Starting phenix.real_space_refine on Thu Mar 5 12:41:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vak_21141/03_2026/6vak_21141.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vak_21141/03_2026/6vak_21141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vak_21141/03_2026/6vak_21141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vak_21141/03_2026/6vak_21141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vak_21141/03_2026/6vak_21141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vak_21141/03_2026/6vak_21141.map" } resolution = 3.48 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= 0.031 sd= 0.566 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 77 5.16 5 C 14707 2.51 5 N 3982 2.21 5 O 4015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22781 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 1, 'GLU:plan': 5, 'PHE:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 2.50, per 1000 atoms: 0.11 Number of scatterers: 22781 At special positions: 0 Unit cell: (147.34, 147.34, 102.82, 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 77 16.00 O 4015 8.00 N 3982 7.00 C 14707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.04 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.04 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.04 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.04 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.04 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.04 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.04 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.04 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 11 sheets defined 75.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 25 through 43 removed outlier: 4.097A pdb=" N ALA A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.507A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 208 " --> pdb=" O CYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.508A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 208 " --> pdb=" O CYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA B 218 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 250 " --> pdb=" O ASN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix removed outlier: 3.508A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 133 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 208 " --> pdb=" O CYS C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA D 43 " --> pdb=" O PHE D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix removed outlier: 3.508A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 133 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR D 208 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 252 removed outlier: 3.864A pdb=" N ALA D 218 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 250 " --> pdb=" O ASN D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR D 282 " --> pdb=" O TRP D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN E 87 " --> pdb=" O VAL E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix removed outlier: 3.508A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL E 176 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR E 208 " --> pdb=" O CYS E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA E 218 " --> pdb=" O TYR E 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE E 250 " --> pdb=" O ASN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR E 282 " --> pdb=" O TRP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Proline residue: F 114 - end of helix removed outlier: 3.507A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL F 176 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR F 208 " --> pdb=" O CYS F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 252 removed outlier: 3.864A pdb=" N ALA F 218 " --> pdb=" O TYR F 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE F 250 " --> pdb=" O ASN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR F 282 " --> pdb=" O TRP F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA G 43 " --> pdb=" O PHE G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 76 through 87 removed outlier: 4.334A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN G 87 " --> pdb=" O VAL G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 124 removed outlier: 5.595A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Proline residue: G 114 - end of helix removed outlier: 3.507A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 153 through 159 Processing helix chain 'G' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL G 176 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU G 183 " --> pdb=" O ARG G 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR G 208 " --> pdb=" O CYS G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA G 218 " --> pdb=" O TYR G 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE G 250 " --> pdb=" O ASN G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR G 282 " --> pdb=" O TRP G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY G 305 " --> pdb=" O LYS G 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA H 43 " --> pdb=" O PHE H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN H 87 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Proline residue: H 114 - end of helix removed outlier: 3.507A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 133 Processing helix chain 'H' and resid 153 through 159 Processing helix chain 'H' and resid 169 through 209 removed outlier: 3.646A pdb=" N GLU H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU H 183 " --> pdb=" O ARG H 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 208 " --> pdb=" O CYS H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 removed outlier: 4.035A pdb=" N GLU H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA H 218 " --> pdb=" O TYR H 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE H 250 " --> pdb=" O ASN H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR H 282 " --> pdb=" O TRP H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY H 305 " --> pdb=" O LYS H 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA I 43 " --> pdb=" O PHE I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN I 87 " --> pdb=" O VAL I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix removed outlier: 3.507A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 133 Processing helix chain 'I' and resid 153 through 159 Processing helix chain 'I' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 176 " --> pdb=" O PHE I 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU I 183 " --> pdb=" O ARG I 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR I 208 " --> pdb=" O CYS I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA I 218 " --> pdb=" O TYR I 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE I 250 " --> pdb=" O ASN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR I 282 " --> pdb=" O TRP I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY I 305 " --> pdb=" O LYS I 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 43 removed outlier: 4.096A pdb=" N ALA J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN J 87 " --> pdb=" O VAL J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Proline residue: J 114 - end of helix removed outlier: 3.508A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 133 Processing helix chain 'J' and resid 153 through 159 Processing helix chain 'J' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL J 176 " --> pdb=" O PHE J 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU J 183 " --> pdb=" O ARG J 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR J 208 " --> pdb=" O CYS J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA J 218 " --> pdb=" O TYR J 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE J 250 " --> pdb=" O ASN J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR J 282 " --> pdb=" O TRP J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY J 305 " --> pdb=" O LYS J 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP K 80 " --> pdb=" O ASN K 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN K 87 " --> pdb=" O VAL K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Proline residue: K 114 - end of helix removed outlier: 3.508A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 133 Processing helix chain 'K' and resid 153 through 159 Processing helix chain 'K' and resid 169 through 209 removed outlier: 3.646A pdb=" N GLU K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL K 176 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU K 183 " --> pdb=" O ARG K 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR K 208 " --> pdb=" O CYS K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 252 removed outlier: 3.864A pdb=" N ALA K 218 " --> pdb=" O TYR K 214 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE K 250 " --> pdb=" O ASN K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR K 282 " --> pdb=" O TRP K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY K 305 " --> pdb=" O LYS K 301 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG A 288 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG B 288 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG C 288 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG D 288 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG E 288 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG F 288 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG G 288 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 288 through 289 removed outlier: 4.086A pdb=" N ARG H 288 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 288 through 289 removed outlier: 4.088A pdb=" N ARG I 288 " --> pdb=" O LEU I 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 288 through 289 removed outlier: 4.088A pdb=" N ARG J 288 " --> pdb=" O LEU J 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG K 288 " --> pdb=" O LEU K 295 " (cutoff:3.500A) 1563 hydrogen bonds defined for protein. 4689 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: 3.83 Time building geometry restraints manager: 2.66 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: 7480 1.34 - 1.46: 5771 1.46 - 1.58: 10047 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 23375 Sorted by residual: bond pdb=" N GLU A 126 " pdb=" CA GLU A 126 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" N GLU E 126 " pdb=" CA GLU E 126 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" N LYS G 163 " pdb=" CA LYS G 163 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.33e+00 bond pdb=" N LYS F 163 " pdb=" CA LYS F 163 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" N GLU C 126 " pdb=" CA GLU C 126 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 ... (remaining 23370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 29873 1.34 - 2.69: 1575 2.69 - 4.03: 382 4.03 - 5.38: 81 5.38 - 6.72: 55 Bond angle restraints: 31966 Sorted by residual: angle pdb=" N ALA K 127 " pdb=" CA ALA K 127 " pdb=" C ALA K 127 " ideal model delta sigma weight residual 113.18 109.09 4.09 1.33e+00 5.65e-01 9.47e+00 angle pdb=" C GLU A 164 " pdb=" N ASN A 165 " pdb=" CA ASN A 165 " ideal model delta sigma weight residual 123.46 119.32 4.14 1.35e+00 5.49e-01 9.40e+00 angle pdb=" C GLU J 164 " pdb=" N ASN J 165 " pdb=" CA ASN J 165 " ideal model delta sigma weight residual 123.46 119.33 4.13 1.35e+00 5.49e-01 9.37e+00 angle pdb=" C GLU F 164 " pdb=" N ASN F 165 " pdb=" CA ASN F 165 " ideal model delta sigma weight residual 123.46 119.35 4.11 1.35e+00 5.49e-01 9.28e+00 angle pdb=" C GLU I 164 " pdb=" N ASN I 165 " pdb=" CA ASN I 165 " ideal model delta sigma weight residual 123.46 119.35 4.11 1.35e+00 5.49e-01 9.27e+00 ... (remaining 31961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 12408 16.83 - 33.67: 968 33.67 - 50.50: 275 50.50 - 67.33: 11 67.33 - 84.17: 55 Dihedral angle restraints: 13717 sinusoidal: 4972 harmonic: 8745 Sorted by residual: dihedral pdb=" CB GLU F 261 " pdb=" CG GLU F 261 " pdb=" CD GLU F 261 " pdb=" OE1 GLU F 261 " ideal model delta sinusoidal sigma weight residual 0.00 -84.17 84.17 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CB GLU B 261 " pdb=" CG GLU B 261 " pdb=" CD GLU B 261 " pdb=" OE1 GLU B 261 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CB GLU I 261 " pdb=" CG GLU I 261 " pdb=" CD GLU I 261 " pdb=" OE1 GLU I 261 " ideal model delta sinusoidal sigma weight residual 0.00 -84.14 84.14 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 13714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2252 0.026 - 0.052: 851 0.052 - 0.077: 322 0.077 - 0.103: 97 0.103 - 0.129: 97 Chirality restraints: 3619 Sorted by residual: chirality pdb=" CA PRO G 50 " pdb=" N PRO G 50 " pdb=" C PRO G 50 " pdb=" CB PRO G 50 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO J 50 " pdb=" N PRO J 50 " pdb=" C PRO J 50 " pdb=" CB PRO J 50 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO D 50 " pdb=" N PRO D 50 " pdb=" C PRO D 50 " pdb=" CB PRO D 50 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 3616 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 160 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 161 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 160 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO J 161 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 161 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 161 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 160 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO D 161 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.025 5.00e-02 4.00e+02 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 215 2.62 - 3.19: 21381 3.19 - 3.76: 34640 3.76 - 4.33: 43772 4.33 - 4.90: 73603 Nonbonded interactions: 173611 Sorted by model distance: nonbonded pdb=" O VAL C 129 " pdb=" OG SER C 133 " model vdw 2.047 3.040 nonbonded pdb=" O VAL E 129 " pdb=" OG SER E 133 " model vdw 2.047 3.040 nonbonded pdb=" O VAL I 129 " pdb=" OG SER I 133 " model vdw 2.047 3.040 nonbonded pdb=" O VAL H 129 " pdb=" OG SER H 133 " model vdw 2.047 3.040 nonbonded pdb=" O VAL F 129 " pdb=" OG SER F 133 " model vdw 2.047 3.040 ... (remaining 173606 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: 0.07 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 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.450 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.004 0.029 23397 Z= 0.203 Angle : 0.766 6.719 32010 Z= 0.453 Chirality : 0.037 0.129 3619 Planarity : 0.005 0.045 4125 Dihedral : 14.359 84.169 7997 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.96 % Allowed : 4.30 % Favored : 92.75 % 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: -2.80 (0.13), residues: 2948 helix: -1.10 (0.10), residues: 2112 sheet: None (None), residues: 0 loop : -3.64 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 159 TYR 0.014 0.001 TYR J 287 PHE 0.021 0.001 PHE A 172 TRP 0.005 0.001 TRP G 189 HIS 0.005 0.001 HIS J 238 Details of bonding type rmsd covalent geometry : bond 0.00409 (23375) covalent geometry : angle 0.76535 (31966) SS BOND : bond 0.00628 ( 22) SS BOND : angle 1.04965 ( 44) hydrogen bonds : bond 0.14663 ( 1563) hydrogen bonds : angle 5.71639 ( 4689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 444 time to evaluate : 0.857 Fit side-chains REVERT: A 190 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8419 (tt) REVERT: B 190 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 205 LEU cc_start: 0.8435 (tp) cc_final: 0.8157 (tt) REVERT: C 190 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8322 (tt) REVERT: D 121 SER cc_start: 0.9052 (t) cc_final: 0.8838 (p) REVERT: E 190 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8144 (tt) REVERT: E 285 TYR cc_start: 0.7781 (t80) cc_final: 0.7386 (t80) REVERT: G 190 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8340 (mp) REVERT: H 190 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (mp) REVERT: H 206 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7962 (tttt) REVERT: I 190 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7808 (mp) outliers start: 66 outliers final: 13 residues processed: 502 average time/residue: 0.1355 time to fit residues: 112.5472 Evaluate side-chains 288 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 222 GLN A 229 GLN A 246 ASN B 45 HIS B 238 HIS B 246 ASN B 277 GLN C 222 GLN C 238 HIS C 246 ASN D 238 HIS D 246 ASN E 238 HIS E 246 ASN F 238 HIS F 246 ASN F 266 ASN G 238 HIS G 246 ASN H 222 GLN H 238 HIS H 246 ASN I 238 HIS I 246 ASN J 45 HIS J 238 HIS J 246 ASN K 238 HIS K 246 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092751 restraints weight = 39178.511| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.67 r_work: 0.2947 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23397 Z= 0.148 Angle : 0.609 6.931 32010 Z= 0.307 Chirality : 0.037 0.161 3619 Planarity : 0.004 0.044 4125 Dihedral : 5.271 47.202 3304 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.55 % Allowed : 13.70 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2948 helix: 0.79 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.98 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 240 TYR 0.016 0.001 TYR F 208 PHE 0.016 0.001 PHE E 172 TRP 0.011 0.001 TRP F 302 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00312 (23375) covalent geometry : angle 0.60813 (31966) SS BOND : bond 0.01373 ( 22) SS BOND : angle 1.12228 ( 44) hydrogen bonds : bond 0.05514 ( 1563) hydrogen bonds : angle 3.97636 ( 4689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 331 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8743 (m-40) cc_final: 0.8276 (m110) REVERT: B 205 LEU cc_start: 0.8642 (tp) cc_final: 0.8324 (tt) REVERT: D 121 SER cc_start: 0.9188 (t) cc_final: 0.8931 (p) REVERT: E 285 TYR cc_start: 0.8020 (t80) cc_final: 0.7394 (t80) REVERT: G 53 ASN cc_start: 0.8817 (m-40) cc_final: 0.8576 (m110) REVERT: I 53 ASN cc_start: 0.8660 (m-40) cc_final: 0.8217 (m110) REVERT: J 137 ASP cc_start: 0.8713 (t0) cc_final: 0.8409 (t0) outliers start: 57 outliers final: 42 residues processed: 368 average time/residue: 0.1281 time to fit residues: 80.6772 Evaluate side-chains 303 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 41 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 240 optimal weight: 0.0000 chunk 27 optimal weight: 70.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 229 GLN A 238 HIS A 277 GLN B 45 HIS B 222 GLN D 45 HIS D 207 HIS D 222 GLN G 207 HIS G 222 GLN H 207 HIS I 207 HIS ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.090540 restraints weight = 39288.705| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.66 r_work: 0.2912 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23397 Z= 0.151 Angle : 0.580 6.897 32010 Z= 0.292 Chirality : 0.037 0.178 3619 Planarity : 0.004 0.050 4125 Dihedral : 4.305 18.723 3267 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.72 % Allowed : 17.33 % Favored : 78.95 % 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: 0.60 (0.16), residues: 2948 helix: 1.45 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 240 TYR 0.019 0.001 TYR H 285 PHE 0.014 0.001 PHE E 172 TRP 0.007 0.001 TRP I 278 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00336 (23375) covalent geometry : angle 0.57992 (31966) SS BOND : bond 0.00456 ( 22) SS BOND : angle 0.76995 ( 44) hydrogen bonds : bond 0.05499 ( 1563) hydrogen bonds : angle 3.81112 ( 4689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8823 (m-40) cc_final: 0.8345 (m110) REVERT: A 206 LYS cc_start: 0.8817 (tmmt) cc_final: 0.8556 (tmtt) REVERT: A 236 GLU cc_start: 0.8962 (tt0) cc_final: 0.8563 (tt0) REVERT: B 205 LEU cc_start: 0.8781 (tp) cc_final: 0.8441 (tt) REVERT: B 206 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8573 (tmtt) REVERT: E 285 TYR cc_start: 0.8057 (t80) cc_final: 0.7368 (t80) REVERT: F 148 PHE cc_start: 0.7261 (m-80) cc_final: 0.6988 (m-80) REVERT: G 285 TYR cc_start: 0.8044 (t80) cc_final: 0.7773 (t80) outliers start: 83 outliers final: 70 residues processed: 356 average time/residue: 0.1287 time to fit residues: 77.4753 Evaluate side-chains 348 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 275 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 HIS C 277 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 GLN ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 GLN K 277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096023 restraints weight = 38983.506| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.61 r_work: 0.2958 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23397 Z= 0.114 Angle : 0.544 6.126 32010 Z= 0.269 Chirality : 0.035 0.173 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.987 16.355 3267 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.27 % Allowed : 19.26 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.16), residues: 2948 helix: 2.07 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.58 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 240 TYR 0.023 0.001 TYR C 285 PHE 0.009 0.001 PHE E 148 TRP 0.005 0.001 TRP K 302 HIS 0.002 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (23375) covalent geometry : angle 0.54450 (31966) SS BOND : bond 0.00434 ( 22) SS BOND : angle 0.50426 ( 44) hydrogen bonds : bond 0.04426 ( 1563) hydrogen bonds : angle 3.37980 ( 4689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 310 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8671 (m-40) cc_final: 0.8166 (m110) REVERT: A 236 GLU cc_start: 0.8977 (tt0) cc_final: 0.8537 (tt0) REVERT: A 285 TYR cc_start: 0.7926 (t80) cc_final: 0.7125 (t80) REVERT: B 205 LEU cc_start: 0.8729 (tp) cc_final: 0.8345 (tt) REVERT: B 206 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8523 (tmtt) REVERT: B 277 GLN cc_start: 0.8215 (mm110) cc_final: 0.7998 (mp10) REVERT: E 285 TYR cc_start: 0.8018 (t80) cc_final: 0.7369 (t80) REVERT: F 148 PHE cc_start: 0.6866 (m-80) cc_final: 0.6658 (m-80) REVERT: G 285 TYR cc_start: 0.8000 (t80) cc_final: 0.7747 (t80) REVERT: I 85 GLU cc_start: 0.8274 (tp30) cc_final: 0.7652 (tp30) REVERT: I 174 GLU cc_start: 0.8459 (tp30) cc_final: 0.8178 (mm-30) REVERT: I 261 GLU cc_start: 0.8512 (tp30) cc_final: 0.8307 (tp30) outliers start: 73 outliers final: 45 residues processed: 352 average time/residue: 0.1223 time to fit residues: 73.1491 Evaluate side-chains 324 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 67 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 255 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 222 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094256 restraints weight = 38819.512| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.78 r_work: 0.2938 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23397 Z= 0.125 Angle : 0.541 5.771 32010 Z= 0.269 Chirality : 0.035 0.163 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.872 15.740 3267 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.40 % Allowed : 20.02 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.16), residues: 2948 helix: 2.29 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.48 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 240 TYR 0.022 0.001 TYR I 285 PHE 0.011 0.001 PHE E 148 TRP 0.005 0.001 TRP H 278 HIS 0.002 0.000 HIS F 45 Details of bonding type rmsd covalent geometry : bond 0.00272 (23375) covalent geometry : angle 0.54108 (31966) SS BOND : bond 0.00193 ( 22) SS BOND : angle 0.61319 ( 44) hydrogen bonds : bond 0.04718 ( 1563) hydrogen bonds : angle 3.40522 ( 4689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 290 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8723 (m-40) cc_final: 0.8221 (m110) REVERT: A 236 GLU cc_start: 0.8960 (tt0) cc_final: 0.8578 (tt0) REVERT: A 285 TYR cc_start: 0.7901 (t80) cc_final: 0.7149 (t80) REVERT: B 205 LEU cc_start: 0.8756 (tp) cc_final: 0.8386 (tt) REVERT: B 206 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8552 (tmtt) REVERT: C 45 HIS cc_start: 0.7890 (m170) cc_final: 0.7687 (m-70) REVERT: C 206 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8341 (tmtt) REVERT: E 285 TYR cc_start: 0.8057 (t80) cc_final: 0.7463 (t80) REVERT: G 285 TYR cc_start: 0.8024 (t80) cc_final: 0.7779 (t80) REVERT: I 85 GLU cc_start: 0.8181 (tp30) cc_final: 0.7542 (tp30) REVERT: I 174 GLU cc_start: 0.8497 (tp30) cc_final: 0.8255 (mm-30) REVERT: I 261 GLU cc_start: 0.8515 (tp30) cc_final: 0.8312 (tp30) outliers start: 76 outliers final: 64 residues processed: 329 average time/residue: 0.1272 time to fit residues: 70.9113 Evaluate side-chains 338 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 199 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089301 restraints weight = 39447.472| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.70 r_work: 0.2884 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23397 Z= 0.179 Angle : 0.569 5.472 32010 Z= 0.288 Chirality : 0.037 0.162 3619 Planarity : 0.004 0.042 4125 Dihedral : 3.986 15.871 3267 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.57 % Allowed : 20.02 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.16), residues: 2948 helix: 2.22 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.47 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 173 TYR 0.021 0.001 TYR C 285 PHE 0.012 0.001 PHE J 148 TRP 0.004 0.001 TRP E 278 HIS 0.002 0.001 HIS I 238 Details of bonding type rmsd covalent geometry : bond 0.00416 (23375) covalent geometry : angle 0.56888 (31966) SS BOND : bond 0.00347 ( 22) SS BOND : angle 0.76394 ( 44) hydrogen bonds : bond 0.05574 ( 1563) hydrogen bonds : angle 3.63553 ( 4689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 272 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8079 (t0) cc_final: 0.7815 (t0) REVERT: A 206 LYS cc_start: 0.8873 (tmmt) cc_final: 0.8597 (tmtt) REVERT: A 236 GLU cc_start: 0.8988 (tt0) cc_final: 0.8618 (tt0) REVERT: B 206 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8522 (tmtt) REVERT: E 148 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: E 285 TYR cc_start: 0.8119 (t80) cc_final: 0.7369 (t80) REVERT: F 148 PHE cc_start: 0.7023 (m-80) cc_final: 0.6192 (m-80) REVERT: G 285 TYR cc_start: 0.7991 (t80) cc_final: 0.7728 (t80) outliers start: 102 outliers final: 92 residues processed: 324 average time/residue: 0.1216 time to fit residues: 67.2589 Evaluate side-chains 360 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 267 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 194 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS C 45 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.091510 restraints weight = 39051.394| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.69 r_work: 0.2916 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23397 Z= 0.135 Angle : 0.541 5.437 32010 Z= 0.271 Chirality : 0.035 0.162 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.861 15.891 3267 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.16 % Allowed : 20.73 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.16), residues: 2948 helix: 2.38 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 240 TYR 0.026 0.001 TYR I 285 PHE 0.008 0.001 PHE J 148 TRP 0.003 0.001 TRP F 278 HIS 0.002 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00300 (23375) covalent geometry : angle 0.54084 (31966) SS BOND : bond 0.00251 ( 22) SS BOND : angle 0.58923 ( 44) hydrogen bonds : bond 0.04908 ( 1563) hydrogen bonds : angle 3.45121 ( 4689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 277 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8781 (m-40) cc_final: 0.8290 (m110) REVERT: A 76 ASN cc_start: 0.8040 (t0) cc_final: 0.7777 (t0) REVERT: A 137 ASP cc_start: 0.8466 (t0) cc_final: 0.8176 (t0) REVERT: A 206 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8591 (tmtt) REVERT: A 236 GLU cc_start: 0.8961 (tt0) cc_final: 0.8557 (tt0) REVERT: A 285 TYR cc_start: 0.7893 (t80) cc_final: 0.7073 (t80) REVERT: B 206 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8526 (tmtt) REVERT: E 148 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: E 285 TYR cc_start: 0.8119 (t80) cc_final: 0.7404 (t80) REVERT: F 148 PHE cc_start: 0.6873 (m-80) cc_final: 0.6145 (m-80) REVERT: G 285 TYR cc_start: 0.8017 (t80) cc_final: 0.7763 (t80) REVERT: K 206 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8523 (tmtt) outliers start: 93 outliers final: 83 residues processed: 323 average time/residue: 0.1219 time to fit residues: 67.6449 Evaluate side-chains 355 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 271 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 103 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 188 optimal weight: 0.0370 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS C 45 HIS D 45 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 GLN ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093089 restraints weight = 38672.671| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.69 r_work: 0.2938 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23397 Z= 0.118 Angle : 0.529 5.357 32010 Z= 0.264 Chirality : 0.034 0.160 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.722 15.815 3267 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.63 % Allowed : 21.59 % Favored : 74.79 % 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: 2.10 (0.16), residues: 2948 helix: 2.56 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 240 TYR 0.027 0.001 TYR I 285 PHE 0.011 0.001 PHE J 148 TRP 0.003 0.000 TRP I 278 HIS 0.004 0.000 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00253 (23375) covalent geometry : angle 0.52926 (31966) SS BOND : bond 0.00192 ( 22) SS BOND : angle 0.52314 ( 44) hydrogen bonds : bond 0.04508 ( 1563) hydrogen bonds : angle 3.33694 ( 4689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 278 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8005 (t0) cc_final: 0.7716 (t0) REVERT: A 206 LYS cc_start: 0.8805 (tmmt) cc_final: 0.8540 (tmtt) REVERT: A 236 GLU cc_start: 0.8923 (tt0) cc_final: 0.8505 (tt0) REVERT: A 285 TYR cc_start: 0.7919 (t80) cc_final: 0.7104 (t80) REVERT: B 206 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8572 (tmtt) REVERT: E 285 TYR cc_start: 0.8092 (t80) cc_final: 0.7399 (t80) REVERT: F 134 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8246 (pp20) REVERT: F 148 PHE cc_start: 0.6845 (m-80) cc_final: 0.6099 (m-80) REVERT: F 206 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8431 (tmtt) REVERT: G 285 TYR cc_start: 0.7994 (t80) cc_final: 0.7737 (t80) REVERT: H 206 LYS cc_start: 0.8751 (tmtt) cc_final: 0.8422 (tmtt) REVERT: J 137 ASP cc_start: 0.8334 (t0) cc_final: 0.8110 (t0) REVERT: K 137 ASP cc_start: 0.8325 (t70) cc_final: 0.8063 (t0) REVERT: K 206 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8487 (tmtt) outliers start: 81 outliers final: 75 residues processed: 322 average time/residue: 0.1224 time to fit residues: 67.1348 Evaluate side-chains 347 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 272 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 279 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 275 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS C 45 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090705 restraints weight = 39251.803| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.71 r_work: 0.2892 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23397 Z= 0.152 Angle : 0.547 5.905 32010 Z= 0.276 Chirality : 0.035 0.161 3619 Planarity : 0.004 0.043 4125 Dihedral : 3.792 15.301 3267 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.99 % Allowed : 21.67 % Favored : 74.34 % 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: 2.03 (0.16), residues: 2948 helix: 2.48 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.15 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 173 TYR 0.028 0.001 TYR I 285 PHE 0.009 0.001 PHE E 172 TRP 0.004 0.001 TRP J 189 HIS 0.003 0.000 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00348 (23375) covalent geometry : angle 0.54692 (31966) SS BOND : bond 0.00221 ( 22) SS BOND : angle 0.67316 ( 44) hydrogen bonds : bond 0.05119 ( 1563) hydrogen bonds : angle 3.47358 ( 4689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 268 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8043 (t0) cc_final: 0.7780 (t0) REVERT: A 137 ASP cc_start: 0.8431 (t0) cc_final: 0.8167 (t0) REVERT: A 206 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8594 (tmtt) REVERT: A 236 GLU cc_start: 0.8956 (tt0) cc_final: 0.8557 (tt0) REVERT: B 206 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8534 (tmtt) REVERT: E 285 TYR cc_start: 0.8127 (t80) cc_final: 0.7390 (t80) REVERT: F 148 PHE cc_start: 0.6945 (m-80) cc_final: 0.6225 (m-80) REVERT: F 206 LYS cc_start: 0.8617 (tmtt) cc_final: 0.8413 (tmtt) REVERT: G 285 TYR cc_start: 0.8016 (t80) cc_final: 0.7773 (t80) REVERT: H 206 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8595 (tmtt) REVERT: J 137 ASP cc_start: 0.8162 (t0) cc_final: 0.7939 (t0) REVERT: K 137 ASP cc_start: 0.8388 (t70) cc_final: 0.8134 (t0) outliers start: 89 outliers final: 86 residues processed: 316 average time/residue: 0.1256 time to fit residues: 67.2360 Evaluate side-chains 347 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 261 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 168 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 86 optimal weight: 0.0000 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 271 optimal weight: 50.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS C 45 HIS D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092024 restraints weight = 38850.127| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.68 r_work: 0.2928 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23397 Z= 0.134 Angle : 0.539 6.836 32010 Z= 0.271 Chirality : 0.035 0.161 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.740 15.240 3267 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.76 % Allowed : 22.08 % Favored : 74.16 % 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: 2.15 (0.16), residues: 2948 helix: 2.55 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.01 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 173 TYR 0.029 0.001 TYR I 285 PHE 0.006 0.001 PHE J 172 TRP 0.003 0.001 TRP F 278 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00299 (23375) covalent geometry : angle 0.53931 (31966) SS BOND : bond 0.00194 ( 22) SS BOND : angle 0.61345 ( 44) hydrogen bonds : bond 0.04815 ( 1563) hydrogen bonds : angle 3.40656 ( 4689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8071 (t0) cc_final: 0.7794 (t0) REVERT: A 137 ASP cc_start: 0.8407 (t0) cc_final: 0.8131 (t0) REVERT: A 206 LYS cc_start: 0.8851 (tmmt) cc_final: 0.8579 (tmtt) REVERT: A 236 GLU cc_start: 0.8943 (tt0) cc_final: 0.8538 (tt0) REVERT: B 206 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8594 (tmtt) REVERT: E 285 TYR cc_start: 0.8139 (t80) cc_final: 0.7398 (t80) REVERT: F 148 PHE cc_start: 0.6977 (m-80) cc_final: 0.6282 (m-80) REVERT: G 285 TYR cc_start: 0.8012 (t80) cc_final: 0.7778 (t80) REVERT: J 137 ASP cc_start: 0.8177 (t0) cc_final: 0.7944 (t0) REVERT: K 137 ASP cc_start: 0.8373 (t70) cc_final: 0.8118 (t0) outliers start: 84 outliers final: 82 residues processed: 312 average time/residue: 0.1222 time to fit residues: 64.9938 Evaluate side-chains 342 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 260 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 291 GLN Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 108 optimal weight: 70.0000 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 60.0000 chunk 65 optimal weight: 0.0670 chunk 172 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091734 restraints weight = 39052.498| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.69 r_work: 0.2905 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23397 Z= 0.136 Angle : 0.543 6.687 32010 Z= 0.273 Chirality : 0.035 0.160 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.736 15.112 3267 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.03 % Allowed : 22.12 % Favored : 73.85 % 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: 2.19 (0.16), residues: 2948 helix: 2.56 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 173 TYR 0.029 0.001 TYR I 285 PHE 0.009 0.001 PHE E 148 TRP 0.003 0.001 TRP F 278 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00307 (23375) covalent geometry : angle 0.54255 (31966) SS BOND : bond 0.00193 ( 22) SS BOND : angle 0.62105 ( 44) hydrogen bonds : bond 0.04892 ( 1563) hydrogen bonds : angle 3.41793 ( 4689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4500.15 seconds wall clock time: 77 minutes 56.72 seconds (4676.72 seconds total)