Starting phenix.real_space_refine on Thu Jan 15 08:53:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdt_34680/01_2026/8hdt_34680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdt_34680/01_2026/8hdt_34680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hdt_34680/01_2026/8hdt_34680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdt_34680/01_2026/8hdt_34680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hdt_34680/01_2026/8hdt_34680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdt_34680/01_2026/8hdt_34680.map" } resolution = 3.17 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= 0.006 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 119 5.16 5 C 15652 2.51 5 N 4263 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24710 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain: "B" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain: "E" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain: "G" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "H" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "I" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "J" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "K" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "L" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "M" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1207 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 9, 'TRANS': 156} Chain: "N" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2323 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Time building chain proxies: 5.65, per 1000 atoms: 0.23 Number of scatterers: 24710 At special positions: 0 Unit cell: (205.639, 205.639, 141.82, 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 119 16.00 O 4676 8.00 N 4263 7.00 C 15652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 60 sheets defined 17.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.524A pdb=" N MET A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 137 removed outlier: 3.613A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 removed outlier: 3.945A pdb=" N GLY A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.867A pdb=" N GLN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.507A pdb=" N GLN B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 138 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.850A pdb=" N GLY B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 179 " --> pdb=" O PHE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 217 through 226 removed outlier: 4.130A pdb=" N ARG B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 114 through 137 removed outlier: 3.557A pdb=" N GLU C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 186 removed outlier: 3.916A pdb=" N GLY C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 114 through 137 removed outlier: 3.543A pdb=" N GLU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 186 removed outlier: 3.921A pdb=" N GLY D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE D 179 " --> pdb=" O PHE D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.679A pdb=" N ASN E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 106' Processing helix chain 'E' and resid 114 through 137 removed outlier: 3.729A pdb=" N ALA E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN E 121 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 186 removed outlier: 3.871A pdb=" N GLY E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'E' and resid 218 through 220 No H-bonds generated for 'chain 'E' and resid 218 through 220' Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 114 through 137 Processing helix chain 'F' and resid 167 through 186 removed outlier: 3.855A pdb=" N GLY F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE F 179 " --> pdb=" O PHE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 226 through 232 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'N' and resid 102 through 110 removed outlier: 3.548A pdb=" N MET N 110 " --> pdb=" O ASN N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 137 removed outlier: 3.749A pdb=" N ALA N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU N 122 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA N 123 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 184 removed outlier: 3.758A pdb=" N GLY N 178 " --> pdb=" O ASP N 174 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE N 179 " --> pdb=" O PHE N 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER N 184 " --> pdb=" O THR N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 205 removed outlier: 3.627A pdb=" N GLN N 203 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE N 204 " --> pdb=" O ALA N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 224 removed outlier: 3.747A pdb=" N LEU N 222 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG N 224 " --> pdb=" O GLN N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 233 removed outlier: 3.864A pdb=" N ALA N 230 " --> pdb=" O ASN N 226 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU N 231 " --> pdb=" O VAL N 227 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR N 232 " --> pdb=" O TYR N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 302 No H-bonds generated for 'chain 'N' and resid 300 through 302' Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.245A pdb=" N TYR A 24 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR B 59 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A 30 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY B 63 " --> pdb=" O TYR A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.245A pdb=" N TYR A 24 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR B 59 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 90 removed outlier: 6.726A pdb=" N THR A 55 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLU E 26 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP A 57 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY E 28 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A 59 " --> pdb=" O GLY E 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 68 through 69 removed outlier: 4.066A pdb=" N GLU A 68 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG E 292 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG E 272 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.658A pdb=" N HIS A 92 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 68 " --> pdb=" O GLY A 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 157 removed outlier: 6.514A pdb=" N THR A 154 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASP A 308 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 156 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG A 254 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 195 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET A 241 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 197 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 25 removed outlier: 7.005A pdb=" N TYR B 24 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N TYR C 59 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR B 30 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N GLY C 63 " --> pdb=" O TYR B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 24 through 25 removed outlier: 7.005A pdb=" N TYR B 24 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N TYR C 59 " --> pdb=" O TYR B 24 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'B' and resid 271 through 275 removed outlier: 3.549A pdb=" N MET B 271 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS B 273 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 290 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 68 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AB5, first strand: chain 'B' and resid 154 through 157 removed outlier: 4.294A pdb=" N THR B 154 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ARG B 254 " --> pdb=" O PRO B 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 31 removed outlier: 6.399A pdb=" N TYR C 24 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR D 59 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLU C 26 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N MET D 61 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N GLY C 28 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 14.893A pdb=" N GLY D 63 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 13.371A pdb=" N TYR C 30 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 275 removed outlier: 3.728A pdb=" N MET C 271 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 292 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N HIS C 273 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 290 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 68 " --> pdb=" O GLY C 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AC1, first strand: chain 'C' and resid 154 through 157 removed outlier: 4.359A pdb=" N THR C 154 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ARG C 254 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 195 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET C 241 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 197 " --> pdb=" O MET C 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 23 through 31 removed outlier: 6.541A pdb=" N TYR D 24 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR F 59 " --> pdb=" O TYR D 24 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU D 26 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 11.354A pdb=" N MET F 61 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 12.747A pdb=" N GLY D 28 " --> pdb=" O MET F 61 " (cutoff:3.500A) removed outlier: 14.935A pdb=" N GLY F 63 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 13.371A pdb=" N TYR D 30 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL F 64 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC4, first strand: chain 'D' and resid 271 through 275 removed outlier: 5.287A pdb=" N ARG D 272 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG D 292 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 68 " --> pdb=" O GLY D 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AC6, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.309A pdb=" N THR D 154 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ARG D 254 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 195 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET D 241 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 197 " --> pdb=" O MET D 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AC8, first strand: chain 'E' and resid 81 through 90 Processing sheet with id=AC9, first strand: chain 'E' and resid 81 through 90 removed outlier: 3.504A pdb=" N TYR F 30 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.685A pdb=" N GLU E 68 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG F 292 " --> pdb=" O ARG F 272 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG F 272 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AD3, first strand: chain 'E' and resid 154 through 157 removed outlier: 4.262A pdb=" N THR E 154 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ARG E 254 " --> pdb=" O PRO E 198 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AD5, first strand: chain 'F' and resid 98 through 101 Processing sheet with id=AD6, first strand: chain 'F' and resid 154 through 157 removed outlier: 4.265A pdb=" N THR F 154 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG F 254 " --> pdb=" O PRO F 198 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 28 through 29 removed outlier: 3.687A pdb=" N GLY G 69 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR G 32 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 98 through 102 Processing sheet with id=AD9, first strand: chain 'G' and resid 123 through 125 removed outlier: 3.631A pdb=" N THR G 123 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY G 134 " --> pdb=" O GLY G 165 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY G 165 " --> pdb=" O GLY G 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 28 through 29 removed outlier: 3.688A pdb=" N GLY H 69 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR H 32 " --> pdb=" O CYS H 54 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 98 through 102 Processing sheet with id=AE3, first strand: chain 'H' and resid 123 through 125 removed outlier: 3.632A pdb=" N THR H 123 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY H 134 " --> pdb=" O GLY H 165 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY H 165 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 28 through 29 removed outlier: 3.687A pdb=" N GLY I 69 " --> pdb=" O VAL I 45 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR I 32 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 98 through 102 Processing sheet with id=AE6, first strand: chain 'I' and resid 123 through 125 removed outlier: 3.632A pdb=" N THR I 123 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY I 134 " --> pdb=" O GLY I 165 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY I 165 " --> pdb=" O GLY I 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.688A pdb=" N GLY J 69 " --> pdb=" O VAL J 45 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR J 32 " --> pdb=" O CYS J 54 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 98 through 102 Processing sheet with id=AE9, first strand: chain 'J' and resid 123 through 125 removed outlier: 3.631A pdb=" N THR J 123 " --> pdb=" O LYS J 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY J 134 " --> pdb=" O GLY J 165 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY J 165 " --> pdb=" O GLY J 134 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 28 through 29 removed outlier: 3.689A pdb=" N GLY K 69 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR K 32 " --> pdb=" O CYS K 54 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 98 through 102 Processing sheet with id=AF3, first strand: chain 'K' and resid 123 through 125 removed outlier: 3.631A pdb=" N THR K 123 " --> pdb=" O LYS K 118 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY K 134 " --> pdb=" O GLY K 165 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY K 165 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 28 through 29 removed outlier: 3.687A pdb=" N GLY L 69 " --> pdb=" O VAL L 45 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR L 32 " --> pdb=" O CYS L 54 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 98 through 102 Processing sheet with id=AF6, first strand: chain 'L' and resid 123 through 125 removed outlier: 3.630A pdb=" N THR L 123 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY L 134 " --> pdb=" O GLY L 165 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 165 " --> pdb=" O GLY L 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 28 through 29 removed outlier: 3.688A pdb=" N GLY M 69 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR M 32 " --> pdb=" O CYS M 54 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 98 through 102 Processing sheet with id=AF9, first strand: chain 'M' and resid 123 through 125 removed outlier: 3.630A pdb=" N THR M 123 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY M 134 " --> pdb=" O GLY M 165 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY M 165 " --> pdb=" O GLY M 134 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 55 through 59 Processing sheet with id=AG2, first strand: chain 'N' and resid 62 through 64 Processing sheet with id=AG3, first strand: chain 'N' and resid 92 through 95 removed outlier: 4.866A pdb=" N ARG N 292 " --> pdb=" O ARG N 272 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG N 272 " --> pdb=" O ARG N 292 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 98 through 101 Processing sheet with id=AG5, first strand: chain 'N' and resid 154 through 157 removed outlier: 6.356A pdb=" N THR N 154 " --> pdb=" O TYR N 306 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP N 308 " --> pdb=" O THR N 154 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL N 156 " --> pdb=" O ASP N 308 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL N 195 " --> pdb=" O ARG N 239 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 265 through 267 739 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8021 1.34 - 1.45: 3942 1.45 - 1.57: 13041 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 25228 Sorted by residual: bond pdb=" N ALA C 71 " pdb=" CA ALA C 71 " ideal model delta sigma weight residual 1.458 1.482 -0.024 6.30e-03 2.52e+04 1.43e+01 bond pdb=" N ILE C 70 " pdb=" CA ILE C 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.23e+00 bond pdb=" N ARG C 73 " pdb=" CA ARG C 73 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 8.01e+00 bond pdb=" N ARG A 73 " pdb=" CA ARG A 73 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.95e+00 bond pdb=" CG TYR E 58 " pdb=" CD1 TYR E 58 " ideal model delta sigma weight residual 1.389 1.335 0.054 2.10e-02 2.27e+03 6.63e+00 ... (remaining 25223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 34092 3.84 - 7.67: 199 7.67 - 11.51: 6 11.51 - 15.35: 1 15.35 - 19.18: 2 Bond angle restraints: 34300 Sorted by residual: angle pdb=" N SER F 75 " pdb=" CA SER F 75 " pdb=" C SER F 75 " ideal model delta sigma weight residual 112.26 131.44 -19.18 1.32e+00 5.74e-01 2.11e+02 angle pdb=" N ARG E 73 " pdb=" CA ARG E 73 " pdb=" C ARG E 73 " ideal model delta sigma weight residual 110.80 127.41 -16.61 2.13e+00 2.20e-01 6.08e+01 angle pdb=" C ALA B 74 " pdb=" CA ALA B 74 " pdb=" CB ALA B 74 " ideal model delta sigma weight residual 111.91 96.87 15.04 2.06e+00 2.36e-01 5.33e+01 angle pdb=" N ARG F 73 " pdb=" CA ARG F 73 " pdb=" C ARG F 73 " ideal model delta sigma weight residual 111.74 119.88 -8.14 1.35e+00 5.49e-01 3.63e+01 angle pdb=" C ALA D 74 " pdb=" CA ALA D 74 " pdb=" CB ALA D 74 " ideal model delta sigma weight residual 109.53 100.44 9.09 1.65e+00 3.67e-01 3.03e+01 ... (remaining 34295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13663 17.94 - 35.87: 1003 35.87 - 53.81: 156 53.81 - 71.75: 75 71.75 - 89.69: 13 Dihedral angle restraints: 14910 sinusoidal: 5656 harmonic: 9254 Sorted by residual: dihedral pdb=" C ALA B 74 " pdb=" N ALA B 74 " pdb=" CA ALA B 74 " pdb=" CB ALA B 74 " ideal model delta harmonic sigma weight residual -122.60 -102.64 -19.96 0 2.50e+00 1.60e-01 6.37e+01 dihedral pdb=" N SER F 75 " pdb=" C SER F 75 " pdb=" CA SER F 75 " pdb=" CB SER F 75 " ideal model delta harmonic sigma weight residual 122.80 138.15 -15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" CA TYR E 58 " pdb=" C TYR E 58 " pdb=" N TYR E 59 " pdb=" CA TYR E 59 " ideal model delta harmonic sigma weight residual 180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 14907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 3836 0.178 - 0.357: 9 0.357 - 0.535: 2 0.535 - 0.713: 2 0.713 - 0.891: 1 Chirality restraints: 3850 Sorted by residual: chirality pdb=" CA SER F 75 " pdb=" N SER F 75 " pdb=" C SER F 75 " pdb=" CB SER F 75 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA ARG E 73 " pdb=" N ARG E 73 " pdb=" C ARG E 73 " pdb=" CB ARG E 73 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ALA B 74 " pdb=" N ALA B 74 " pdb=" C ALA B 74 " pdb=" CB ALA B 74 " both_signs ideal model delta sigma weight residual False 2.48 3.04 -0.55 2.00e-01 2.50e+01 7.62e+00 ... (remaining 3847 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 39 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 40 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 40 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 40 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 234 " -0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO C 235 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 78 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C GLU K 78 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU K 78 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN K 79 " 0.017 2.00e-02 2.50e+03 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 3 2.09 - 2.79: 6000 2.79 - 3.49: 30552 3.49 - 4.20: 53821 4.20 - 4.90: 96357 Nonbonded interactions: 186733 Sorted by model distance: nonbonded pdb=" CZ3 TRP N 163 " pdb=" CD1 ILE N 205 " model vdw 1.382 3.760 nonbonded pdb=" CE3 TRP N 163 " pdb=" CD1 ILE N 205 " model vdw 1.674 3.760 nonbonded pdb=" NH1 ARG D 209 " pdb=" O ASN D 212 " model vdw 2.071 3.120 nonbonded pdb=" O LEU E 147 " pdb=" OH TYR E 306 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR A 191 " pdb=" OE1 GLU A 231 " model vdw 2.111 3.040 ... (remaining 186728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 48.420 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.690 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.006 0.062 25228 Z= 0.272 Angle : 0.871 19.182 34300 Z= 0.509 Chirality : 0.058 0.891 3850 Planarity : 0.006 0.103 4452 Dihedral : 13.899 89.685 9058 Min Nonbonded Distance : 1.382 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.36 % Allowed : 4.60 % Favored : 93.03 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.13), residues: 3234 helix: -0.23 (0.22), residues: 535 sheet: -0.27 (0.24), residues: 470 loop : -2.80 (0.11), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG N 38 TYR 0.024 0.002 TYR N 47 PHE 0.024 0.002 PHE E 15 TRP 0.014 0.002 TRP A 183 HIS 0.004 0.001 HIS D 202 Details of bonding type rmsd covalent geometry : bond 0.00599 (25228) covalent geometry : angle 0.87102 (34300) hydrogen bonds : bond 0.16906 ( 729) hydrogen bonds : angle 6.88353 ( 2028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 570 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6895 (mp10) REVERT: A 145 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7668 (mmtt) REVERT: B 85 GLU cc_start: 0.7853 (tp30) cc_final: 0.7097 (mt-10) REVERT: B 109 ILE cc_start: 0.8007 (mm) cc_final: 0.7785 (mm) REVERT: B 216 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 33 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6530 (ptt90) REVERT: D 103 GLU cc_start: 0.5699 (mm-30) cc_final: 0.3894 (pt0) REVERT: E 73 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7373 (ptt180) REVERT: E 205 ILE cc_start: 0.8175 (mt) cc_final: 0.7899 (pt) REVERT: G 113 ASP cc_start: 0.8139 (m-30) cc_final: 0.7912 (m-30) REVERT: I 19 MET cc_start: 0.8674 (ttm) cc_final: 0.8445 (ttm) REVERT: J 154 MET cc_start: 0.8492 (ptt) cc_final: 0.8285 (ptt) REVERT: K 105 ASP cc_start: 0.6291 (t70) cc_final: 0.6071 (t70) REVERT: M 143 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: N 128 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7247 (mm-30) REVERT: N 145 LYS cc_start: 0.7319 (mmtp) cc_final: 0.7115 (mmtt) REVERT: N 302 LYS cc_start: 0.8313 (mttm) cc_final: 0.7190 (pttt) outliers start: 60 outliers final: 11 residues processed: 599 average time/residue: 0.1836 time to fit residues: 168.4745 Evaluate side-chains 400 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 387 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 143 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.2980 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 92 HIS B 162 ASN B 268 HIS G 47 GLN H 47 GLN H 79 ASN I 47 GLN K 47 GLN M 79 ASN N 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099860 restraints weight = 38113.728| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.76 r_work: 0.3004 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25228 Z= 0.232 Angle : 0.749 7.638 34300 Z= 0.400 Chirality : 0.053 0.226 3850 Planarity : 0.006 0.096 4452 Dihedral : 6.000 56.024 3622 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.36 % Allowed : 12.04 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.13), residues: 3234 helix: -0.01 (0.22), residues: 551 sheet: -1.00 (0.20), residues: 711 loop : -2.79 (0.11), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 73 TYR 0.025 0.002 TYR N 47 PHE 0.024 0.002 PHE G 14 TRP 0.040 0.002 TRP N 163 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00540 (25228) covalent geometry : angle 0.74864 (34300) hydrogen bonds : bond 0.05453 ( 729) hydrogen bonds : angle 5.31299 ( 2028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 409 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8083 (mm-40) cc_final: 0.6888 (mp10) REVERT: A 53 ILE cc_start: 0.8503 (mt) cc_final: 0.8193 (pt) REVERT: A 103 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6077 (tp30) REVERT: B 24 TYR cc_start: 0.8475 (t80) cc_final: 0.8244 (t80) REVERT: B 84 MET cc_start: 0.8480 (tpp) cc_final: 0.8072 (tpp) REVERT: B 128 GLU cc_start: 0.7865 (mp0) cc_final: 0.7644 (mt-10) REVERT: C 33 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.6713 (ptt90) REVERT: C 241 MET cc_start: 0.9036 (mmp) cc_final: 0.8625 (mmt) REVERT: C 267 MET cc_start: 0.8937 (ttt) cc_final: 0.8693 (ttt) REVERT: D 15 PHE cc_start: 0.8626 (m-10) cc_final: 0.8349 (m-10) REVERT: D 75 SER cc_start: 0.8088 (p) cc_final: 0.7709 (t) REVERT: D 103 GLU cc_start: 0.6871 (mm-30) cc_final: 0.4077 (pt0) REVERT: D 223 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8154 (mt0) REVERT: D 265 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8217 (mp) REVERT: E 107 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8473 (tt0) REVERT: E 145 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7636 (mmtm) REVERT: H 148 ASN cc_start: 0.8376 (t0) cc_final: 0.8154 (t0) REVERT: J 126 ASN cc_start: 0.8378 (t0) cc_final: 0.8171 (t0) REVERT: J 136 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8065 (ttt-90) REVERT: K 125 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8324 (p) REVERT: L 55 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8568 (pttt) REVERT: M 19 MET cc_start: 0.8804 (ttm) cc_final: 0.8550 (ttm) REVERT: M 143 ASP cc_start: 0.8236 (m-30) cc_final: 0.7981 (m-30) REVERT: N 84 MET cc_start: 0.8757 (mtm) cc_final: 0.8546 (mtt) REVERT: N 124 ARG cc_start: 0.7842 (mpt-90) cc_final: 0.7574 (mtm180) REVERT: N 128 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8143 (mm-30) REVERT: N 145 LYS cc_start: 0.7870 (mmtp) cc_final: 0.7519 (mmtt) REVERT: N 191 TYR cc_start: 0.8187 (m-10) cc_final: 0.7970 (m-10) REVERT: N 193 ASP cc_start: 0.8558 (t0) cc_final: 0.8323 (t0) REVERT: N 231 GLU cc_start: 0.6798 (tt0) cc_final: 0.6588 (mm-30) outliers start: 60 outliers final: 41 residues processed: 450 average time/residue: 0.1706 time to fit residues: 120.1979 Evaluate side-chains 380 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 253 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 143 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 202 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN H 79 ASN I 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.094449 restraints weight = 38382.239| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.72 r_work: 0.2915 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 25228 Z= 0.281 Angle : 0.765 8.168 34300 Z= 0.410 Chirality : 0.054 0.183 3850 Planarity : 0.007 0.095 4452 Dihedral : 5.931 37.694 3601 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.90 % Allowed : 15.55 % Favored : 80.56 % 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: -2.57 (0.13), residues: 3234 helix: 0.19 (0.23), residues: 548 sheet: -0.40 (0.22), residues: 575 loop : -2.82 (0.11), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 299 TYR 0.024 0.002 TYR K 4 PHE 0.026 0.002 PHE G 14 TRP 0.014 0.002 TRP B 183 HIS 0.006 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00688 (25228) covalent geometry : angle 0.76501 (34300) hydrogen bonds : bond 0.06328 ( 729) hydrogen bonds : angle 5.34316 ( 2028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 372 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8205 (pp30) REVERT: A 15 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 21 GLN cc_start: 0.8229 (mm-40) cc_final: 0.6692 (mp10) REVERT: A 53 ILE cc_start: 0.8495 (mt) cc_final: 0.8106 (pt) REVERT: A 103 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6040 (tp30) REVERT: B 53 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8320 (pt) REVERT: B 128 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: B 216 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7850 (mt-10) REVERT: C 33 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7093 (ptt90) REVERT: C 241 MET cc_start: 0.9107 (mmp) cc_final: 0.8893 (mmm) REVERT: C 267 MET cc_start: 0.8844 (ttt) cc_final: 0.8580 (ttt) REVERT: D 38 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6675 (ptt90) REVERT: D 57 ASP cc_start: 0.8284 (m-30) cc_final: 0.7908 (m-30) REVERT: D 75 SER cc_start: 0.8134 (p) cc_final: 0.7876 (t) REVERT: D 103 GLU cc_start: 0.6886 (mm-30) cc_final: 0.4099 (pt0) REVERT: D 223 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7914 (mt0) REVERT: D 265 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8302 (mp) REVERT: E 57 ASP cc_start: 0.8510 (p0) cc_final: 0.8212 (p0) REVERT: E 93 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9041 (tp) REVERT: E 96 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8244 (tt) REVERT: E 107 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8636 (tt0) REVERT: F 130 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.6995 (tpt) REVERT: G 41 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: G 81 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7409 (p) REVERT: J 1 MET cc_start: 0.4090 (OUTLIER) cc_final: 0.3847 (ttp) REVERT: J 17 GLU cc_start: 0.8463 (tp30) cc_final: 0.8246 (tp30) REVERT: J 136 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8118 (ttt-90) REVERT: L 28 ILE cc_start: 0.8466 (mm) cc_final: 0.8234 (mm) REVERT: N 76 ASP cc_start: 0.6572 (m-30) cc_final: 0.6119 (t70) REVERT: N 124 ARG cc_start: 0.8072 (mpt-90) cc_final: 0.7781 (mtm180) REVERT: N 128 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8080 (mm-30) REVERT: N 145 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7838 (mmtt) REVERT: N 191 TYR cc_start: 0.8309 (m-10) cc_final: 0.8061 (m-10) REVERT: N 193 ASP cc_start: 0.8562 (t0) cc_final: 0.8239 (t0) outliers start: 99 outliers final: 69 residues processed: 441 average time/residue: 0.1696 time to fit residues: 117.1359 Evaluate side-chains 418 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain G residue 41 PHE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 253 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 127 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 203 optimal weight: 0.4980 chunk 307 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN D 12 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 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 = 0.3227 r_free = 0.3227 target = 0.111828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.099548 restraints weight = 37728.421| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.76 r_work: 0.2972 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25228 Z= 0.126 Angle : 0.595 6.759 34300 Z= 0.319 Chirality : 0.048 0.169 3850 Planarity : 0.005 0.089 4452 Dihedral : 5.123 40.431 3600 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.56 % Allowed : 17.71 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.14), residues: 3234 helix: 0.68 (0.23), residues: 548 sheet: -0.75 (0.20), residues: 721 loop : -2.69 (0.11), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 209 TYR 0.019 0.001 TYR C 39 PHE 0.018 0.001 PHE D 221 TRP 0.010 0.001 TRP E 69 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00270 (25228) covalent geometry : angle 0.59452 (34300) hydrogen bonds : bond 0.04122 ( 729) hydrogen bonds : angle 4.94785 ( 2028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 0.917 Fit side-chains REVERT: A 15 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7003 (t80) REVERT: A 21 GLN cc_start: 0.8250 (mm-40) cc_final: 0.6732 (mp10) REVERT: A 53 ILE cc_start: 0.8466 (mt) cc_final: 0.8078 (pt) REVERT: A 103 GLU cc_start: 0.6586 (mm-30) cc_final: 0.5997 (tp30) REVERT: B 53 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8301 (pt) REVERT: B 84 MET cc_start: 0.8494 (tpp) cc_final: 0.8286 (tpp) REVERT: B 128 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: B 170 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: C 33 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7109 (ptt90) REVERT: C 267 MET cc_start: 0.8728 (ttt) cc_final: 0.8416 (ttt) REVERT: D 38 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7441 (ptt90) REVERT: D 103 GLU cc_start: 0.6438 (mm-30) cc_final: 0.4249 (pm20) REVERT: D 219 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7389 (tt) REVERT: D 223 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7928 (mt0) REVERT: D 234 ARG cc_start: 0.7975 (mpp80) cc_final: 0.7729 (mtm-85) REVERT: E 130 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7438 (tpt) REVERT: E 145 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7754 (mmtm) REVERT: E 191 TYR cc_start: 0.8438 (m-80) cc_final: 0.7612 (m-80) REVERT: G 81 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7258 (p) REVERT: H 1 MET cc_start: 0.4995 (ttp) cc_final: 0.4698 (ttp) REVERT: I 51 ASP cc_start: 0.7838 (t70) cc_final: 0.7606 (t0) REVERT: I 136 ARG cc_start: 0.8100 (ttp-170) cc_final: 0.7666 (ttt90) REVERT: J 136 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7962 (ttt-90) REVERT: K 105 ASP cc_start: 0.6839 (t70) cc_final: 0.6546 (t70) REVERT: K 125 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8252 (p) REVERT: N 38 ARG cc_start: 0.7230 (ptt-90) cc_final: 0.7011 (ptt-90) REVERT: N 84 MET cc_start: 0.8766 (ttm) cc_final: 0.8504 (ttt) REVERT: N 128 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8069 (mm-30) REVERT: N 145 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7845 (mmtt) REVERT: N 302 LYS cc_start: 0.8632 (mttm) cc_final: 0.7069 (pttt) outliers start: 65 outliers final: 40 residues processed: 415 average time/residue: 0.1764 time to fit residues: 114.0014 Evaluate side-chains 384 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 253 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 319 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN E 202 HIS H 79 ASN J 79 ASN N 203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.095764 restraints weight = 37975.983| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.70 r_work: 0.2929 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25228 Z= 0.203 Angle : 0.663 6.906 34300 Z= 0.355 Chirality : 0.051 0.172 3850 Planarity : 0.005 0.085 4452 Dihedral : 5.396 40.425 3600 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.09 % Allowed : 18.18 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.14), residues: 3234 helix: 0.69 (0.23), residues: 548 sheet: -0.73 (0.20), residues: 705 loop : -2.75 (0.11), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 209 TYR 0.019 0.002 TYR C 39 PHE 0.019 0.002 PHE D 221 TRP 0.010 0.001 TRP B 183 HIS 0.004 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00491 (25228) covalent geometry : angle 0.66263 (34300) hydrogen bonds : bond 0.05176 ( 729) hydrogen bonds : angle 5.01785 ( 2028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 330 time to evaluate : 1.040 Fit side-chains REVERT: A 12 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8207 (pp30) REVERT: A 15 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7331 (t80) REVERT: A 21 GLN cc_start: 0.8270 (mm-40) cc_final: 0.6692 (mp10) REVERT: A 53 ILE cc_start: 0.8495 (mt) cc_final: 0.8063 (pt) REVERT: A 103 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6449 (mm-30) REVERT: B 53 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8238 (pt) REVERT: B 128 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: B 170 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: B 203 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8591 (mt0) REVERT: C 33 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7282 (ptt90) REVERT: C 267 MET cc_start: 0.8732 (ttt) cc_final: 0.8498 (ttt) REVERT: D 38 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7502 (ptt90) REVERT: D 103 GLU cc_start: 0.6742 (mm-30) cc_final: 0.4236 (pm20) REVERT: D 219 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7476 (tt) REVERT: D 223 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7890 (mt0) REVERT: D 234 ARG cc_start: 0.8058 (mpp80) cc_final: 0.7852 (mtm-85) REVERT: D 265 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8227 (mp) REVERT: E 93 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8997 (tp) REVERT: E 130 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7483 (tpt) REVERT: E 145 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7876 (mmtm) REVERT: F 130 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.6962 (tpt) REVERT: G 41 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: G 81 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7202 (p) REVERT: G 94 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8613 (tmm) REVERT: H 11 ASP cc_start: 0.7986 (p0) cc_final: 0.7305 (t70) REVERT: H 49 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7998 (m) REVERT: I 51 ASP cc_start: 0.7901 (t70) cc_final: 0.7653 (t0) REVERT: I 80 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8124 (mp) REVERT: I 136 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7694 (ttt180) REVERT: J 1 MET cc_start: 0.3242 (OUTLIER) cc_final: 0.3009 (ttp) REVERT: J 136 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8081 (ttt-90) REVERT: K 105 ASP cc_start: 0.6945 (t70) cc_final: 0.6597 (t70) REVERT: K 125 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8288 (p) REVERT: M 27 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7925 (t0) REVERT: N 38 ARG cc_start: 0.7301 (ptt-90) cc_final: 0.6991 (ptt-90) REVERT: N 76 ASP cc_start: 0.6771 (m-30) cc_final: 0.6404 (t70) REVERT: N 84 MET cc_start: 0.8771 (ttm) cc_final: 0.8453 (ttt) REVERT: N 128 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8091 (mm-30) REVERT: N 145 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7887 (mmtt) REVERT: N 302 LYS cc_start: 0.8639 (mttm) cc_final: 0.7119 (pttt) outliers start: 104 outliers final: 68 residues processed: 404 average time/residue: 0.1734 time to fit residues: 108.6895 Evaluate side-chains 407 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 318 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 41 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 79 ASN Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 253 SER Chi-restraints excluded: chain N residue 293 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 139 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 246 optimal weight: 0.0050 chunk 204 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 overall best weight: 6.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN I 79 ASN J 79 ASN ** J 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.093913 restraints weight = 38179.926| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.70 r_work: 0.2894 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 25228 Z= 0.246 Angle : 0.697 7.182 34300 Z= 0.374 Chirality : 0.052 0.172 3850 Planarity : 0.006 0.089 4452 Dihedral : 5.620 40.310 3600 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.27 % Allowed : 18.02 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3234 helix: 0.58 (0.23), residues: 551 sheet: -0.78 (0.20), residues: 705 loop : -2.81 (0.11), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 31 TYR 0.018 0.002 TYR D 39 PHE 0.021 0.002 PHE D 221 TRP 0.016 0.002 TRP B 163 HIS 0.005 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00604 (25228) covalent geometry : angle 0.69721 (34300) hydrogen bonds : bond 0.05593 ( 729) hydrogen bonds : angle 5.10506 ( 2028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 320 time to evaluate : 0.964 Fit side-chains REVERT: A 12 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8188 (pp30) REVERT: A 15 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 21 GLN cc_start: 0.8311 (mm-40) cc_final: 0.6675 (mp10) REVERT: A 53 ILE cc_start: 0.8493 (mt) cc_final: 0.8046 (pt) REVERT: A 103 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6323 (mm-30) REVERT: B 128 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: B 130 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8034 (tmm) REVERT: B 170 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: B 203 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: B 216 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 33 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7279 (ptt90) REVERT: D 38 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7504 (ptt90) REVERT: D 103 GLU cc_start: 0.6856 (mm-30) cc_final: 0.4126 (pt0) REVERT: D 130 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8227 (tpt) REVERT: D 223 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7889 (mt0) REVERT: D 265 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8286 (mp) REVERT: E 21 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: E 93 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9035 (tp) REVERT: E 130 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7513 (tpt) REVERT: F 130 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.6998 (tpt) REVERT: G 41 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8501 (m-10) REVERT: G 81 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7232 (p) REVERT: G 94 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8608 (tmm) REVERT: H 11 ASP cc_start: 0.8021 (p0) cc_final: 0.7698 (t70) REVERT: H 41 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: H 49 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7945 (m) REVERT: I 80 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8200 (mp) REVERT: I 136 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7695 (ttt180) REVERT: J 1 MET cc_start: 0.3792 (OUTLIER) cc_final: 0.3453 (ttp) REVERT: J 136 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8079 (ttt-90) REVERT: K 105 ASP cc_start: 0.6976 (t70) cc_final: 0.6630 (t70) REVERT: L 28 ILE cc_start: 0.8488 (mm) cc_final: 0.8248 (mm) REVERT: M 27 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7997 (t0) REVERT: N 38 ARG cc_start: 0.7274 (ptt-90) cc_final: 0.6957 (ptt-90) REVERT: N 84 MET cc_start: 0.8777 (ttm) cc_final: 0.8455 (ttt) REVERT: N 128 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8122 (mm-30) REVERT: N 145 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7959 (mmtt) REVERT: N 302 LYS cc_start: 0.8637 (mttm) cc_final: 0.7129 (pttt) outliers start: 134 outliers final: 88 residues processed: 414 average time/residue: 0.1795 time to fit residues: 115.7458 Evaluate side-chains 419 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 310 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 41 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 41 PHE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 253 SER Chi-restraints excluded: chain N residue 293 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 23 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096651 restraints weight = 37934.291| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.70 r_work: 0.2931 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25228 Z= 0.147 Angle : 0.603 6.548 34300 Z= 0.324 Chirality : 0.048 0.166 3850 Planarity : 0.005 0.085 4452 Dihedral : 5.151 42.780 3600 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.01 % Allowed : 19.36 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.14), residues: 3234 helix: 0.85 (0.23), residues: 553 sheet: -0.70 (0.20), residues: 726 loop : -2.74 (0.11), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 31 TYR 0.017 0.001 TYR C 39 PHE 0.018 0.001 PHE D 221 TRP 0.010 0.001 TRP D 183 HIS 0.002 0.001 HIS E 268 Details of bonding type rmsd covalent geometry : bond 0.00341 (25228) covalent geometry : angle 0.60293 (34300) hydrogen bonds : bond 0.04350 ( 729) hydrogen bonds : angle 4.86987 ( 2028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 319 time to evaluate : 1.050 Fit side-chains REVERT: A 15 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7180 (t80) REVERT: A 21 GLN cc_start: 0.8378 (mm-40) cc_final: 0.6664 (mp10) REVERT: A 53 ILE cc_start: 0.8451 (mt) cc_final: 0.8034 (pt) REVERT: A 103 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6314 (mm-30) REVERT: B 84 MET cc_start: 0.8493 (tpp) cc_final: 0.8112 (tpp) REVERT: B 128 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: B 130 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7989 (tmm) REVERT: B 170 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: C 33 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7299 (ptt90) REVERT: D 103 GLU cc_start: 0.6560 (mm-30) cc_final: 0.4262 (pm20) REVERT: D 191 TYR cc_start: 0.8440 (m-80) cc_final: 0.8184 (m-80) REVERT: D 223 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7853 (mt0) REVERT: E 130 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7604 (tpt) REVERT: G 81 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7138 (p) REVERT: G 94 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8566 (tmm) REVERT: H 11 ASP cc_start: 0.7965 (p0) cc_final: 0.7403 (t70) REVERT: H 41 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: H 49 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7912 (m) REVERT: I 51 ASP cc_start: 0.7839 (t70) cc_final: 0.7609 (t0) REVERT: I 136 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7672 (ttt180) REVERT: J 136 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8036 (ttt-90) REVERT: K 105 ASP cc_start: 0.6878 (t70) cc_final: 0.6515 (t70) REVERT: L 118 LYS cc_start: 0.8348 (tttm) cc_final: 0.8138 (tttm) REVERT: N 38 ARG cc_start: 0.7262 (ptt-90) cc_final: 0.6949 (ptt-90) REVERT: N 84 MET cc_start: 0.8793 (ttm) cc_final: 0.8509 (ttt) REVERT: N 128 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8183 (mm-30) REVERT: N 145 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8053 (mmtt) REVERT: N 302 LYS cc_start: 0.8633 (mttm) cc_final: 0.7129 (pttt) outliers start: 102 outliers final: 72 residues processed: 393 average time/residue: 0.1820 time to fit residues: 111.3376 Evaluate side-chains 402 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 321 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 41 PHE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 41 PHE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 253 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 194 optimal weight: 10.0000 chunk 273 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 287 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094519 restraints weight = 38141.719| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.69 r_work: 0.2904 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25228 Z= 0.207 Angle : 0.661 7.915 34300 Z= 0.354 Chirality : 0.050 0.168 3850 Planarity : 0.005 0.084 4452 Dihedral : 5.417 44.484 3600 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.25 % Allowed : 19.68 % Favored : 76.07 % 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: -2.38 (0.13), residues: 3234 helix: 0.74 (0.23), residues: 555 sheet: -0.82 (0.20), residues: 685 loop : -2.72 (0.11), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 31 TYR 0.018 0.002 TYR D 39 PHE 0.023 0.002 PHE D 221 TRP 0.010 0.001 TRP D 183 HIS 0.004 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00501 (25228) covalent geometry : angle 0.66097 (34300) hydrogen bonds : bond 0.05190 ( 729) hydrogen bonds : angle 4.97688 ( 2028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 311 time to evaluate : 0.943 Fit side-chains REVERT: A 12 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8240 (pp30) REVERT: A 15 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 53 ILE cc_start: 0.8480 (mt) cc_final: 0.8029 (pt) REVERT: A 103 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6341 (mm-30) REVERT: B 128 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 130 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7973 (tmm) REVERT: B 170 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: B 216 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7729 (mt-10) REVERT: C 33 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7294 (ptt90) REVERT: D 103 GLU cc_start: 0.6793 (mm-30) cc_final: 0.4254 (pm20) REVERT: D 130 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8181 (tpt) REVERT: D 170 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: D 191 TYR cc_start: 0.8451 (m-80) cc_final: 0.8191 (m-80) REVERT: D 223 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7870 (mt0) REVERT: D 265 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8234 (mp) REVERT: E 21 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: E 130 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.7570 (tpt) REVERT: F 130 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.6935 (tpt) REVERT: G 41 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8484 (m-10) REVERT: G 81 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7066 (p) REVERT: G 94 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8588 (tmm) REVERT: H 1 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4325 (ttt) REVERT: H 11 ASP cc_start: 0.7976 (p0) cc_final: 0.7741 (t70) REVERT: H 41 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8092 (m-10) REVERT: H 49 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7895 (m) REVERT: I 51 ASP cc_start: 0.7842 (t70) cc_final: 0.7578 (t0) REVERT: I 125 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7184 (p) REVERT: I 136 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7675 (ttt180) REVERT: J 1 MET cc_start: 0.3764 (OUTLIER) cc_final: 0.3415 (ttp) REVERT: J 136 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8092 (ttt-90) REVERT: L 28 ILE cc_start: 0.8463 (mm) cc_final: 0.8233 (mm) REVERT: N 38 ARG cc_start: 0.7266 (ptt-90) cc_final: 0.6951 (ptt-90) REVERT: N 84 MET cc_start: 0.8804 (ttm) cc_final: 0.8505 (ttt) REVERT: N 145 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8070 (mmtt) REVERT: N 302 LYS cc_start: 0.8638 (mttm) cc_final: 0.7135 (pttt) outliers start: 108 outliers final: 83 residues processed: 386 average time/residue: 0.1772 time to fit residues: 106.9049 Evaluate side-chains 399 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 297 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 41 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 41 PHE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 41 PHE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 253 SER Chi-restraints excluded: chain N residue 293 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 201 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 269 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 315 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN ** J 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095207 restraints weight = 38235.039| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.70 r_work: 0.2914 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25228 Z= 0.181 Angle : 0.637 7.256 34300 Z= 0.342 Chirality : 0.049 0.169 3850 Planarity : 0.005 0.084 4452 Dihedral : 5.322 46.615 3600 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.53 % Allowed : 19.48 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 3234 helix: 0.81 (0.23), residues: 555 sheet: -0.80 (0.20), residues: 685 loop : -2.71 (0.11), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 31 TYR 0.017 0.002 TYR C 39 PHE 0.019 0.001 PHE D 221 TRP 0.010 0.001 TRP D 183 HIS 0.003 0.001 HIS E 268 Details of bonding type rmsd covalent geometry : bond 0.00433 (25228) covalent geometry : angle 0.63687 (34300) hydrogen bonds : bond 0.04835 ( 729) hydrogen bonds : angle 4.92782 ( 2028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 303 time to evaluate : 0.992 Fit side-chains REVERT: A 12 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8224 (pp30) REVERT: A 15 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7312 (t80) REVERT: A 53 ILE cc_start: 0.8448 (mt) cc_final: 0.8002 (pt) REVERT: A 103 GLU cc_start: 0.6730 (mm-30) cc_final: 0.6374 (mm-30) REVERT: B 84 MET cc_start: 0.8512 (tpp) cc_final: 0.8127 (tpp) REVERT: B 128 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: B 130 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: B 170 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: B 216 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 241 MET cc_start: 0.8765 (mmp) cc_final: 0.8547 (mmm) REVERT: B 302 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8623 (mptt) REVERT: C 33 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7296 (ptt90) REVERT: D 103 GLU cc_start: 0.6686 (mm-30) cc_final: 0.4219 (pm20) REVERT: D 130 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8114 (tpt) REVERT: D 191 TYR cc_start: 0.8451 (m-80) cc_final: 0.8200 (m-80) REVERT: D 223 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7885 (mt0) REVERT: D 265 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8163 (mp) REVERT: E 130 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7554 (tpt) REVERT: F 130 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.6916 (tpt) REVERT: G 41 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: G 81 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7094 (p) REVERT: G 94 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8600 (tmm) REVERT: H 41 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: H 49 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7893 (m) REVERT: I 51 ASP cc_start: 0.7818 (t70) cc_final: 0.7563 (t0) REVERT: I 125 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7134 (p) REVERT: I 136 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7684 (ttt180) REVERT: J 1 MET cc_start: 0.3895 (OUTLIER) cc_final: 0.3541 (ttp) REVERT: J 136 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8061 (ttt-90) REVERT: L 28 ILE cc_start: 0.8429 (mm) cc_final: 0.8220 (mm) REVERT: L 136 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8143 (ttt90) REVERT: N 38 ARG cc_start: 0.7231 (ptt-90) cc_final: 0.6937 (ptt-90) REVERT: N 84 MET cc_start: 0.8805 (ttm) cc_final: 0.8514 (ttt) REVERT: N 145 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8046 (mmtt) REVERT: N 302 LYS cc_start: 0.8638 (mttm) cc_final: 0.7133 (pttt) outliers start: 115 outliers final: 90 residues processed: 384 average time/residue: 0.1719 time to fit residues: 103.2411 Evaluate side-chains 406 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 300 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 41 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 41 PHE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 41 PHE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 253 SER Chi-restraints excluded: chain N residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 231 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 118 optimal weight: 0.0670 chunk 251 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 272 optimal weight: 0.0050 overall best weight: 3.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN ** J 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.095987 restraints weight = 37923.656| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.73 r_work: 0.2919 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25228 Z= 0.157 Angle : 0.623 7.325 34300 Z= 0.334 Chirality : 0.049 0.225 3850 Planarity : 0.005 0.083 4452 Dihedral : 5.243 47.192 3600 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 4.13 % Allowed : 19.91 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.14), residues: 3234 helix: 0.88 (0.23), residues: 556 sheet: -0.80 (0.20), residues: 706 loop : -2.69 (0.11), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 234 TYR 0.018 0.001 TYR C 39 PHE 0.018 0.001 PHE D 221 TRP 0.010 0.001 TRP D 183 HIS 0.003 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00362 (25228) covalent geometry : angle 0.62314 (34300) hydrogen bonds : bond 0.04596 ( 729) hydrogen bonds : angle 4.89360 ( 2028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 306 time to evaluate : 0.737 Fit side-chains REVERT: A 12 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8180 (pp30) REVERT: A 15 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7300 (t80) REVERT: A 53 ILE cc_start: 0.8446 (mt) cc_final: 0.7998 (pt) REVERT: A 103 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6258 (mm-30) REVERT: B 84 MET cc_start: 0.8496 (tpp) cc_final: 0.8098 (tpp) REVERT: B 128 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: B 130 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7963 (tmm) REVERT: B 170 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: B 216 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 241 MET cc_start: 0.8772 (mmp) cc_final: 0.8552 (mmm) REVERT: B 302 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8616 (mptt) REVERT: C 33 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7279 (ptt90) REVERT: D 57 ASP cc_start: 0.8354 (m-30) cc_final: 0.8122 (m-30) REVERT: D 103 GLU cc_start: 0.6655 (mm-30) cc_final: 0.4283 (pm20) REVERT: D 130 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8101 (tpt) REVERT: D 170 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: D 191 TYR cc_start: 0.8441 (m-80) cc_final: 0.8196 (m-80) REVERT: D 223 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7904 (mt0) REVERT: E 21 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: E 130 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: F 130 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: G 81 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7016 (p) REVERT: G 94 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8580 (tmm) REVERT: H 1 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4937 (ttt) REVERT: H 41 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8077 (m-10) REVERT: H 49 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7903 (m) REVERT: I 125 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.7167 (p) REVERT: I 136 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7650 (ttt180) REVERT: J 1 MET cc_start: 0.3796 (OUTLIER) cc_final: 0.3436 (ttp) REVERT: J 136 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8044 (ttt-90) REVERT: L 28 ILE cc_start: 0.8396 (mm) cc_final: 0.8190 (mm) REVERT: L 136 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8118 (ttt90) REVERT: N 38 ARG cc_start: 0.7221 (ptt-90) cc_final: 0.6919 (ptt-90) REVERT: N 84 MET cc_start: 0.8822 (ttm) cc_final: 0.8525 (ttt) REVERT: N 145 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8037 (mmtt) REVERT: N 302 LYS cc_start: 0.8630 (mttm) cc_final: 0.7120 (pttt) outliers start: 105 outliers final: 84 residues processed: 378 average time/residue: 0.1745 time to fit residues: 102.6788 Evaluate side-chains 402 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 301 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 41 PHE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 41 PHE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain N residue 47 TYR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 205 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 253 SER Chi-restraints excluded: chain N residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 285 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 246 optimal weight: 0.0570 chunk 168 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN D 12 GLN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN N 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098383 restraints weight = 37914.020| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.71 r_work: 0.2964 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25228 Z= 0.122 Angle : 0.577 7.451 34300 Z= 0.308 Chirality : 0.047 0.170 3850 Planarity : 0.005 0.080 4452 Dihedral : 4.892 49.554 3600 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.38 % Allowed : 20.54 % Favored : 76.07 % 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: -2.13 (0.14), residues: 3234 helix: 1.09 (0.23), residues: 556 sheet: -0.69 (0.20), residues: 712 loop : -2.61 (0.11), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 234 TYR 0.017 0.001 TYR C 39 PHE 0.017 0.001 PHE D 221 TRP 0.011 0.001 TRP E 69 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00271 (25228) covalent geometry : angle 0.57706 (34300) hydrogen bonds : bond 0.03833 ( 729) hydrogen bonds : angle 4.72099 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7522.60 seconds wall clock time: 129 minutes 12.25 seconds (7752.25 seconds total)