Starting phenix.real_space_refine on Sun Sep 29 12:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/09_2024/6vak_21141.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/09_2024/6vak_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/09_2024/6vak_21141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/09_2024/6vak_21141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/09_2024/6vak_21141.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/09_2024/6vak_21141.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 6.26, per 1000 atoms: 0.27 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=2, 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 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: 5.89 Conformation dependent library (CDL) restraints added in 3.0 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: 1.96 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: 6.36 Time building geometry restraints manager: 6.78 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: 12378 16.83 - 33.67: 958 33.67 - 50.50: 255 50.50 - 67.33: 11 67.33 - 84.17: 55 Dihedral angle restraints: 13657 sinusoidal: 4912 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 13654 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: 2.03 - 2.60: 174 2.60 - 3.18: 20920 3.18 - 3.75: 34886 3.75 - 4.33: 43803 4.33 - 4.90: 73888 Nonbonded interactions: 173671 Sorted by model distance: nonbonded pdb=" SG CYS J 46 " pdb=" SG CYS J 130 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 46 " pdb=" SG CYS F 130 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 46 " pdb=" SG CYS C 130 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS K 46 " pdb=" SG CYS K 130 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 46 " pdb=" SG CYS B 130 " model vdw 2.029 3.760 ... (remaining 173666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.550 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 40.630 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.050 ------------------------------------------------------------------------------- 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 23375 Z= 0.268 Angle : 0.765 6.719 31966 Z= 0.453 Chirality : 0.037 0.129 3619 Planarity : 0.005 0.045 4125 Dihedral : 14.359 84.169 7997 Min Nonbonded Distance : 2.029 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP G 189 HIS 0.005 0.001 HIS J 238 PHE 0.021 0.001 PHE A 172 TYR 0.014 0.001 TYR J 287 ARG 0.003 0.000 ARG F 159 *********************** 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 fitting. rotamer outliers: 66 poor density : 444 time to evaluate : 2.718 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: 0.9053 (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: 0.8339 (mp) REVERT: H 190 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8290 (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: 0.2829 time to fit residues: 232.6465 Evaluate side-chains 288 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 268 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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 250 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 238 HIS A 246 ASN B 45 HIS B 53 ASN 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 207 HIS J 238 HIS J 246 ASN K 238 HIS K 246 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23375 Z= 0.226 Angle : 0.616 6.982 31966 Z= 0.311 Chirality : 0.037 0.155 3619 Planarity : 0.004 0.044 4125 Dihedral : 5.345 47.847 3304 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.51 % Allowed : 14.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 2948 helix: 0.71 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 302 HIS 0.005 0.001 HIS J 207 PHE 0.017 0.001 PHE E 172 TYR 0.015 0.001 TYR F 208 ARG 0.004 0.000 ARG A 240 *********************** 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 396 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 340 time to evaluate : 2.446 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: A 53 ASN cc_start: 0.8108 (m-40) cc_final: 0.7775 (m110) REVERT: E 285 TYR cc_start: 0.7778 (t80) cc_final: 0.7391 (t80) outliers start: 56 outliers final: 38 residues processed: 378 average time/residue: 0.2617 time to fit residues: 167.5183 Evaluate side-chains 297 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 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 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 198 LEU 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 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 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 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 129 VAL 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 129 VAL 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 149 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 270 optimal weight: 70.0000 chunk 291 optimal weight: 2.9990 chunk 240 optimal weight: 0.0000 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 216 optimal weight: 80.0000 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 277 GLN B 45 HIS C 45 HIS D 45 HIS D 222 GLN E 53 ASN G 222 GLN H 53 ASN J 277 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23375 Z= 0.177 Angle : 0.563 6.907 31966 Z= 0.283 Chirality : 0.036 0.159 3619 Planarity : 0.004 0.046 4125 Dihedral : 4.287 15.990 3267 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.82 % Allowed : 18.41 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2948 helix: 1.61 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP G 302 HIS 0.003 0.001 HIS K 238 PHE 0.010 0.001 PHE E 148 TYR 0.019 0.001 TYR H 285 ARG 0.003 0.000 ARG K 240 *********************** 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 390 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 327 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.7960 (m-40) cc_final: 0.7633 (m110) REVERT: A 285 TYR cc_start: 0.7745 (t80) cc_final: 0.7188 (t80) REVERT: B 126 GLU cc_start: 0.7822 (pp20) cc_final: 0.7619 (pt0) REVERT: D 285 TYR cc_start: 0.7851 (t80) cc_final: 0.7380 (t80) REVERT: E 285 TYR cc_start: 0.7769 (t80) cc_final: 0.7290 (t80) REVERT: G 48 CYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7051 (p) outliers start: 63 outliers final: 47 residues processed: 364 average time/residue: 0.2742 time to fit residues: 167.8631 Evaluate side-chains 325 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 277 GLN 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 C residue 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 239 SER 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 E residue 73 ILE 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 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 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 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 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 148 PHE 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 129 VAL 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 266 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 40.0000 chunk 287 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 256 optimal weight: 0.0570 chunk 77 optimal weight: 0.0010 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 45 HIS C 45 HIS C 277 GLN D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23375 Z= 0.146 Angle : 0.538 6.215 31966 Z= 0.268 Chirality : 0.034 0.168 3619 Planarity : 0.004 0.045 4125 Dihedral : 3.994 16.919 3267 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.60 % Allowed : 19.39 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.16), residues: 2948 helix: 2.10 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 278 HIS 0.002 0.001 HIS K 238 PHE 0.010 0.001 PHE E 148 TYR 0.021 0.001 TYR C 285 ARG 0.002 0.000 ARG K 240 *********************** 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 372 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 314 time to evaluate : 2.446 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: A 53 ASN cc_start: 0.7808 (m-40) cc_final: 0.7486 (m110) REVERT: A 285 TYR cc_start: 0.7684 (t80) cc_final: 0.7163 (t80) REVERT: D 285 TYR cc_start: 0.7694 (t80) cc_final: 0.7329 (t80) REVERT: E 285 TYR cc_start: 0.7698 (t80) cc_final: 0.7420 (t80) REVERT: F 48 CYS cc_start: 0.7557 (m) cc_final: 0.7163 (p) REVERT: G 48 CYS cc_start: 0.7282 (m) cc_final: 0.6746 (p) REVERT: I 85 GLU cc_start: 0.7773 (tp30) cc_final: 0.7456 (tp30) REVERT: I 148 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.3330 (t80) REVERT: J 48 CYS cc_start: 0.7211 (m) cc_final: 0.6832 (p) REVERT: J 190 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8232 (tt) REVERT: K 48 CYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6890 (p) outliers start: 58 outliers final: 35 residues processed: 344 average time/residue: 0.2610 time to fit residues: 153.0415 Evaluate side-chains 313 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 129 VAL 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 129 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 48 CYS 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 201 LEU 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 148 PHE Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 190 LEU 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 129 VAL 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 239 optimal weight: 0.3980 chunk 162 optimal weight: 70.0000 chunk 4 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 0 optimal weight: 60.0000 chunk 146 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** A 277 GLN B 45 HIS B 277 GLN C 45 HIS D 45 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN G 45 HIS K 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23375 Z= 0.158 Angle : 0.527 5.649 31966 Z= 0.263 Chirality : 0.034 0.162 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.827 14.510 3267 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.13 % Allowed : 20.56 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 2948 helix: 2.37 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.49 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 189 HIS 0.002 0.000 HIS G 45 PHE 0.011 0.001 PHE E 148 TYR 0.022 0.001 TYR I 285 ARG 0.001 0.000 ARG K 173 *********************** 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 fitting. rotamer outliers: 70 poor density : 296 time to evaluate : 2.317 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: A 53 ASN cc_start: 0.7875 (m-40) cc_final: 0.7575 (m110) REVERT: A 285 TYR cc_start: 0.7669 (t80) cc_final: 0.7188 (t80) REVERT: B 48 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6918 (p) REVERT: D 285 TYR cc_start: 0.7767 (t80) cc_final: 0.7410 (t80) REVERT: E 285 TYR cc_start: 0.7743 (t80) cc_final: 0.7450 (t80) REVERT: F 48 CYS cc_start: 0.7510 (m) cc_final: 0.7143 (p) REVERT: G 48 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6763 (p) REVERT: I 48 CYS cc_start: 0.7345 (m) cc_final: 0.6742 (p) REVERT: I 85 GLU cc_start: 0.7659 (tp30) cc_final: 0.7355 (tp30) REVERT: I 148 PHE cc_start: 0.5343 (OUTLIER) cc_final: 0.3464 (t80) REVERT: J 48 CYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6868 (p) REVERT: J 190 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8280 (tt) REVERT: K 48 CYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6753 (p) outliers start: 70 outliers final: 50 residues processed: 331 average time/residue: 0.2719 time to fit residues: 151.1845 Evaluate side-chains 333 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 277 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 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 73 ILE Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 148 PHE 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 73 ILE Chi-restraints excluded: chain F residue 79 THR 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 236 GLU 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 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 201 LEU 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 148 PHE 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 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 190 LEU 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 129 VAL 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 96 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 168 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 95 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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 53 ASN B 222 GLN C 45 HIS D 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23375 Z= 0.161 Angle : 0.521 5.507 31966 Z= 0.260 Chirality : 0.034 0.166 3619 Planarity : 0.004 0.043 4125 Dihedral : 3.713 15.224 3267 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.54 % Allowed : 20.69 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2948 helix: 2.53 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.34 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 278 HIS 0.002 0.000 HIS G 45 PHE 0.008 0.001 PHE E 148 TYR 0.023 0.001 TYR I 285 ARG 0.001 0.000 ARG G 173 *********************** 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 364 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 285 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.7875 (m-40) cc_final: 0.7585 (m110) REVERT: A 285 TYR cc_start: 0.7682 (t80) cc_final: 0.7183 (t80) REVERT: B 48 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7075 (p) REVERT: D 285 TYR cc_start: 0.7771 (t80) cc_final: 0.7411 (t80) REVERT: E 285 TYR cc_start: 0.7731 (t80) cc_final: 0.7429 (t80) REVERT: F 48 CYS cc_start: 0.7619 (m) cc_final: 0.7300 (p) REVERT: G 48 CYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6800 (p) REVERT: H 217 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6491 (mt-10) REVERT: I 48 CYS cc_start: 0.7353 (m) cc_final: 0.6878 (p) REVERT: I 148 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.3712 (t80) REVERT: J 48 CYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6653 (p) REVERT: J 190 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8305 (tt) REVERT: K 48 CYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6965 (p) outliers start: 79 outliers final: 62 residues processed: 330 average time/residue: 0.2967 time to fit residues: 160.1423 Evaluate side-chains 342 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 274 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 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 73 ILE 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 129 VAL 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 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 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 202 THR Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 239 SER 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 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 201 LEU 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 148 PHE 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 190 LEU 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 148 PHE Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 241 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 45 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS D 207 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS H 207 HIS ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23375 Z= 0.270 Angle : 0.561 6.027 31966 Z= 0.286 Chirality : 0.036 0.163 3619 Planarity : 0.004 0.042 4125 Dihedral : 3.897 14.657 3267 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.48 % Allowed : 20.56 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.16), residues: 2948 helix: 2.38 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.32 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 302 HIS 0.003 0.001 HIS D 45 PHE 0.009 0.001 PHE K 148 TYR 0.026 0.001 TYR I 285 ARG 0.008 0.000 ARG F 179 *********************** 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 fitting. rotamer outliers: 100 poor density : 270 time to evaluate : 2.530 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: A 206 LYS cc_start: 0.8233 (tmtt) cc_final: 0.7987 (tmtt) REVERT: E 285 TYR cc_start: 0.7808 (t80) cc_final: 0.7351 (t80) REVERT: H 217 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6809 (mt-10) outliers start: 100 outliers final: 84 residues processed: 323 average time/residue: 0.2767 time to fit residues: 149.5052 Evaluate side-chains 347 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 263 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 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 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 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 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 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 202 THR Chi-restraints excluded: chain F residue 236 GLU 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 73 ILE Chi-restraints excluded: chain G residue 79 THR 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 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP 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 202 THR Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN 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 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 129 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 5.9990 chunk 114 optimal weight: 0.0670 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 141 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS D 45 HIS I 45 HIS J 222 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23375 Z= 0.142 Angle : 0.524 6.134 31966 Z= 0.262 Chirality : 0.034 0.192 3619 Planarity : 0.004 0.044 4125 Dihedral : 3.685 14.618 3267 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.33 % Allowed : 22.84 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2948 helix: 2.66 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.06 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 80 HIS 0.003 0.001 HIS E 147 PHE 0.008 0.001 PHE J 148 TYR 0.026 0.001 TYR I 285 ARG 0.005 0.000 ARG F 179 *********************** 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 329 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 2.124 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: A 53 ASN cc_start: 0.7736 (m-40) cc_final: 0.7435 (m110) REVERT: D 285 TYR cc_start: 0.7780 (t80) cc_final: 0.7442 (t80) REVERT: E 285 TYR cc_start: 0.7801 (t80) cc_final: 0.7468 (t80) REVERT: F 48 CYS cc_start: 0.7639 (m) cc_final: 0.7267 (p) REVERT: I 48 CYS cc_start: 0.7391 (m) cc_final: 0.6952 (p) outliers start: 52 outliers final: 47 residues processed: 310 average time/residue: 0.2959 time to fit residues: 150.0380 Evaluate side-chains 307 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 260 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A 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 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 148 PHE 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 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 202 THR Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN 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 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 201 LEU 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 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 148 PHE 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 260 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 160 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 70.0000 chunk 241 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23375 Z= 0.201 Angle : 0.540 6.712 31966 Z= 0.272 Chirality : 0.035 0.164 3619 Planarity : 0.004 0.042 4125 Dihedral : 3.707 14.227 3267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.09 % Allowed : 22.44 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.16), residues: 2948 helix: 2.70 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.05 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 302 HIS 0.007 0.001 HIS C 45 PHE 0.010 0.001 PHE J 148 TYR 0.027 0.001 TYR I 285 ARG 0.009 0.000 ARG B 179 *********************** 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 329 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 260 time to evaluate : 2.483 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: E 285 TYR cc_start: 0.7839 (t80) cc_final: 0.7440 (t80) REVERT: F 48 CYS cc_start: 0.7844 (m) cc_final: 0.7385 (p) REVERT: F 148 PHE cc_start: 0.6134 (m-80) cc_final: 0.5864 (m-80) REVERT: I 85 GLU cc_start: 0.7691 (tp30) cc_final: 0.7154 (tp30) outliers start: 69 outliers final: 66 residues processed: 306 average time/residue: 0.2802 time to fit residues: 144.1377 Evaluate side-chains 319 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 253 time to evaluate : 2.376 ------------------------------------------------------------------------------- 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 291 GLN Chi-restraints excluded: chain B residue 48 CYS 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 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE 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 202 THR Chi-restraints excluded: chain E residue 291 GLN 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 236 GLU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 257 ASN 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 129 VAL 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 201 LEU Chi-restraints excluded: chain H residue 202 THR 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 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 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 148 PHE 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 175 optimal weight: 0.8980 chunk 282 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 272 optimal weight: 0.1980 chunk 235 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS H 53 ASN I 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23375 Z= 0.143 Angle : 0.527 6.401 31966 Z= 0.263 Chirality : 0.034 0.163 3619 Planarity : 0.004 0.043 4125 Dihedral : 3.569 14.026 3267 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.24 % Allowed : 23.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.16), residues: 2948 helix: 2.84 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -1.93 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 80 HIS 0.004 0.001 HIS C 45 PHE 0.015 0.001 PHE F 148 TYR 0.029 0.001 TYR I 285 ARG 0.008 0.000 ARG B 179 ********************** 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 353 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 2.704 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 85 GLU cc_start: 0.7730 (tp30) cc_final: 0.7483 (tp30) REVERT: B 205 LEU cc_start: 0.8684 (tt) cc_final: 0.8400 (tp) REVERT: E 285 TYR cc_start: 0.7806 (t80) cc_final: 0.7454 (t80) REVERT: E 291 GLN cc_start: 0.7032 (pt0) cc_final: 0.6832 (mt0) REVERT: F 48 CYS cc_start: 0.7591 (m) cc_final: 0.7226 (p) REVERT: H 85 GLU cc_start: 0.7567 (tp30) cc_final: 0.7303 (tp30) REVERT: I 48 CYS cc_start: 0.7417 (m) cc_final: 0.6990 (p) REVERT: K 239 SER cc_start: 0.8580 (p) cc_final: 0.8349 (p) outliers start: 50 outliers final: 44 residues processed: 333 average time/residue: 0.3068 time to fit residues: 165.7080 Evaluate side-chains 334 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 290 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS 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 B residue 48 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 291 GLN 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 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 202 THR 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 257 ASN Chi-restraints excluded: chain G residue 101 LEU 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 201 LEU 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 101 LEU Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 148 PHE 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 187 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 0.0060 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 43 optimal weight: 2.9990 overall best weight: 1.0012 ------------------------------------------------------------------------------- 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 ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS I 45 HIS ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094508 restraints weight = 39073.171| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.64 r_work: 0.2984 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23375 Z= 0.157 Angle : 0.533 5.725 31966 Z= 0.266 Chirality : 0.034 0.162 3619 Planarity : 0.004 0.043 4125 Dihedral : 3.565 14.209 3267 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.37 % Allowed : 24.05 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.16), residues: 2948 helix: 2.87 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -1.94 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP K 278 HIS 0.004 0.001 HIS F 238 PHE 0.019 0.001 PHE D 148 TYR 0.028 0.001 TYR I 285 ARG 0.008 0.000 ARG B 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.02 seconds wall clock time: 78 minutes 22.52 seconds (4702.52 seconds total)