Starting phenix.real_space_refine on Sat Feb 7 12:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nye_49932/02_2026/9nye_49932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nye_49932/02_2026/9nye_49932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nye_49932/02_2026/9nye_49932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nye_49932/02_2026/9nye_49932.map" model { file = "/net/cci-nas-00/data/ceres_data/9nye_49932/02_2026/9nye_49932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nye_49932/02_2026/9nye_49932.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16392 atoms to isotropic. 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 64 5.16 5 C 12824 2.51 5 N 3192 2.21 5 O 3512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19592 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2449 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 40 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 2.64, per 1000 atoms: 0.13 Number of scatterers: 19592 At special positions: 0 Unit cell: (111.15, 111.15, 181.45, 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 64 16.00 O 3512 8.00 N 3192 7.00 C 12824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 873.1 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 54.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.803A pdb=" N THR A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 180 removed outlier: 4.017A pdb=" N LYS A 180 " --> pdb=" O ARG A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 180' Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 4.418A pdb=" N ALA A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 252 Processing helix chain 'A' and resid 262 through 296 Processing helix chain 'B' and resid 17 through 30 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 59 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.803A pdb=" N THR B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 removed outlier: 4.017A pdb=" N LYS B 180 " --> pdb=" O ARG B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 180' Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.418A pdb=" N ALA B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 252 Processing helix chain 'B' and resid 262 through 296 Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.942A pdb=" N GLN C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.802A pdb=" N THR C 176 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 removed outlier: 4.017A pdb=" N LYS C 180 " --> pdb=" O ARG C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 181 through 187 removed outlier: 3.823A pdb=" N GLY C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 removed outlier: 4.418A pdb=" N ALA C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 252 Processing helix chain 'C' and resid 262 through 296 Processing helix chain 'D' and resid 17 through 30 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 59 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.803A pdb=" N THR D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 180 removed outlier: 4.017A pdb=" N LYS D 180 " --> pdb=" O ARG D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 180' Processing helix chain 'D' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.418A pdb=" N ALA D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 252 Processing helix chain 'D' and resid 262 through 296 Processing helix chain 'E' and resid 17 through 30 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 172 through 176 removed outlier: 3.802A pdb=" N THR E 176 " --> pdb=" O PRO E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 4.017A pdb=" N LYS E 180 " --> pdb=" O ARG E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY E 187 " --> pdb=" O PHE E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 223 removed outlier: 4.417A pdb=" N ALA E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 252 Processing helix chain 'E' and resid 262 through 296 Processing helix chain 'F' and resid 17 through 30 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER F 59 " --> pdb=" O ASP F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 169 Processing helix chain 'F' and resid 172 through 176 removed outlier: 3.803A pdb=" N THR F 176 " --> pdb=" O PRO F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 180 removed outlier: 4.016A pdb=" N LYS F 180 " --> pdb=" O ARG F 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 180' Processing helix chain 'F' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY F 187 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 removed outlier: 4.418A pdb=" N ALA F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 252 Processing helix chain 'F' and resid 262 through 296 Processing helix chain 'G' and resid 17 through 30 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER G 59 " --> pdb=" O ASP G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 Processing helix chain 'G' and resid 102 through 113 removed outlier: 4.128A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 146 removed outlier: 3.633A pdb=" N MET G 146 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 169 Processing helix chain 'G' and resid 172 through 176 removed outlier: 3.802A pdb=" N THR G 176 " --> pdb=" O PRO G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 180 removed outlier: 4.016A pdb=" N LYS G 180 " --> pdb=" O ARG G 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 180' Processing helix chain 'G' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY G 187 " --> pdb=" O PHE G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 223 removed outlier: 4.417A pdb=" N ALA G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 252 Processing helix chain 'G' and resid 262 through 296 Processing helix chain 'H' and resid 17 through 30 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 48 through 59 removed outlier: 3.941A pdb=" N GLN H 52 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER H 59 " --> pdb=" O ASP H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 Processing helix chain 'H' and resid 102 through 113 removed outlier: 4.129A pdb=" N GLU H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 removed outlier: 3.634A pdb=" N MET H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 169 Processing helix chain 'H' and resid 172 through 176 removed outlier: 3.802A pdb=" N THR H 176 " --> pdb=" O PRO H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 180 removed outlier: 4.016A pdb=" N LYS H 180 " --> pdb=" O ARG H 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 177 through 180' Processing helix chain 'H' and resid 181 through 187 removed outlier: 3.822A pdb=" N GLY H 187 " --> pdb=" O PHE H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 223 removed outlier: 4.417A pdb=" N ALA H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE H 221 " --> pdb=" O LEU H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 252 Processing helix chain 'H' and resid 262 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.330A pdb=" N ILE A 117 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL A 193 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 119 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE A 195 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR A 121 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG A 159 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 6 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS A 64 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 38 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 66 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS A 40 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 68 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN A 42 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 65 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU D 306 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A 67 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 307 removed outlier: 6.972A pdb=" N ASN B 67 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 306 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 65 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS B 64 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 38 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 66 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS B 40 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 68 " --> pdb=" O CYS B 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN B 42 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER B 6 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG B 159 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 117 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL B 193 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR B 119 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE B 195 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR B 121 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 303 through 307 removed outlier: 6.979A pdb=" N ASN C 67 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 306 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 65 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS C 64 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE C 38 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 66 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS C 40 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU C 68 " --> pdb=" O CYS C 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN C 42 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER C 6 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG C 159 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE C 117 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL C 193 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR C 119 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE C 195 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR C 121 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 303 through 307 removed outlier: 6.977A pdb=" N ASN D 67 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 306 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 65 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS D 64 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 38 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL D 66 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS D 40 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 68 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN D 42 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER D 6 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG D 159 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 117 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL D 193 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR D 119 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE D 195 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR D 121 " --> pdb=" O PHE D 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 190 through 195 removed outlier: 6.330A pdb=" N ILE E 117 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL E 193 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR E 119 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE E 195 " --> pdb=" O TYR E 119 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR E 121 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG E 159 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER E 6 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LYS E 64 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 38 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL E 66 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS E 40 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 68 " --> pdb=" O CYS E 40 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN E 42 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE E 65 " --> pdb=" O LEU H 306 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU H 306 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN E 67 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 303 through 307 removed outlier: 6.971A pdb=" N ASN F 67 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU E 306 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 65 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LYS F 64 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 38 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL F 66 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS F 40 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU F 68 " --> pdb=" O CYS F 40 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN F 42 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER F 6 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG F 159 " --> pdb=" O PRO F 92 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE F 117 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL F 193 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR F 119 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE F 195 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR F 121 " --> pdb=" O PHE F 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 303 through 307 removed outlier: 6.978A pdb=" N ASN G 67 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU F 306 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE G 65 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS G 64 " --> pdb=" O TYR G 36 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE G 38 " --> pdb=" O LYS G 64 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL G 66 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS G 40 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU G 68 " --> pdb=" O CYS G 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN G 42 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER G 6 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG G 159 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE G 117 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL G 193 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR G 119 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE G 195 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR G 121 " --> pdb=" O PHE G 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 303 through 307 removed outlier: 6.973A pdb=" N ASN H 67 " --> pdb=" O SER G 304 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU G 306 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE H 65 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS H 64 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE H 38 " --> pdb=" O LYS H 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL H 66 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS H 40 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU H 68 " --> pdb=" O CYS H 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN H 42 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER H 6 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG H 159 " --> pdb=" O PRO H 92 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE H 117 " --> pdb=" O THR H 191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL H 193 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR H 119 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE H 195 " --> pdb=" O TYR H 119 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR H 121 " --> pdb=" O PHE H 195 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6035 1.34 - 1.45: 2746 1.45 - 1.57: 11123 1.57 - 1.69: 0 1.69 - 1.80: 112 Bond restraints: 20016 Sorted by residual: bond pdb=" C ALA E 136 " pdb=" N LYS E 137 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.36e-02 5.41e+03 4.69e+01 bond pdb=" C ALA C 136 " pdb=" N LYS C 137 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.36e-02 5.41e+03 4.68e+01 bond pdb=" C ALA B 136 " pdb=" N LYS B 137 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.36e-02 5.41e+03 4.68e+01 bond pdb=" C ALA D 136 " pdb=" N LYS D 137 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.36e-02 5.41e+03 4.68e+01 bond pdb=" C ALA G 136 " pdb=" N LYS G 137 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.36e-02 5.41e+03 4.68e+01 ... (remaining 20011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 25873 1.45 - 2.89: 950 2.89 - 4.34: 274 4.34 - 5.79: 55 5.79 - 7.23: 24 Bond angle restraints: 27176 Sorted by residual: angle pdb=" CA ALA C 136 " pdb=" C ALA C 136 " pdb=" N LYS C 137 " ideal model delta sigma weight residual 118.17 123.53 -5.36 1.33e+00 5.65e-01 1.62e+01 angle pdb=" CA ALA A 136 " pdb=" C ALA A 136 " pdb=" N LYS A 137 " ideal model delta sigma weight residual 118.17 123.53 -5.36 1.33e+00 5.65e-01 1.62e+01 angle pdb=" CA ALA F 136 " pdb=" C ALA F 136 " pdb=" N LYS F 137 " ideal model delta sigma weight residual 118.17 123.53 -5.36 1.33e+00 5.65e-01 1.62e+01 angle pdb=" CA ALA G 136 " pdb=" C ALA G 136 " pdb=" N LYS G 137 " ideal model delta sigma weight residual 118.17 123.52 -5.35 1.33e+00 5.65e-01 1.62e+01 angle pdb=" CA ALA D 136 " pdb=" C ALA D 136 " pdb=" N LYS D 137 " ideal model delta sigma weight residual 118.17 123.51 -5.34 1.33e+00 5.65e-01 1.61e+01 ... (remaining 27171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 10241 16.31 - 32.62: 1127 32.62 - 48.93: 456 48.93 - 65.25: 80 65.25 - 81.56: 16 Dihedral angle restraints: 11920 sinusoidal: 4752 harmonic: 7168 Sorted by residual: dihedral pdb=" CD ARG E 175 " pdb=" NE ARG E 175 " pdb=" CZ ARG E 175 " pdb=" NH1 ARG E 175 " ideal model delta sinusoidal sigma weight residual 0.00 -81.17 81.17 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CD ARG G 175 " pdb=" NE ARG G 175 " pdb=" CZ ARG G 175 " pdb=" NH1 ARG G 175 " ideal model delta sinusoidal sigma weight residual 0.00 -81.16 81.16 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CD ARG H 175 " pdb=" NE ARG H 175 " pdb=" CZ ARG H 175 " pdb=" NH1 ARG H 175 " ideal model delta sinusoidal sigma weight residual 0.00 -81.15 81.15 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 11917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2127 0.040 - 0.079: 699 0.079 - 0.119: 222 0.119 - 0.159: 56 0.159 - 0.199: 24 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CA THR C 155 " pdb=" N THR C 155 " pdb=" C THR C 155 " pdb=" CB THR C 155 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA THR E 155 " pdb=" N THR E 155 " pdb=" C THR E 155 " pdb=" CB THR E 155 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA THR D 155 " pdb=" N THR D 155 " pdb=" C THR D 155 " pdb=" CB THR D 155 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 3125 not shown) Planarity restraints: 3384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 175 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG B 175 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 175 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 175 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 175 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 175 " -1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG G 175 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 175 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG G 175 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG G 175 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 175 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 175 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 175 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 175 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 175 " 0.019 2.00e-02 2.50e+03 ... (remaining 3381 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2771 2.76 - 3.29: 18365 3.29 - 3.83: 32473 3.83 - 4.36: 38585 4.36 - 4.90: 66598 Nonbonded interactions: 158792 Sorted by model distance: nonbonded pdb=" OD1 ASP D 99 " pdb=" NH2 ARG D 197 " model vdw 2.221 3.120 nonbonded pdb=" OD1 ASP C 99 " pdb=" NH2 ARG C 197 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP E 99 " pdb=" NH2 ARG E 197 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP A 99 " pdb=" NH2 ARG A 197 " model vdw 2.223 3.120 nonbonded pdb=" OD1 ASP G 99 " pdb=" NH2 ARG G 197 " model vdw 2.223 3.120 ... (remaining 158787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 20016 Z= 0.364 Angle : 0.715 7.235 27176 Z= 0.441 Chirality : 0.047 0.199 3128 Planarity : 0.025 0.493 3384 Dihedral : 16.461 81.558 7312 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.20 % Allowed : 19.75 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2408 helix: 0.78 (0.15), residues: 1208 sheet: 1.07 (0.26), residues: 312 loop : -1.74 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 177 TYR 0.013 0.002 TYR B 12 PHE 0.008 0.001 PHE C 72 TRP 0.010 0.002 TRP C 231 HIS 0.001 0.000 HIS G 20 Details of bonding type rmsd covalent geometry : bond 0.00564 (20016) covalent geometry : angle 0.71475 (27176) hydrogen bonds : bond 0.13445 ( 960) hydrogen bonds : angle 4.89429 ( 2856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 0.796 Fit side-chains outliers start: 67 outliers final: 18 residues processed: 348 average time/residue: 0.6738 time to fit residues: 262.8434 Evaluate side-chains 294 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 62 GLN B 58 GLN B 62 GLN C 58 GLN C 62 GLN D 58 GLN D 62 GLN E 58 GLN E 62 GLN F 58 GLN F 62 GLN G 58 GLN G 62 GLN H 58 GLN H 62 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.204516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170310 restraints weight = 16521.301| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.23 r_work: 0.3316 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20016 Z= 0.227 Angle : 0.672 7.061 27176 Z= 0.357 Chirality : 0.048 0.173 3128 Planarity : 0.007 0.049 3384 Dihedral : 5.643 31.805 2708 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 8.44 % Allowed : 16.70 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2408 helix: 0.77 (0.15), residues: 1224 sheet: 0.43 (0.25), residues: 360 loop : -1.89 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 177 TYR 0.015 0.002 TYR G 57 PHE 0.015 0.002 PHE E 223 TRP 0.014 0.002 TRP A 231 HIS 0.001 0.000 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00547 (20016) covalent geometry : angle 0.67215 (27176) hydrogen bonds : bond 0.05420 ( 960) hydrogen bonds : angle 3.96070 ( 2856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 275 time to evaluate : 0.829 Fit side-chains REVERT: A 19 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7390 (pm20) REVERT: A 33 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7757 (mptp) REVERT: A 241 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6833 (mp) REVERT: A 310 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: B 19 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7428 (pm20) REVERT: B 33 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7758 (mptp) REVERT: B 241 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6817 (mp) REVERT: B 310 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: C 19 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7410 (pm20) REVERT: C 33 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7752 (mptp) REVERT: C 215 PHE cc_start: 0.4518 (OUTLIER) cc_final: 0.3567 (p90) REVERT: C 241 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6841 (mp) REVERT: C 310 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: D 19 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7409 (pm20) REVERT: D 33 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7753 (mptp) REVERT: D 241 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6808 (mp) REVERT: D 310 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: E 19 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7395 (pm20) REVERT: E 33 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7758 (mptp) REVERT: E 241 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6813 (mp) REVERT: E 310 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: F 19 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7425 (pm20) REVERT: F 33 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7758 (mptp) REVERT: F 241 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6869 (mp) REVERT: F 310 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: G 19 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7400 (pm20) REVERT: G 33 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (mptp) REVERT: G 241 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6814 (mp) REVERT: G 310 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: H 19 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7431 (pm20) REVERT: H 33 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7759 (mptp) REVERT: H 241 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6876 (mp) REVERT: H 310 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7813 (mm-30) outliers start: 177 outliers final: 44 residues processed: 397 average time/residue: 0.6398 time to fit residues: 285.8664 Evaluate side-chains 327 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 310 GLU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 SER Chi-restraints excluded: chain H residue 310 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN B 277 GLN C 58 GLN C 277 GLN D 58 GLN D 277 GLN E 58 GLN E 277 GLN F 58 GLN F 277 GLN G 58 GLN G 277 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.206242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.175615 restraints weight = 16636.357| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.07 r_work: 0.3423 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20016 Z= 0.141 Angle : 0.567 7.012 27176 Z= 0.300 Chirality : 0.043 0.160 3128 Planarity : 0.005 0.035 3384 Dihedral : 4.794 17.820 2680 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.53 % Allowed : 18.99 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2408 helix: 1.09 (0.15), residues: 1224 sheet: 0.48 (0.26), residues: 360 loop : -1.74 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 177 TYR 0.013 0.001 TYR A 57 PHE 0.009 0.001 PHE H 223 TRP 0.015 0.002 TRP H 231 HIS 0.000 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00324 (20016) covalent geometry : angle 0.56696 (27176) hydrogen bonds : bond 0.04262 ( 960) hydrogen bonds : angle 3.62839 ( 2856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 247 time to evaluate : 0.756 Fit side-chains REVERT: A 19 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7240 (pm20) REVERT: A 241 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6199 (mp) REVERT: B 19 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7253 (pm20) REVERT: B 241 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6193 (mp) REVERT: C 19 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7263 (pm20) REVERT: D 19 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7259 (pm20) REVERT: D 241 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6189 (mp) REVERT: E 19 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7248 (pm20) REVERT: E 241 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6172 (mp) REVERT: F 19 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7255 (pm20) REVERT: F 241 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6169 (mp) REVERT: G 19 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7255 (pm20) REVERT: G 241 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6180 (mp) REVERT: H 19 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7249 (pm20) REVERT: H 215 PHE cc_start: 0.3724 (OUTLIER) cc_final: 0.3109 (p90) REVERT: H 241 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6203 (mp) outliers start: 116 outliers final: 33 residues processed: 310 average time/residue: 0.6401 time to fit residues: 224.0077 Evaluate side-chains 274 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 267 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN B 277 GLN C 58 GLN C 277 GLN D 58 GLN D 277 GLN E 58 GLN E 277 GLN F 58 GLN F 277 GLN G 58 GLN G 277 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.202425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170204 restraints weight = 16546.880| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.15 r_work: 0.3312 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 20016 Z= 0.317 Angle : 0.765 7.007 27176 Z= 0.405 Chirality : 0.052 0.189 3128 Planarity : 0.007 0.046 3384 Dihedral : 5.504 19.463 2680 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.73 % Allowed : 18.61 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2408 helix: 0.64 (0.15), residues: 1216 sheet: 0.30 (0.25), residues: 352 loop : -2.08 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 177 TYR 0.017 0.003 TYR A 57 PHE 0.019 0.003 PHE C 223 TRP 0.016 0.003 TRP H 185 HIS 0.001 0.000 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00783 (20016) covalent geometry : angle 0.76518 (27176) hydrogen bonds : bond 0.06238 ( 960) hydrogen bonds : angle 4.08280 ( 2856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 244 time to evaluate : 0.710 Fit side-chains REVERT: A 11 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: A 19 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7629 (pm20) REVERT: A 33 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7847 (mptp) REVERT: A 241 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6959 (mp) REVERT: A 296 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7699 (ttpp) REVERT: B 11 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: B 19 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7633 (pm20) REVERT: B 33 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7843 (mptp) REVERT: B 241 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6942 (mp) REVERT: B 296 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7731 (ttpp) REVERT: C 11 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8285 (mtt) REVERT: C 19 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7648 (pm20) REVERT: C 33 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7847 (mptp) REVERT: C 241 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6945 (mp) REVERT: C 296 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7698 (ttpp) REVERT: D 11 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: D 19 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7635 (pm20) REVERT: D 33 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7846 (mptp) REVERT: D 241 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6954 (mp) REVERT: D 296 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: E 11 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: E 19 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7627 (pm20) REVERT: E 33 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7852 (mptp) REVERT: E 241 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6947 (mp) REVERT: E 296 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7730 (ttpp) REVERT: F 11 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8285 (mtt) REVERT: F 19 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7622 (pm20) REVERT: F 33 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7840 (mptp) REVERT: F 241 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6967 (mp) REVERT: F 296 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7722 (ttpp) REVERT: G 11 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: G 19 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7640 (pm20) REVERT: G 33 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7847 (mptp) REVERT: G 241 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6947 (mp) REVERT: G 296 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7731 (ttpp) REVERT: H 11 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: H 19 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7635 (pm20) REVERT: H 33 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7840 (mptp) REVERT: H 241 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6979 (mp) REVERT: H 296 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7697 (ttpp) outliers start: 141 outliers final: 74 residues processed: 337 average time/residue: 0.7121 time to fit residues: 267.5569 Evaluate side-chains 354 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 248 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 296 LYS Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 LYS Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 LYS Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 296 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN B 277 GLN C 58 GLN C 277 GLN D 58 GLN E 58 GLN E 277 GLN F 58 GLN F 277 GLN G 58 GLN G 277 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.204919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.172626 restraints weight = 16616.804| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.32 r_work: 0.3300 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20016 Z= 0.147 Angle : 0.570 6.935 27176 Z= 0.302 Chirality : 0.044 0.166 3128 Planarity : 0.005 0.040 3384 Dihedral : 4.935 19.225 2680 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.96 % Allowed : 20.75 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2408 helix: 1.07 (0.15), residues: 1216 sheet: 0.31 (0.26), residues: 360 loop : -1.91 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 177 TYR 0.012 0.002 TYR A 57 PHE 0.010 0.001 PHE H 223 TRP 0.015 0.002 TRP F 231 HIS 0.001 0.000 HIS H 20 Details of bonding type rmsd covalent geometry : bond 0.00339 (20016) covalent geometry : angle 0.56954 (27176) hydrogen bonds : bond 0.04348 ( 960) hydrogen bonds : angle 3.62114 ( 2856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 272 time to evaluate : 0.968 Fit side-chains REVERT: A 19 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7515 (pm20) REVERT: A 241 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6750 (mp) REVERT: B 19 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7516 (pm20) REVERT: B 96 ASP cc_start: 0.8241 (p0) cc_final: 0.8018 (p0) REVERT: B 215 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.4145 (p90) REVERT: B 241 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6740 (mp) REVERT: C 19 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7513 (pm20) REVERT: C 161 MET cc_start: 0.8752 (mtm) cc_final: 0.8484 (mtm) REVERT: C 215 PHE cc_start: 0.4889 (OUTLIER) cc_final: 0.4185 (p90) REVERT: C 241 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6728 (mp) REVERT: D 19 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7524 (pm20) REVERT: D 96 ASP cc_start: 0.8252 (p0) cc_final: 0.8039 (p0) REVERT: D 215 PHE cc_start: 0.4873 (OUTLIER) cc_final: 0.4145 (p90) REVERT: D 241 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6740 (mp) REVERT: E 19 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7503 (pm20) REVERT: E 241 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6739 (mp) REVERT: F 19 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7533 (pm20) REVERT: F 96 ASP cc_start: 0.8253 (p0) cc_final: 0.8039 (p0) REVERT: F 241 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6763 (mp) REVERT: G 19 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7506 (pm20) REVERT: G 241 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6730 (mp) REVERT: H 19 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7500 (pm20) REVERT: H 96 ASP cc_start: 0.8244 (p0) cc_final: 0.8032 (p0) REVERT: H 215 PHE cc_start: 0.4854 (OUTLIER) cc_final: 0.4140 (p90) REVERT: H 241 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6770 (mp) outliers start: 83 outliers final: 20 residues processed: 324 average time/residue: 0.6987 time to fit residues: 252.8525 Evaluate side-chains 288 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 241 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 225 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 58 GLN C 58 GLN D 58 GLN D 277 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.207600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.174623 restraints weight = 16364.389| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.27 r_work: 0.3308 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20016 Z= 0.161 Angle : 0.589 6.697 27176 Z= 0.309 Chirality : 0.044 0.162 3128 Planarity : 0.005 0.039 3384 Dihedral : 4.900 20.404 2680 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.01 % Allowed : 20.90 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2408 helix: 1.16 (0.15), residues: 1216 sheet: 0.29 (0.26), residues: 360 loop : -1.87 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 177 TYR 0.013 0.002 TYR E 57 PHE 0.011 0.001 PHE C 223 TRP 0.015 0.002 TRP E 231 HIS 0.000 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00379 (20016) covalent geometry : angle 0.58928 (27176) hydrogen bonds : bond 0.04405 ( 960) hydrogen bonds : angle 3.60856 ( 2856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 254 time to evaluate : 0.783 Fit side-chains REVERT: A 19 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7504 (pm20) REVERT: A 161 MET cc_start: 0.8724 (mtm) cc_final: 0.8441 (mtm) REVERT: A 215 PHE cc_start: 0.4869 (OUTLIER) cc_final: 0.4177 (p90) REVERT: A 241 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6766 (mp) REVERT: B 19 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7499 (pm20) REVERT: B 161 MET cc_start: 0.8735 (mtm) cc_final: 0.8458 (mtm) REVERT: B 215 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4157 (p90) REVERT: B 241 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6747 (mp) REVERT: C 19 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7513 (pm20) REVERT: C 161 MET cc_start: 0.8746 (mtm) cc_final: 0.8474 (mtm) REVERT: C 215 PHE cc_start: 0.4876 (OUTLIER) cc_final: 0.4167 (p90) REVERT: D 19 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7529 (pm20) REVERT: D 161 MET cc_start: 0.8727 (mtm) cc_final: 0.8444 (mtm) REVERT: D 215 PHE cc_start: 0.4873 (OUTLIER) cc_final: 0.4148 (p90) REVERT: D 241 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6747 (mp) REVERT: E 19 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7495 (pm20) REVERT: E 161 MET cc_start: 0.8744 (mtm) cc_final: 0.8462 (mtm) REVERT: E 241 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6751 (mp) REVERT: F 19 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7522 (pm20) REVERT: F 161 MET cc_start: 0.8724 (mtm) cc_final: 0.8442 (mtm) REVERT: F 215 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4168 (p90) REVERT: F 241 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6752 (mp) REVERT: G 19 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7503 (pm20) REVERT: G 161 MET cc_start: 0.8724 (mtm) cc_final: 0.8443 (mtm) REVERT: G 215 PHE cc_start: 0.4886 (OUTLIER) cc_final: 0.4166 (p90) REVERT: G 241 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6748 (mp) REVERT: H 19 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7499 (pm20) REVERT: H 161 MET cc_start: 0.8746 (mtm) cc_final: 0.8463 (mtm) REVERT: H 215 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4141 (p90) REVERT: H 241 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6759 (mp) outliers start: 84 outliers final: 54 residues processed: 319 average time/residue: 0.6447 time to fit residues: 231.1580 Evaluate side-chains 322 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 254 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 267 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 164 optimal weight: 0.8980 chunk 109 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN C 58 GLN D 58 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.209203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.175078 restraints weight = 16689.323| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.28 r_work: 0.3337 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20016 Z= 0.108 Angle : 0.525 6.855 27176 Z= 0.274 Chirality : 0.042 0.221 3128 Planarity : 0.005 0.035 3384 Dihedral : 4.540 20.284 2680 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.48 % Allowed : 22.47 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2408 helix: 1.39 (0.15), residues: 1232 sheet: 0.53 (0.27), residues: 352 loop : -1.66 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 177 TYR 0.011 0.001 TYR A 57 PHE 0.006 0.001 PHE D 195 TRP 0.016 0.001 TRP A 231 HIS 0.001 0.000 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00231 (20016) covalent geometry : angle 0.52545 (27176) hydrogen bonds : bond 0.03474 ( 960) hydrogen bonds : angle 3.36278 ( 2856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 0.718 Fit side-chains REVERT: A 19 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7418 (pm20) REVERT: A 161 MET cc_start: 0.8733 (mtm) cc_final: 0.8467 (mtm) REVERT: B 19 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7415 (pm20) REVERT: B 161 MET cc_start: 0.8792 (mtm) cc_final: 0.8520 (mtm) REVERT: C 19 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7427 (pm20) REVERT: C 161 MET cc_start: 0.8727 (mtm) cc_final: 0.8473 (mtm) REVERT: C 241 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6663 (mp) REVERT: D 19 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7426 (pm20) REVERT: D 161 MET cc_start: 0.8753 (mtm) cc_final: 0.8481 (mtm) REVERT: E 19 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7457 (pm20) REVERT: E 161 MET cc_start: 0.8785 (mtm) cc_final: 0.8516 (mtm) REVERT: F 19 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7463 (pm20) REVERT: F 161 MET cc_start: 0.8728 (mtm) cc_final: 0.8464 (mtm) REVERT: G 19 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7427 (pm20) REVERT: G 161 MET cc_start: 0.8757 (mtm) cc_final: 0.8487 (mtm) REVERT: H 19 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7455 (pm20) REVERT: H 161 MET cc_start: 0.8775 (mtm) cc_final: 0.8504 (mtm) outliers start: 52 outliers final: 23 residues processed: 313 average time/residue: 0.6705 time to fit residues: 234.9068 Evaluate side-chains 262 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 215 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 139 optimal weight: 0.0010 chunk 24 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 161 optimal weight: 0.0270 chunk 194 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN B 277 GLN C 58 GLN C 277 GLN D 52 GLN D 58 GLN D 277 GLN E 52 GLN E 58 GLN E 277 GLN F 52 GLN F 58 GLN F 277 GLN G 58 GLN G 277 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.202580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166413 restraints weight = 16623.376| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.45 r_work: 0.3227 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20016 Z= 0.218 Angle : 0.694 7.369 27176 Z= 0.360 Chirality : 0.047 0.211 3128 Planarity : 0.006 0.041 3384 Dihedral : 5.127 25.038 2680 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.48 % Allowed : 22.81 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2408 helix: 1.04 (0.15), residues: 1224 sheet: 0.40 (0.26), residues: 352 loop : -1.82 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 177 TYR 0.016 0.002 TYR A 57 PHE 0.014 0.002 PHE H 223 TRP 0.013 0.002 TRP E 231 HIS 0.000 0.000 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00530 (20016) covalent geometry : angle 0.69426 (27176) hydrogen bonds : bond 0.04967 ( 960) hydrogen bonds : angle 3.77748 ( 2856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 250 time to evaluate : 0.804 Fit side-chains REVERT: A 19 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7549 (pm20) REVERT: A 33 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7858 (mptp) REVERT: A 161 MET cc_start: 0.8874 (mtm) cc_final: 0.8615 (mtm) REVERT: B 19 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7530 (pm20) REVERT: B 161 MET cc_start: 0.8896 (mtm) cc_final: 0.8636 (mtm) REVERT: C 19 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7551 (pm20) REVERT: C 161 MET cc_start: 0.8959 (mtm) cc_final: 0.8704 (mtm) REVERT: C 241 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6784 (mp) REVERT: D 19 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7567 (pm20) REVERT: D 161 MET cc_start: 0.8888 (mtm) cc_final: 0.8630 (mtm) REVERT: E 19 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7540 (pm20) REVERT: E 161 MET cc_start: 0.8908 (mtm) cc_final: 0.8653 (mtm) REVERT: F 19 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7540 (pm20) REVERT: F 161 MET cc_start: 0.8875 (mtm) cc_final: 0.8618 (mtm) REVERT: G 19 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7557 (pm20) REVERT: G 161 MET cc_start: 0.8893 (mtm) cc_final: 0.8634 (mtm) REVERT: H 19 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7537 (pm20) REVERT: H 33 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7870 (mptp) REVERT: H 161 MET cc_start: 0.8902 (mtm) cc_final: 0.8644 (mtm) outliers start: 73 outliers final: 45 residues processed: 319 average time/residue: 0.6755 time to fit residues: 241.4786 Evaluate side-chains 298 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 304 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 238 optimal weight: 0.0670 chunk 200 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN C 58 GLN D 58 GLN E 52 GLN E 58 GLN F 52 GLN F 58 GLN G 58 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.205895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.171395 restraints weight = 16634.300| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.33 r_work: 0.3347 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20016 Z= 0.120 Angle : 0.564 6.686 27176 Z= 0.291 Chirality : 0.043 0.196 3128 Planarity : 0.005 0.037 3384 Dihedral : 4.748 25.876 2680 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.15 % Allowed : 23.66 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2408 helix: 1.31 (0.15), residues: 1224 sheet: 0.47 (0.27), residues: 352 loop : -1.63 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 177 TYR 0.011 0.001 TYR A 57 PHE 0.007 0.001 PHE H 223 TRP 0.015 0.001 TRP A 231 HIS 0.001 0.000 HIS G 20 Details of bonding type rmsd covalent geometry : bond 0.00263 (20016) covalent geometry : angle 0.56358 (27176) hydrogen bonds : bond 0.03663 ( 960) hydrogen bonds : angle 3.44709 ( 2856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.766 Fit side-chains REVERT: A 19 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7472 (pm20) REVERT: A 161 MET cc_start: 0.8736 (mtm) cc_final: 0.8460 (mtm) REVERT: A 241 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6734 (mp) REVERT: B 19 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7471 (pm20) REVERT: B 161 MET cc_start: 0.8758 (mtm) cc_final: 0.8475 (mtm) REVERT: B 241 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6681 (mp) REVERT: C 19 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7485 (pm20) REVERT: C 161 MET cc_start: 0.8757 (mtm) cc_final: 0.8498 (mtm) REVERT: C 241 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6692 (mp) REVERT: D 19 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7490 (pm20) REVERT: D 161 MET cc_start: 0.8741 (mtm) cc_final: 0.8457 (mtm) REVERT: D 180 LYS cc_start: 0.8357 (mttt) cc_final: 0.8138 (mttp) REVERT: D 215 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.4176 (p90) REVERT: D 241 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6689 (mp) REVERT: E 19 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7470 (pm20) REVERT: E 161 MET cc_start: 0.8755 (mtm) cc_final: 0.8476 (mtm) REVERT: E 180 LYS cc_start: 0.8356 (mttt) cc_final: 0.8133 (mttp) REVERT: E 241 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6707 (mp) REVERT: F 19 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7472 (pm20) REVERT: F 161 MET cc_start: 0.8735 (mtm) cc_final: 0.8461 (mtm) REVERT: F 180 LYS cc_start: 0.8348 (mttt) cc_final: 0.8129 (mttp) REVERT: F 241 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6721 (mp) REVERT: G 19 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7478 (pm20) REVERT: G 102 GLU cc_start: 0.8283 (mp0) cc_final: 0.7928 (mp0) REVERT: G 161 MET cc_start: 0.8744 (mtm) cc_final: 0.8461 (mtm) REVERT: G 180 LYS cc_start: 0.8349 (mttt) cc_final: 0.8131 (mttp) REVERT: G 241 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6695 (mp) REVERT: H 19 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7475 (pm20) REVERT: H 161 MET cc_start: 0.8754 (mtm) cc_final: 0.8471 (mtm) REVERT: H 215 PHE cc_start: 0.4806 (OUTLIER) cc_final: 0.4180 (p90) REVERT: H 241 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6745 (mp) outliers start: 45 outliers final: 22 residues processed: 284 average time/residue: 0.6926 time to fit residues: 219.6842 Evaluate side-chains 279 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 40 optimal weight: 0.0000 chunk 66 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 277 GLN B 58 GLN C 58 GLN C 277 GLN D 58 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.208621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.175700 restraints weight = 16635.062| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.35 r_work: 0.3358 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20016 Z= 0.112 Angle : 0.547 7.110 27176 Z= 0.282 Chirality : 0.042 0.191 3128 Planarity : 0.005 0.038 3384 Dihedral : 4.565 26.663 2680 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.05 % Allowed : 23.62 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2408 helix: 1.33 (0.15), residues: 1240 sheet: 0.59 (0.28), residues: 352 loop : -1.46 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 177 TYR 0.012 0.001 TYR C 57 PHE 0.006 0.001 PHE H 223 TRP 0.015 0.001 TRP A 231 HIS 0.000 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00245 (20016) covalent geometry : angle 0.54705 (27176) hydrogen bonds : bond 0.03415 ( 960) hydrogen bonds : angle 3.35877 ( 2856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.813 Fit side-chains REVERT: A 19 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7444 (pm20) REVERT: A 161 MET cc_start: 0.8748 (mtm) cc_final: 0.8488 (mtm) REVERT: A 180 LYS cc_start: 0.8219 (mttt) cc_final: 0.7970 (mttp) REVERT: A 215 PHE cc_start: 0.4797 (OUTLIER) cc_final: 0.4205 (p90) REVERT: A 241 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6683 (mp) REVERT: B 19 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7445 (pm20) REVERT: B 161 MET cc_start: 0.8753 (mtm) cc_final: 0.8487 (mtm) REVERT: B 180 LYS cc_start: 0.8219 (mttt) cc_final: 0.7974 (mttp) REVERT: B 241 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6663 (mp) REVERT: C 19 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7460 (pm20) REVERT: C 161 MET cc_start: 0.8726 (mtm) cc_final: 0.8477 (mtm) REVERT: C 180 LYS cc_start: 0.8225 (mttt) cc_final: 0.7976 (mttp) REVERT: D 19 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7474 (pm20) REVERT: D 161 MET cc_start: 0.8732 (mtm) cc_final: 0.8465 (mtm) REVERT: D 180 LYS cc_start: 0.8232 (mttt) cc_final: 0.7968 (mttp) REVERT: D 215 PHE cc_start: 0.4804 (OUTLIER) cc_final: 0.4202 (p90) REVERT: D 241 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6674 (mp) REVERT: E 19 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7454 (pm20) REVERT: E 161 MET cc_start: 0.8745 (mtm) cc_final: 0.8481 (mtm) REVERT: E 180 LYS cc_start: 0.8225 (mttt) cc_final: 0.7980 (mttp) REVERT: E 241 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6654 (mp) REVERT: F 19 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7445 (pm20) REVERT: F 161 MET cc_start: 0.8742 (mtm) cc_final: 0.8483 (mtm) REVERT: F 180 LYS cc_start: 0.8237 (mttt) cc_final: 0.7974 (mttp) REVERT: F 215 PHE cc_start: 0.4792 (OUTLIER) cc_final: 0.4198 (p90) REVERT: F 241 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6654 (mp) REVERT: G 19 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7419 (pm20) REVERT: G 102 GLU cc_start: 0.8336 (mp0) cc_final: 0.8042 (mp0) REVERT: G 161 MET cc_start: 0.8744 (mtm) cc_final: 0.8477 (mtm) REVERT: G 180 LYS cc_start: 0.8234 (mttt) cc_final: 0.7971 (mttp) REVERT: G 215 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.4195 (p90) REVERT: G 241 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6646 (mp) REVERT: H 19 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7448 (pm20) REVERT: H 161 MET cc_start: 0.8748 (mtm) cc_final: 0.8481 (mtm) REVERT: H 180 LYS cc_start: 0.8226 (mttt) cc_final: 0.7977 (mttp) REVERT: H 241 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6694 (mp) outliers start: 43 outliers final: 19 residues processed: 294 average time/residue: 0.6672 time to fit residues: 220.2311 Evaluate side-chains 280 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 215 PHE Chi-restraints excluded: chain H residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 58 GLN A 277 GLN B 58 GLN B 277 GLN C 58 GLN D 58 GLN D 277 GLN E 52 GLN E 58 GLN E 277 GLN F 52 GLN F 58 GLN F 277 GLN G 58 GLN G 277 GLN H 52 GLN H 58 GLN H 277 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.205343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.171555 restraints weight = 16899.984| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.42 r_work: 0.3323 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20016 Z= 0.118 Angle : 0.560 7.223 27176 Z= 0.287 Chirality : 0.043 0.189 3128 Planarity : 0.005 0.040 3384 Dihedral : 4.564 26.849 2680 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.19 % Allowed : 23.95 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2408 helix: 1.36 (0.15), residues: 1232 sheet: 0.58 (0.27), residues: 352 loop : -1.43 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 177 TYR 0.012 0.001 TYR A 57 PHE 0.007 0.001 PHE B 223 TRP 0.014 0.001 TRP G 231 HIS 0.000 0.000 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00262 (20016) covalent geometry : angle 0.55999 (27176) hydrogen bonds : bond 0.03538 ( 960) hydrogen bonds : angle 3.37966 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6480.00 seconds wall clock time: 111 minutes 13.39 seconds (6673.39 seconds total)