIS 0.012 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11737) covalent geometry : angle 0.66441 / 0.34 (15973) SS BOND : bond 0.00474 / 0.27 ( 14) SS BOND : angle 1.02289 / 0.70 ( 28) hydrogen bonds : bond 0.03719 / 2.42 ( 321) hydrogen bonds : angle 6.92538 / 4.94 ( 813) link_NAG-ASN : bond 0.00342 / 0.17 ( 5) link_NAG-ASN : angle 2.68223 / 1.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 322 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.7641 (p) cc_final: 0.7362 (t) REVERT: A 119 MET cc_start: 0.6498 (tpp) cc_final: 0.6275 (tpp) REVERT: B 36 TRP cc_start: 0.7599 (m100) cc_final: 0.6035 (m100) REVERT: B 112 GLN cc_start: 0.8111 (tp40) cc_final: 0.7672 (tp-100) REVERT: C 80 TYR cc_start: 0.6157 (m-80) cc_final: 0.5824 (m-80) REVERT: D 39 LYS cc_start: 0.7246 (tptt) cc_final: 0.6945 (tptp) REVERT: D 79 GLN cc_start: 0.6271 (mp10) cc_final: 0.5957 (mp10) REVERT: F 53 ARG cc_start: 0.6639 (mtm110) cc_final: 0.6239 (mtm110) REVERT: F 163 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7382 (p) REVERT: G 105 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7273 (tp) outliers start: 68 outliers final: 43 residues processed: 356 average time/residue: 0.1027 time to fit residues: 52.2303 Evaluate side-chains 364 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 TRP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 90 optimal weight: 0.1980 chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN E 175 GLN F 65 ASN G 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.117936 restraints weight = 25446.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121185 restraints weight = 14115.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123336 restraints weight = 9157.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124729 restraints weight = 6629.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125663 restraints weight = 5242.142| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11756 Z= 0.104 Angle : 0.626 9.424 16016 Z= 0.316 Chirality : 0.044 0.251 1813 Planarity : 0.005 0.061 2028 Dihedral : 5.265 59.948 1704 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 5.35 % Allowed : 30.58 % Favored : 64.07 % 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: -0.93 (0.21), residues: 1454 helix: -1.25 (0.69), residues: 41 sheet: 0.29 (0.22), residues: 546 loop : -1.23 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.015 0.001 TYR F 140 PHE 0.014 0.001 PHE G 192 TRP 0.016 0.001 TRP C 169 HIS 0.010 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11737) covalent geometry : angle 0.62105 / 0.31 (15973) SS BOND : bond 0.00326 / 0.19 ( 14) SS BOND : angle 0.75525 / 0.52 ( 28) hydrogen bonds : bond 0.03127 / 2.07 ( 321) hydrogen bonds : angle 6.40594 / 4.51 ( 813) link_NAG-ASN : bond 0.00180 / 0.09 ( 5) link_NAG-ASN : angle 2.47486 / 1.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.7613 (p) cc_final: 0.7400 (t) REVERT: A 85 ARG cc_start: 0.7018 (tmm-80) cc_final: 0.6682 (ttp80) REVERT: A 119 MET cc_start: 0.6391 (tpp) cc_final: 0.6071 (tpp) REVERT: C 95 TYR cc_start: 0.7682 (m-80) cc_final: 0.7142 (m-80) REVERT: D 79 GLN cc_start: 0.6562 (mp10) cc_final: 0.6288 (mp10) REVERT: D 86 TYR cc_start: 0.7691 (m-10) cc_final: 0.7447 (m-10) REVERT: E 89 GLU cc_start: 0.7113 (mp0) cc_final: 0.6669 (mp0) REVERT: F 81 ASP cc_start: 0.7042 (m-30) cc_final: 0.6803 (m-30) REVERT: G 105 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7256 (mm) REVERT: G 192 PHE cc_start: 0.7186 (m-80) cc_final: 0.6671 (m-80) outliers start: 68 outliers final: 38 residues processed: 359 average time/residue: 0.1042 time to fit residues: 53.3084 Evaluate side-chains 350 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 41 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.0060 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN F 49 GLN G 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.142745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115710 restraints weight = 25464.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119010 restraints weight = 14133.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121125 restraints weight = 9157.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122551 restraints weight = 6646.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123490 restraints weight = 5270.001| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11756 Z= 0.144 Angle : 0.660 9.486 16016 Z= 0.337 Chirality : 0.044 0.232 1813 Planarity : 0.005 0.065 2028 Dihedral : 5.233 55.234 1702 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 7.31 % Allowed : 28.77 % Favored : 63.92 % 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: -0.97 (0.21), residues: 1454 helix: -1.18 (0.69), residues: 41 sheet: 0.37 (0.22), residues: 519 loop : -1.29 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 55 TYR 0.015 0.002 TYR A 95 PHE 0.025 0.002 PHE C 137 TRP 0.019 0.001 TRP C 169 HIS 0.013 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (11737) covalent geometry : angle 0.65471 / 0.34 (15973) SS BOND : bond 0.00572 / 0.32 ( 14) SS BOND : angle 1.03501 / 0.71 ( 28) hydrogen bonds : bond 0.03612 / 2.34 ( 321) hydrogen bonds : angle 6.47762 / 4.56 ( 813) link_NAG-ASN : bond 0.00510 / 0.24 ( 5) link_NAG-ASN : angle 2.61679 / 1.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.7661 (p) cc_final: 0.7451 (t) REVERT: A 85 ARG cc_start: 0.7117 (tmm-80) cc_final: 0.6757 (ttp80) REVERT: A 119 MET cc_start: 0.6350 (tpp) cc_final: 0.5695 (tpp) REVERT: B 36 TRP cc_start: 0.7552 (m100) cc_final: 0.6130 (m100) REVERT: C 95 TYR cc_start: 0.7744 (m-80) cc_final: 0.7257 (m-80) REVERT: D 79 GLN cc_start: 0.6630 (mp10) cc_final: 0.6338 (mp10) REVERT: E 98 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.4962 (ttp80) REVERT: F 49 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: F 52 LYS cc_start: 0.7669 (mppt) cc_final: 0.7464 (mppt) REVERT: F 78 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6625 (tm-30) REVERT: G 105 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7190 (tp) REVERT: G 152 TRP cc_start: 0.7165 (m100) cc_final: 0.6947 (m100) outliers start: 93 outliers final: 71 residues processed: 365 average time/residue: 0.1022 time to fit residues: 53.2457 Evaluate side-chains 378 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 304 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 73 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN F 68 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.142033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114899 restraints weight = 25256.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118177 restraints weight = 14064.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120321 restraints weight = 9125.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121684 restraints weight = 6633.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122643 restraints weight = 5276.830| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11756 Z= 0.158 Angle : 0.678 9.495 16016 Z= 0.345 Chirality : 0.044 0.231 1813 Planarity : 0.005 0.061 2028 Dihedral : 5.352 55.409 1702 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 7.31 % Allowed : 28.62 % Favored : 64.07 % 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: -0.97 (0.21), residues: 1454 helix: -1.23 (0.70), residues: 41 sheet: 0.32 (0.23), residues: 525 loop : -1.27 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 55 TYR 0.016 0.002 TYR A 95 PHE 0.022 0.002 PHE G 192 TRP 0.018 0.002 TRP C 169 HIS 0.010 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11737) covalent geometry : angle 0.67258 / 0.34 (15973) SS BOND : bond 0.00608 / 0.38 ( 14) SS BOND : angle 1.20333 / 0.85 ( 28) hydrogen bonds : bond 0.03738 / 2.43 ( 321) hydrogen bonds : angle 6.53160 / 4.59 ( 813) link_NAG-ASN : bond 0.00549 / 0.26 ( 5) link_NAG-ASN : angle 2.44233 / 1.43 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 316 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.7657 (p) cc_final: 0.7444 (t) REVERT: A 119 MET cc_start: 0.6300 (tpp) cc_final: 0.5634 (tpp) REVERT: B 112 GLN cc_start: 0.8156 (tp40) cc_final: 0.7776 (tp-100) REVERT: B 190 LYS cc_start: 0.2519 (OUTLIER) cc_final: 0.2279 (mttp) REVERT: C 95 TYR cc_start: 0.7723 (m-80) cc_final: 0.7361 (m-80) REVERT: E 98 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.4973 (ttp80) REVERT: G 101 ILE cc_start: 0.7628 (pt) cc_final: 0.7379 (mt) REVERT: G 105 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7172 (tp) outliers start: 93 outliers final: 72 residues processed: 369 average time/residue: 0.0999 time to fit residues: 52.3079 Evaluate side-chains 385 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 310 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 38 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 160 GLN E 175 GLN G 30 ASN G 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.142935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115808 restraints weight = 25287.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119116 restraints weight = 14049.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121256 restraints weight = 9095.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122686 restraints weight = 6603.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123617 restraints weight = 5221.542| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11756 Z= 0.125 Angle : 0.659 9.413 16016 Z= 0.331 Chirality : 0.044 0.243 1813 Planarity : 0.005 0.061 2028 Dihedral : 5.198 56.082 1702 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.91 % Favored : 94.02 % Rotamer: Outliers : 7.15 % Allowed : 29.48 % Favored : 63.36 % 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: -0.93 (0.21), residues: 1454 helix: -1.18 (0.71), residues: 41 sheet: 0.34 (0.23), residues: 522 loop : -1.24 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 55 TYR 0.015 0.001 TYR A 95 PHE 0.018 0.001 PHE G 192 TRP 0.019 0.001 TRP C 169 HIS 0.009 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (11737) covalent geometry : angle 0.65403 / 0.33 (15973) SS BOND : bond 0.00460 / 0.26 ( 14) SS BOND : angle 0.97228 / 0.65 ( 28) hydrogen bonds : bond 0.03332 / 2.18 ( 321) hydrogen bonds : angle 6.33452 / 4.43 ( 813) link_NAG-ASN : bond 0.00357 / 0.17 ( 5) link_NAG-ASN : angle 2.48586 / 1.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 313 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 SER cc_start: 0.4947 (m) cc_final: 0.4600 (p) REVERT: B 112 GLN cc_start: 0.8158 (tp40) cc_final: 0.7837 (tp-100) REVERT: B 190 LYS cc_start: 0.2630 (OUTLIER) cc_final: 0.2290 (mttp) REVERT: C 95 TYR cc_start: 0.7707 (m-80) cc_final: 0.7269 (m-80) REVERT: D 79 GLN cc_start: 0.6385 (mp10) cc_final: 0.6108 (mp10) REVERT: F 49 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: F 78 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6522 (tm-30) REVERT: G 105 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7209 (mm) REVERT: G 192 PHE cc_start: 0.7249 (m-80) cc_final: 0.6920 (m-80) outliers start: 91 outliers final: 73 residues processed: 375 average time/residue: 0.1068 time to fit residues: 57.3085 Evaluate side-chains 382 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 TRP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 238 PHE Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 130 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN E 175 GLN E 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.141196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114089 restraints weight = 25155.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117359 restraints weight = 14013.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119515 restraints weight = 9124.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120903 restraints weight = 6627.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121845 restraints weight = 5253.035| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11756 Z= 0.178 Angle : 0.715 9.475 16016 Z= 0.362 Chirality : 0.045 0.223 1813 Planarity : 0.005 0.057 2028 Dihedral : 5.471 54.883 1702 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer: Outliers : 7.63 % Allowed : 29.87 % Favored : 62.50 % 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: -1.02 (0.21), residues: 1454 helix: -1.24 (0.70), residues: 41 sheet: 0.37 (0.23), residues: 504 loop : -1.33 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 55 TYR 0.015 0.002 TYR A 95 PHE 0.026 0.002 PHE G 192 TRP 0.023 0.002 TRP C 169 HIS 0.010 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (11737) covalent geometry : angle 0.70993 / 0.36 (15973) SS BOND : bond 0.00596 / 0.33 ( 14) SS BOND : angle 1.39541 / 1.02 ( 28) hydrogen bonds : bond 0.03938 / 2.54 ( 321) hydrogen bonds : angle 6.54119 / 4.58 ( 813) link_NAG-ASN : bond 0.00726 / 0.35 ( 5) link_NAG-ASN : angle 2.44965 / 1.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 315 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 TRP cc_start: 0.7584 (m100) cc_final: 0.7069 (m100) REVERT: B 190 LYS cc_start: 0.2623 (OUTLIER) cc_final: 0.2373 (mttp) REVERT: C 95 TYR cc_start: 0.7724 (m-80) cc_final: 0.7405 (m-80) REVERT: C 215 HIS cc_start: 0.6746 (t70) cc_final: 0.6384 (t70) REVERT: D 54 ARG cc_start: 0.6820 (ptp-170) cc_final: 0.6272 (ptt180) REVERT: D 79 GLN cc_start: 0.6391 (mp10) cc_final: 0.6149 (mp10) REVERT: E 43 LYS cc_start: 0.7360 (mmmt) cc_final: 0.7130 (mmmt) REVERT: E 98 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.4937 (ttp80) REVERT: F 44 VAL cc_start: 0.8445 (t) cc_final: 0.8163 (p) REVERT: G 101 ILE cc_start: 0.7635 (pt) cc_final: 0.7367 (mt) REVERT: G 105 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7239 (mm) outliers start: 97 outliers final: 81 residues processed: 372 average time/residue: 0.1100 time to fit residues: 57.7883 Evaluate side-chains 388 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 304 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 TRP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 32 PHE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 238 PHE Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 127 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 48 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 175 GLN G 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.142462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115447 restraints weight = 25028.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118727 restraints weight = 13944.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120906 restraints weight = 9048.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122306 restraints weight = 6553.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123191 restraints weight = 5194.621| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11756 Z= 0.134 Angle : 0.697 9.436 16016 Z= 0.350 Chirality : 0.044 0.241 1813 Planarity : 0.005 0.059 2028 Dihedral : 5.324 56.131 1702 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 7.23 % Allowed : 31.05 % Favored : 61.71 % 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: -1.00 (0.21), residues: 1454 helix: -1.29 (0.69), residues: 41 sheet: 0.43 (0.23), residues: 505 loop : -1.35 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 55 TYR 0.015 0.001 TYR A 95 PHE 0.021 0.001 PHE G 192 TRP 0.024 0.001 TRP C 169 HIS 0.013 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11737) covalent geometry : angle 0.69109 / 0.35 (15973) SS BOND : bond 0.00524 / 0.28 ( 14) SS BOND : angle 1.34182 / 0.98 ( 28) hydrogen bonds : bond 0.03469 / 2.27 ( 321) hydrogen bonds : angle 6.34414 / 4.43 ( 813) link_NAG-ASN : bond 0.00428 / 0.21 ( 5) link_NAG-ASN : angle 2.51973 / 1.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 310 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 TRP cc_start: 0.7551 (m100) cc_final: 0.6867 (m100) REVERT: B 190 LYS cc_start: 0.2636 (OUTLIER) cc_final: 0.2356 (mttp) REVERT: C 95 TYR cc_start: 0.7691 (m-80) cc_final: 0.7276 (m-80) REVERT: C 215 HIS cc_start: 0.6720 (t70) cc_final: 0.6351 (t70) REVERT: E 98 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.4808 (ttp80) REVERT: F 44 VAL cc_start: 0.8411 (t) cc_final: 0.8122 (p) REVERT: F 78 GLN cc_start: 0.6924 (tm-30) cc_final: 0.6596 (tm-30) REVERT: G 105 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7185 (mm) REVERT: G 192 PHE cc_start: 0.7239 (m-80) cc_final: 0.6901 (m-80) REVERT: G 281 GLU cc_start: 0.6298 (pm20) cc_final: 0.5934 (pm20) outliers start: 92 outliers final: 78 residues processed: 366 average time/residue: 0.1045 time to fit residues: 54.3582 Evaluate side-chains 388 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 307 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 TRP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 32 PHE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN D 37 GLN E 175 GLN ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.140815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113766 restraints weight = 25013.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116999 restraints weight = 14001.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119105 restraints weight = 9143.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120548 restraints weight = 6666.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121505 restraints weight = 5287.674| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11756 Z= 0.192 Angle : 0.748 10.335 16016 Z= 0.381 Chirality : 0.045 0.217 1813 Planarity : 0.005 0.057 2028 Dihedral : 5.597 54.863 1702 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 7.39 % Allowed : 30.97 % Favored : 61.64 % 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 (0.21), residues: 1454 helix: -1.28 (0.70), residues: 41 sheet: 0.29 (0.22), residues: 548 loop : -1.43 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 55 TYR 0.016 0.002 TYR G 145 PHE 0.028 0.002 PHE G 192 TRP 0.027 0.002 TRP C 169 HIS 0.010 0.002 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (11737) covalent geometry : angle 0.74170 / 0.38 (15973) SS BOND : bond 0.00651 / 0.35 ( 14) SS BOND : angle 1.76906 / 1.34 ( 28) hydrogen bonds : bond 0.04059 / 2.61 ( 321) hydrogen bonds : angle 6.56306 / 4.60 ( 813) link_NAG-ASN : bond 0.00736 / 0.35 ( 5) link_NAG-ASN : angle 2.47394 / 1.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 314 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ASN cc_start: 0.4997 (OUTLIER) cc_final: 0.4535 (p0) REVERT: B 190 LYS cc_start: 0.2643 (OUTLIER) cc_final: 0.2363 (mttp) REVERT: C 95 TYR cc_start: 0.7725 (m-80) cc_final: 0.7396 (m-80) REVERT: C 125 THR cc_start: 0.7116 (m) cc_final: 0.6524 (t) REVERT: C 166 THR cc_start: 0.7647 (m) cc_final: 0.7334 (p) REVERT: C 215 HIS cc_start: 0.6866 (t70) cc_final: 0.6491 (t70) REVERT: D 38 GLN cc_start: 0.6783 (tp40) cc_final: 0.6407 (tp40) REVERT: D 166 GLN cc_start: 0.5461 (tt0) cc_final: 0.4841 (pt0) REVERT: E 98 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.4780 (ttp80) REVERT: F 44 VAL cc_start: 0.8472 (t) cc_final: 0.8192 (p) REVERT: F 78 GLN cc_start: 0.6944 (tm-30) cc_final: 0.6569 (tm-30) REVERT: G 101 ILE cc_start: 0.7670 (pt) cc_final: 0.7401 (mt) REVERT: G 105 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7156 (tp) REVERT: G 192 PHE cc_start: 0.7227 (m-80) cc_final: 0.6841 (m-80) REVERT: G 224 GLU cc_start: 0.7221 (mp0) cc_final: 0.6869 (mp0) outliers start: 94 outliers final: 78 residues processed: 370 average time/residue: 0.1116 time to fit residues: 58.4331 Evaluate side-chains 394 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 312 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 TRP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 32 PHE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 238 PHE Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 109 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 117 optimal weight: 0.0050 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.3292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN B 132 ASN G 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116559 restraints weight = 25289.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119798 restraints weight = 14058.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121945 restraints weight = 9137.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123372 restraints weight = 6632.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124297 restraints weight = 5240.856| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11756 Z= 0.123 Angle : 0.712 9.673 16016 Z= 0.356 Chirality : 0.044 0.250 1813 Planarity : 0.005 0.059 2028 Dihedral : 5.274 56.447 1702 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 5.42 % Allowed : 33.02 % Favored : 61.56 % 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: -0.98 (0.21), residues: 1454 helix: -1.18 (0.71), residues: 41 sheet: 0.43 (0.23), residues: 520 loop : -1.36 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 55 TYR 0.015 0.001 TYR A 95 PHE 0.022 0.001 PHE G 168 TRP 0.025 0.001 TRP C 169 HIS 0.008 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (11737) covalent geometry : angle 0.70662 / 0.35 (15973) SS BOND : bond 0.00486 / 0.27 ( 14) SS BOND : angle 1.27788 / 1.00 ( 28) hydrogen bonds : bond 0.03210 / 2.10 ( 321) hydrogen bonds : angle 6.18820 / 4.32 ( 813) link_NAG-ASN : bond 0.00241 / 0.12 ( 5) link_NAG-ASN : angle 2.45474 / 1.47 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 TRP cc_start: 0.7556 (m100) cc_final: 0.6278 (m100) REVERT: B 132 ASN cc_start: 0.4671 (OUTLIER) cc_final: 0.4199 (p0) REVERT: C 67 ARG cc_start: 0.4721 (ttm110) cc_final: 0.4434 (mtm-85) REVERT: C 95 TYR cc_start: 0.7655 (m-80) cc_final: 0.7245 (m-80) REVERT: C 166 THR cc_start: 0.7608 (m) cc_final: 0.7314 (p) REVERT: C 215 HIS cc_start: 0.6728 (t70) cc_final: 0.6372 (t70) REVERT: D 166 GLN cc_start: 0.5306 (tt0) cc_final: 0.4774 (pt0) REVERT: F 44 VAL cc_start: 0.8376 (t) cc_final: 0.8110 (p) REVERT: F 78 GLN cc_start: 0.6874 (tm-30) cc_final: 0.6579 (tm-30) REVERT: G 105 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7152 (tp) REVERT: G 121 ASN cc_start: 0.6916 (t0) cc_final: 0.6669 (t0) REVERT: G 192 PHE cc_start: 0.7263 (m-80) cc_final: 0.6866 (m-80) REVERT: G 224 GLU cc_start: 0.7083 (mp0) cc_final: 0.6722 (mp0) outliers start: 69 outliers final: 60 residues processed: 357 average time/residue: 0.1117 time to fit residues: 56.1703 Evaluate side-chains 369 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 TRP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 238 PHE Chi-restraints excluded: chain G residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 135 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 99 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.142680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115787 restraints weight = 25221.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119001 restraints weight = 14091.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121165 restraints weight = 9191.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.122592 restraints weight = 6675.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123480 restraints weight = 5284.249| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11756 Z= 0.136 Angle : 0.713 11.281 16016 Z= 0.358 Chirality : 0.044 0.236 1813 Planarity : 0.005 0.058 2028 Dihedral : 5.283 55.832 1702 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 5.58 % Allowed : 32.78 % Favored : 61.64 % 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: -0.93 (0.21), residues: 1454 helix: -1.17 (0.71), residues: 41 sheet: 0.49 (0.23), residues: 522 loop : -1.35 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 55 TYR 0.014 0.001 TYR A 95 PHE 0.022 0.002 PHE G 168 TRP 0.029 0.002 TRP C 169 HIS 0.009 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11737) covalent geometry : angle 0.70797 / 0.36 (15973) SS BOND : bond 0.00540 / 0.29 ( 14) SS BOND : angle 1.45623 / 1.13 ( 28) hydrogen bonds : bond 0.03391 / 2.20 ( 321) hydrogen bonds : angle 6.19205 / 4.32 ( 813) link_NAG-ASN : bond 0.00423 / 0.20 ( 5) link_NAG-ASN : angle 2.27289 / 1.34 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.92 seconds wall clock time: 42 minutes 22.85 seconds (2542.85 seconds total)