Starting phenix.real_space_refine on Thu Mar 5 07:00:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7brm_30160/03_2026/7brm_30160.cif Found real_map, /net/cci-nas-00/data/ceres_data/7brm_30160/03_2026/7brm_30160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7brm_30160/03_2026/7brm_30160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7brm_30160/03_2026/7brm_30160.map" model { file = "/net/cci-nas-00/data/ceres_data/7brm_30160/03_2026/7brm_30160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7brm_30160/03_2026/7brm_30160.cif" } resolution = 3.6 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 12780 2.51 5 N 3537 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20277 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "a" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, C, D, E, F, G, H, I, b, c, d, e, f, g, h, i Time building chain proxies: 2.35, per 1000 atoms: 0.12 Number of scatterers: 20277 At special positions: 0 Unit cell: (130, 131, 116, 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 81 16.00 O 3879 8.00 N 3537 7.00 C 12780 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: 1.93 Conformation dependent library (CDL) restraints added in 897.8 milliseconds 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4842 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 19 sheets defined 30.6% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.542A pdb=" N LYS A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 100 through 116 Processing helix chain 'B' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN B 261 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.541A pdb=" N LYS B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 100 through 116 Processing helix chain 'C' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 100 through 116 Processing helix chain 'D' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN D 261 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.820A pdb=" N LYS E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 100 through 116 Processing helix chain 'E' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG E 249 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN E 261 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.822A pdb=" N LYS F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 100 through 116 Processing helix chain 'F' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG F 249 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 250 " --> pdb=" O GLY F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN F 261 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG F 269 " --> pdb=" O LEU F 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 100 through 116 Processing helix chain 'G' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG G 249 " --> pdb=" O ASP G 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN G 261 " --> pdb=" O ALA G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 271 removed outlier: 3.542A pdb=" N LYS G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 269 " --> pdb=" O LEU G 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS H 37 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 100 through 116 Processing helix chain 'H' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG H 249 " --> pdb=" O ASP H 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY H 250 " --> pdb=" O GLY H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN H 261 " --> pdb=" O ALA H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 100 through 116 Processing helix chain 'I' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG I 249 " --> pdb=" O ASP I 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 250 " --> pdb=" O GLY I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN I 261 " --> pdb=" O ALA I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 271 removed outlier: 3.542A pdb=" N LYS I 267 " --> pdb=" O ASP I 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG I 269 " --> pdb=" O LEU I 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 37 No H-bonds generated for 'chain 'a' and resid 35 through 37' Processing helix chain 'a' and resid 38 through 48 removed outlier: 3.516A pdb=" N LEU a 43 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 37 No H-bonds generated for 'chain 'c' and resid 35 through 37' Processing helix chain 'c' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU c 43 " --> pdb=" O GLY c 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 37 No H-bonds generated for 'chain 'd' and resid 35 through 37' Processing helix chain 'd' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU d 43 " --> pdb=" O GLY d 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 37 No H-bonds generated for 'chain 'e' and resid 35 through 37' Processing helix chain 'e' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU e 43 " --> pdb=" O GLY e 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 37 No H-bonds generated for 'chain 'f' and resid 35 through 37' Processing helix chain 'f' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU f 43 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 37 No H-bonds generated for 'chain 'g' and resid 35 through 37' Processing helix chain 'g' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU g 43 " --> pdb=" O GLY g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 37 No H-bonds generated for 'chain 'h' and resid 35 through 37' Processing helix chain 'h' and resid 38 through 48 removed outlier: 3.514A pdb=" N LEU h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 37 No H-bonds generated for 'chain 'i' and resid 35 through 37' Processing helix chain 'i' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE A 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 96 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 51 " --> pdb=" O LEU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 150 through 157 removed outlier: 3.939A pdb=" N LYS C 150 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 167 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 171 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 145 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 173 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 173 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR D 145 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 171 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 162 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA D 203 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP D 164 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 201 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN D 166 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR D 199 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 168 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU D 197 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP D 170 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR D 195 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 172 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER D 193 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 174 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN D 191 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 176 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER D 189 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 215 " --> pdb=" O ARG D 207 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 214 through 224 current: chain 'E' and resid 186 through 208 removed outlier: 6.755A pdb=" N VAL E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER E 189 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU E 176 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN E 191 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 174 " --> pdb=" O ASN E 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER E 193 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 172 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR E 195 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP E 170 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU E 197 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN E 168 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR E 199 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN E 166 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 201 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP E 164 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 203 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY E 162 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 171 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 145 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA E 173 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.900A pdb=" N THR E 222 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 171 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B 145 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 173 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 173 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 145 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN A 171 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 162 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 203 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP A 164 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 201 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 166 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 199 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A 168 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 197 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP A 170 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 195 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 172 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 193 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 174 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 191 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 176 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 189 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 215 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 222 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS I 150 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR I 167 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY I 162 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA I 203 " --> pdb=" O GLY I 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP I 164 " --> pdb=" O VAL I 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL I 201 " --> pdb=" O ASP I 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN I 166 " --> pdb=" O TYR I 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR I 199 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN I 168 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU I 197 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP I 170 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR I 195 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE I 172 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER I 193 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL I 174 " --> pdb=" O ASN I 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN I 191 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU I 176 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER I 189 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 178 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 207 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 215 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR I 222 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS G 150 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR G 167 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN G 171 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR G 145 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA G 173 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 173 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B 145 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 171 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 162 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 203 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 164 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B 201 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 166 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 199 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN B 168 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 197 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP B 170 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 195 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 172 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 193 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL B 174 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 191 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 176 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 189 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 178 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 207 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 215 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 222 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 150 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 167 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN A 171 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 145 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 173 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 173 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 145 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 171 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 162 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 203 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP C 164 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL C 201 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN C 166 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR C 199 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 168 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 197 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP C 170 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR C 195 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 172 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER C 193 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 174 " --> pdb=" O ASN C 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 191 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 176 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER C 189 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 207 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 215 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 222 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS D 150 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D 167 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 162 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA D 203 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP D 164 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 201 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN D 166 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR D 199 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 168 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU D 197 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP D 170 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR D 195 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 172 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER D 193 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 174 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN D 191 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 176 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER D 189 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 215 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 153 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 222 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS F 150 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 167 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN F 171 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR F 145 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA F 173 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA F 173 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR F 145 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN F 171 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY F 162 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA F 203 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP F 164 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL F 201 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN F 166 " --> pdb=" O TYR F 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR F 199 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN F 168 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU F 197 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP F 170 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR F 195 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE F 172 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER F 193 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL F 174 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN F 191 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU F 176 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER F 189 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 178 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 207 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 215 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 222 " --> pdb=" O SER H 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS H 150 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR H 167 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 171 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR H 145 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA H 173 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA I 173 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR I 145 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN I 171 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR I 167 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS I 150 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 222 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 215 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 189 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 176 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 191 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 174 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 193 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 172 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 195 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP A 170 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 197 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A 168 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 199 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 166 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 201 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP A 164 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 203 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 162 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN A 171 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 145 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 173 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.545A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA H 173 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR H 145 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 171 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY H 162 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA H 203 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP H 164 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL H 201 " --> pdb=" O ASP H 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN H 166 " --> pdb=" O TYR H 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR H 199 " --> pdb=" O GLN H 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN H 168 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU H 197 " --> pdb=" O GLN H 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP H 170 " --> pdb=" O THR H 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR H 195 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 172 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER H 193 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL H 174 " --> pdb=" O ASN H 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN H 191 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU H 176 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER H 189 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG H 207 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 215 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY E 153 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR H 222 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS E 150 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 167 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 171 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 145 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA E 173 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 173 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 145 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 171 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 167 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 150 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR G 222 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 215 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 207 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL G 178 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER G 189 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU G 176 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN G 191 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL G 174 " --> pdb=" O ASN G 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER G 193 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE G 172 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR G 195 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP G 170 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU G 197 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN G 168 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR G 199 " --> pdb=" O GLN G 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN G 166 " --> pdb=" O TYR G 199 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL G 201 " --> pdb=" O ASP G 164 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP G 164 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA G 203 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY G 162 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN G 171 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR G 145 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA G 173 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE D 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU D 96 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 51 " --> pdb=" O LEU D 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE E 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU E 96 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 51 " --> pdb=" O LEU E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.277A pdb=" N ILE F 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU F 96 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL F 51 " --> pdb=" O LEU F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.275A pdb=" N ILE H 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU H 96 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 51 " --> pdb=" O LEU H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 49 through 52 removed outlier: 6.275A pdb=" N ILE I 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU I 96 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL I 51 " --> pdb=" O LEU I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 813 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.56 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: 6834 1.34 - 1.45: 3405 1.45 - 1.57: 10263 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 20646 Sorted by residual: bond pdb=" C ARG C 91 " pdb=" N TRP C 92 " ideal model delta sigma weight residual 1.332 1.305 0.028 1.40e-02 5.10e+03 3.94e+00 bond pdb=" C ARG H 91 " pdb=" N TRP H 92 " ideal model delta sigma weight residual 1.332 1.305 0.028 1.40e-02 5.10e+03 3.86e+00 bond pdb=" C ARG E 91 " pdb=" N TRP E 92 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.78e+00 bond pdb=" C ARG A 91 " pdb=" N TRP A 92 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.78e+00 bond pdb=" C ARG B 91 " pdb=" N TRP B 92 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.73e+00 ... (remaining 20641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 24842 1.20 - 2.39: 2501 2.39 - 3.59: 475 3.59 - 4.78: 157 4.78 - 5.98: 42 Bond angle restraints: 28017 Sorted by residual: angle pdb=" N VAL C 266 " pdb=" CA VAL C 266 " pdb=" C VAL C 266 " ideal model delta sigma weight residual 113.42 107.44 5.98 1.17e+00 7.31e-01 2.61e+01 angle pdb=" N VAL A 266 " pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 113.42 107.46 5.96 1.17e+00 7.31e-01 2.59e+01 angle pdb=" N VAL D 266 " pdb=" CA VAL D 266 " pdb=" C VAL D 266 " ideal model delta sigma weight residual 113.42 107.47 5.95 1.17e+00 7.31e-01 2.58e+01 angle pdb=" N VAL I 266 " pdb=" CA VAL I 266 " pdb=" C VAL I 266 " ideal model delta sigma weight residual 113.42 107.48 5.94 1.17e+00 7.31e-01 2.58e+01 angle pdb=" N VAL B 266 " pdb=" CA VAL B 266 " pdb=" C VAL B 266 " ideal model delta sigma weight residual 113.42 107.50 5.92 1.17e+00 7.31e-01 2.56e+01 ... (remaining 28012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.16: 10487 13.16 - 26.33: 1402 26.33 - 39.49: 468 39.49 - 52.65: 72 52.65 - 65.81: 36 Dihedral angle restraints: 12465 sinusoidal: 4923 harmonic: 7542 Sorted by residual: dihedral pdb=" CA GLN A 99 " pdb=" C GLN A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLN B 99 " pdb=" C GLN B 99 " pdb=" N GLY B 100 " pdb=" CA GLY B 100 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLN D 99 " pdb=" C GLN D 99 " pdb=" N GLY D 100 " pdb=" CA GLY D 100 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 12462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1451 0.029 - 0.058: 1027 0.058 - 0.087: 410 0.087 - 0.115: 224 0.115 - 0.144: 56 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA PHE b 32 " pdb=" N PHE b 32 " pdb=" C PHE b 32 " pdb=" CB PHE b 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA PHE c 32 " pdb=" N PHE c 32 " pdb=" C PHE c 32 " pdb=" CB PHE c 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE i 32 " pdb=" N PHE i 32 " pdb=" C PHE i 32 " pdb=" CB PHE i 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 3165 not shown) Planarity restraints: 3699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 94 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO I 95 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 94 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 95 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 94 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO F 95 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 95 " -0.025 5.00e-02 4.00e+02 ... (remaining 3696 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 732 2.68 - 3.24: 21043 3.24 - 3.79: 32333 3.79 - 4.35: 42853 4.35 - 4.90: 75035 Nonbonded interactions: 171996 Sorted by model distance: nonbonded pdb=" OG1 THR A 132 " pdb=" OG1 THR I 183 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR E 183 " pdb=" OG1 THR H 132 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR C 132 " pdb=" OG1 THR D 183 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR A 183 " pdb=" OG1 THR B 132 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR D 132 " pdb=" OG1 THR F 183 " model vdw 2.204 3.040 ... (remaining 171991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.011 0.069 20646 Z= 0.462 Angle : 0.831 5.980 28017 Z= 0.484 Chirality : 0.048 0.144 3168 Planarity : 0.004 0.045 3699 Dihedral : 13.834 65.814 7623 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.24 (0.16), residues: 2583 helix: -2.35 (0.15), residues: 819 sheet: -1.49 (0.21), residues: 648 loop : -2.25 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 269 TYR 0.007 0.002 TYR I 211 PHE 0.023 0.003 PHE h 32 TRP 0.016 0.002 TRP C 252 HIS 0.002 0.001 HIS F 41 Details of bonding type rmsd covalent geometry : bond 0.01053 (20646) covalent geometry : angle 0.83082 (28017) hydrogen bonds : bond 0.19279 ( 713) hydrogen bonds : angle 9.06334 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 PHE cc_start: 0.8297 (t80) cc_final: 0.7409 (t80) REVERT: C 213 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7536 (mmt180) REVERT: D 88 LYS cc_start: 0.8876 (tptp) cc_final: 0.8530 (tptt) REVERT: D 221 TYR cc_start: 0.8867 (t80) cc_final: 0.8580 (t80) REVERT: E 109 LYS cc_start: 0.8732 (mttt) cc_final: 0.8457 (mtmm) REVERT: F 164 ASP cc_start: 0.8277 (p0) cc_final: 0.8025 (p0) REVERT: G 221 TYR cc_start: 0.8788 (t80) cc_final: 0.8515 (t80) REVERT: H 88 LYS cc_start: 0.8865 (tptp) cc_final: 0.8487 (tptt) REVERT: I 164 ASP cc_start: 0.8043 (p0) cc_final: 0.7803 (p0) REVERT: b 32 PHE cc_start: 0.7439 (p90) cc_final: 0.6370 (p90) REVERT: b 52 TYR cc_start: 0.8097 (m-80) cc_final: 0.7716 (m-10) REVERT: c 44 ASN cc_start: 0.8653 (m-40) cc_final: 0.8421 (m-40) REVERT: d 44 ASN cc_start: 0.8602 (m-40) cc_final: 0.8274 (m110) REVERT: h 49 GLN cc_start: 0.7436 (mm110) cc_final: 0.6819 (mm-40) REVERT: i 44 ASN cc_start: 0.8673 (m-40) cc_final: 0.8431 (m110) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1797 time to fit residues: 109.0550 Evaluate side-chains 330 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 270 HIS ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 270 HIS D 77 GLN D 148 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 270 HIS ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 270 HIS ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 GLN F 270 HIS G 148 ASN ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 270 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 270 HIS ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 GLN I 270 HIS a 31 ASN b 31 ASN b 44 ASN b 49 GLN c 31 ASN e 31 ASN e 44 ASN g 31 ASN i 31 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109681 restraints weight = 28979.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112882 restraints weight = 15203.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114905 restraints weight = 9612.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116143 restraints weight = 7019.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116932 restraints weight = 5691.848| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20646 Z= 0.135 Angle : 0.603 6.570 28017 Z= 0.327 Chirality : 0.044 0.191 3168 Planarity : 0.004 0.032 3699 Dihedral : 5.151 26.557 2835 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.64 % Allowed : 15.53 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.17), residues: 2583 helix: -1.12 (0.17), residues: 801 sheet: -0.89 (0.24), residues: 594 loop : -1.95 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 28 TYR 0.022 0.001 TYR E 158 PHE 0.022 0.002 PHE d 32 TRP 0.008 0.002 TRP B 252 HIS 0.004 0.001 HIS C 270 Details of bonding type rmsd covalent geometry : bond 0.00299 (20646) covalent geometry : angle 0.60338 (28017) hydrogen bonds : bond 0.03828 ( 713) hydrogen bonds : angle 5.65157 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 387 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8750 (tptp) cc_final: 0.8482 (tptt) REVERT: B 211 TYR cc_start: 0.7888 (t80) cc_final: 0.7545 (t80) REVERT: C 88 LYS cc_start: 0.8749 (tptp) cc_final: 0.8518 (tptt) REVERT: C 211 TYR cc_start: 0.7750 (t80) cc_final: 0.7549 (t80) REVERT: C 212 GLN cc_start: 0.7726 (mt0) cc_final: 0.7519 (mt0) REVERT: C 213 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7594 (mmt180) REVERT: D 38 ASP cc_start: 0.7915 (t0) cc_final: 0.7642 (t0) REVERT: D 88 LYS cc_start: 0.8770 (tptp) cc_final: 0.8557 (tptt) REVERT: D 213 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7446 (mmt180) REVERT: D 221 TYR cc_start: 0.8794 (t80) cc_final: 0.8494 (t80) REVERT: E 109 LYS cc_start: 0.8579 (mttt) cc_final: 0.8287 (mtmm) REVERT: E 159 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7748 (t80) REVERT: E 211 TYR cc_start: 0.7988 (t80) cc_final: 0.7719 (t80) REVERT: E 212 GLN cc_start: 0.7843 (mt0) cc_final: 0.7433 (mt0) REVERT: F 212 GLN cc_start: 0.7775 (mt0) cc_final: 0.7363 (mm110) REVERT: F 213 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7761 (mmt180) REVERT: G 97 GLU cc_start: 0.7352 (tt0) cc_final: 0.7143 (tt0) REVERT: G 119 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8513 (m) REVERT: H 88 LYS cc_start: 0.8739 (tptp) cc_final: 0.8359 (tptt) REVERT: H 109 LYS cc_start: 0.8628 (mttt) cc_final: 0.8291 (mtmm) REVERT: H 180 ASN cc_start: 0.8690 (t0) cc_final: 0.8470 (t0) REVERT: a 28 ARG cc_start: 0.6637 (mmt180) cc_final: 0.5916 (mmt180) REVERT: b 49 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7386 (mm-40) REVERT: b 52 TYR cc_start: 0.7970 (m-80) cc_final: 0.7607 (m-10) REVERT: h 49 GLN cc_start: 0.7466 (mm110) cc_final: 0.6825 (mm-40) outliers start: 36 outliers final: 14 residues processed: 404 average time/residue: 0.1749 time to fit residues: 103.3258 Evaluate side-chains 345 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 PHE Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain b residue 49 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 61 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS F 148 ASN ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 GLN c 31 ASN e 31 ASN g 49 GLN i 31 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106373 restraints weight = 29346.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109532 restraints weight = 15526.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111544 restraints weight = 9945.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112766 restraints weight = 7318.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113551 restraints weight = 5981.838| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20646 Z= 0.238 Angle : 0.631 7.373 28017 Z= 0.341 Chirality : 0.045 0.157 3168 Planarity : 0.003 0.032 3699 Dihedral : 5.103 26.610 2835 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 2.60 % Allowed : 16.12 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.17), residues: 2583 helix: -0.64 (0.18), residues: 810 sheet: -0.50 (0.25), residues: 504 loop : -1.58 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 213 TYR 0.016 0.001 TYR I 54 PHE 0.025 0.002 PHE b 32 TRP 0.014 0.002 TRP B 252 HIS 0.002 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00556 (20646) covalent geometry : angle 0.63116 (28017) hydrogen bonds : bond 0.03661 ( 713) hydrogen bonds : angle 5.22398 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7841 (tt0) cc_final: 0.7492 (tm-30) REVERT: A 218 GLU cc_start: 0.7378 (tt0) cc_final: 0.6661 (mt-10) REVERT: B 88 LYS cc_start: 0.8767 (tptp) cc_final: 0.8502 (tptt) REVERT: B 216 GLU cc_start: 0.7803 (tt0) cc_final: 0.7514 (tt0) REVERT: B 218 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6444 (mt-10) REVERT: C 88 LYS cc_start: 0.8803 (tptp) cc_final: 0.8597 (tptt) REVERT: D 38 ASP cc_start: 0.7957 (t0) cc_final: 0.7719 (t0) REVERT: D 88 LYS cc_start: 0.8851 (tptp) cc_final: 0.8621 (tptt) REVERT: D 213 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7395 (mmt180) REVERT: E 159 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7748 (t80) REVERT: F 109 LYS cc_start: 0.8612 (mttt) cc_final: 0.8228 (ttmm) REVERT: F 212 GLN cc_start: 0.7809 (mt0) cc_final: 0.7463 (mm110) REVERT: H 88 LYS cc_start: 0.8826 (tptp) cc_final: 0.8418 (tptt) REVERT: H 109 LYS cc_start: 0.8633 (mttt) cc_final: 0.8318 (mtmm) REVERT: H 159 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7495 (t80) REVERT: H 218 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6564 (mt-10) REVERT: a 28 ARG cc_start: 0.6755 (mmt180) cc_final: 0.6469 (mmt180) REVERT: b 52 TYR cc_start: 0.7915 (m-80) cc_final: 0.7550 (m-10) REVERT: f 28 ARG cc_start: 0.6958 (mmt-90) cc_final: 0.6694 (mmt180) REVERT: h 49 GLN cc_start: 0.7463 (mm110) cc_final: 0.6931 (mm-40) outliers start: 57 outliers final: 32 residues processed: 381 average time/residue: 0.1598 time to fit residues: 90.4504 Evaluate side-chains 357 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 323 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 226 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN E 77 GLN ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109869 restraints weight = 29069.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113106 restraints weight = 15287.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115154 restraints weight = 9706.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116385 restraints weight = 7105.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117214 restraints weight = 5788.044| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20646 Z= 0.128 Angle : 0.562 6.935 28017 Z= 0.304 Chirality : 0.043 0.150 3168 Planarity : 0.003 0.024 3699 Dihedral : 4.854 25.607 2835 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.60 % Allowed : 16.80 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 2583 helix: -0.04 (0.19), residues: 810 sheet: -0.54 (0.24), residues: 594 loop : -1.40 (0.20), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.025 0.001 TYR B 211 PHE 0.026 0.002 PHE i 32 TRP 0.009 0.002 TRP F 252 HIS 0.002 0.000 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00293 (20646) covalent geometry : angle 0.56178 (28017) hydrogen bonds : bond 0.03073 ( 713) hydrogen bonds : angle 4.84577 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 358 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8613 (t0) cc_final: 0.8375 (t0) REVERT: A 218 GLU cc_start: 0.7313 (tt0) cc_final: 0.6829 (mt-10) REVERT: B 88 LYS cc_start: 0.8618 (tptp) cc_final: 0.8413 (tptt) REVERT: B 216 GLU cc_start: 0.7720 (tt0) cc_final: 0.7513 (tt0) REVERT: B 218 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: C 88 LYS cc_start: 0.8698 (tptp) cc_final: 0.8476 (tptt) REVERT: D 38 ASP cc_start: 0.7917 (t0) cc_final: 0.7637 (t0) REVERT: D 88 LYS cc_start: 0.8736 (tptp) cc_final: 0.8345 (tptt) REVERT: D 97 GLU cc_start: 0.7353 (tt0) cc_final: 0.6975 (tt0) REVERT: D 213 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7203 (mmt180) REVERT: E 159 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7827 (t80) REVERT: E 197 LEU cc_start: 0.8643 (tp) cc_final: 0.8440 (tp) REVERT: E 213 ARG cc_start: 0.8009 (mmt-90) cc_final: 0.7669 (mmt180) REVERT: G 38 ASP cc_start: 0.8090 (t0) cc_final: 0.7611 (t0) REVERT: H 88 LYS cc_start: 0.8731 (tptp) cc_final: 0.8283 (tptt) REVERT: H 159 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7292 (t80) REVERT: a 28 ARG cc_start: 0.6681 (mmt180) cc_final: 0.6429 (mmt180) REVERT: b 52 TYR cc_start: 0.7798 (m-80) cc_final: 0.7505 (m-10) REVERT: h 44 ASN cc_start: 0.8550 (m-40) cc_final: 0.8206 (m-40) REVERT: h 49 GLN cc_start: 0.7370 (mm110) cc_final: 0.6919 (mm-40) outliers start: 57 outliers final: 28 residues processed: 395 average time/residue: 0.1605 time to fit residues: 93.6862 Evaluate side-chains 359 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 159 PHE Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS B 102 GLN B 148 ASN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107892 restraints weight = 29265.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111079 restraints weight = 15488.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113062 restraints weight = 9912.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114362 restraints weight = 7304.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115099 restraints weight = 5955.562| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20646 Z= 0.213 Angle : 0.600 8.440 28017 Z= 0.325 Chirality : 0.044 0.163 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.938 26.312 2835 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 2.55 % Allowed : 16.80 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.94 (0.18), residues: 2583 helix: 0.05 (0.19), residues: 819 sheet: -0.51 (0.24), residues: 567 loop : -1.07 (0.20), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.020 0.001 TYR H 211 PHE 0.030 0.002 PHE i 32 TRP 0.017 0.002 TRP F 252 HIS 0.002 0.001 HIS E 41 Details of bonding type rmsd covalent geometry : bond 0.00498 (20646) covalent geometry : angle 0.59968 (28017) hydrogen bonds : bond 0.03342 ( 713) hydrogen bonds : angle 4.83450 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7808 (t0) cc_final: 0.7518 (t0) REVERT: A 180 ASN cc_start: 0.8660 (t0) cc_final: 0.8426 (t0) REVERT: A 218 GLU cc_start: 0.7338 (tt0) cc_final: 0.6874 (mt-10) REVERT: B 88 LYS cc_start: 0.8662 (tptp) cc_final: 0.8449 (tptt) REVERT: B 216 GLU cc_start: 0.7687 (tt0) cc_final: 0.7455 (tt0) REVERT: B 218 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: C 88 LYS cc_start: 0.8727 (tptp) cc_final: 0.8512 (tptt) REVERT: D 88 LYS cc_start: 0.8823 (tptp) cc_final: 0.8592 (tptt) REVERT: D 97 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: D 213 ARG cc_start: 0.8106 (mmt-90) cc_final: 0.7249 (mmt180) REVERT: E 213 ARG cc_start: 0.8022 (mmt-90) cc_final: 0.7624 (mmt180) REVERT: F 213 ARG cc_start: 0.8340 (mmp80) cc_final: 0.7767 (mmt180) REVERT: G 38 ASP cc_start: 0.8073 (t0) cc_final: 0.7720 (t0) REVERT: H 88 LYS cc_start: 0.8769 (tptp) cc_final: 0.8334 (tptt) REVERT: H 159 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.6969 (t80) REVERT: H 213 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7598 (mmt180) REVERT: H 218 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6567 (mt-10) REVERT: I 38 ASP cc_start: 0.8123 (t0) cc_final: 0.7875 (t0) REVERT: a 28 ARG cc_start: 0.6668 (mmt180) cc_final: 0.5813 (mmt180) REVERT: b 52 TYR cc_start: 0.7945 (m-80) cc_final: 0.7724 (m-10) REVERT: e 28 ARG cc_start: 0.7362 (mmt180) cc_final: 0.6950 (mmt180) REVERT: h 49 GLN cc_start: 0.7395 (mm110) cc_final: 0.7078 (mm-40) outliers start: 56 outliers final: 33 residues processed: 374 average time/residue: 0.1612 time to fit residues: 89.5355 Evaluate side-chains 361 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 159 PHE Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 117 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 160 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111066 restraints weight = 28725.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114276 restraints weight = 15130.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116308 restraints weight = 9635.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117567 restraints weight = 7076.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118252 restraints weight = 5778.041| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20646 Z= 0.129 Angle : 0.553 6.968 28017 Z= 0.301 Chirality : 0.043 0.158 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.759 25.456 2835 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.50 % Allowed : 17.40 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.90 (0.18), residues: 2583 helix: 0.34 (0.19), residues: 810 sheet: -0.64 (0.22), residues: 657 loop : -1.18 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 26 TYR 0.017 0.001 TYR C 221 PHE 0.024 0.001 PHE E 159 TRP 0.010 0.002 TRP F 252 HIS 0.002 0.000 HIS E 270 Details of bonding type rmsd covalent geometry : bond 0.00298 (20646) covalent geometry : angle 0.55283 (28017) hydrogen bonds : bond 0.02996 ( 713) hydrogen bonds : angle 4.65303 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7842 (t0) cc_final: 0.7590 (t0) REVERT: A 180 ASN cc_start: 0.8546 (t0) cc_final: 0.8266 (t0) REVERT: A 218 GLU cc_start: 0.7218 (tt0) cc_final: 0.6901 (mt-10) REVERT: B 164 ASP cc_start: 0.8414 (p0) cc_final: 0.8207 (p0) REVERT: D 88 LYS cc_start: 0.8751 (tptp) cc_final: 0.8363 (tptt) REVERT: D 213 ARG cc_start: 0.8056 (mmt-90) cc_final: 0.7200 (mmt180) REVERT: F 158 TYR cc_start: 0.8003 (t80) cc_final: 0.7687 (t80) REVERT: G 38 ASP cc_start: 0.8013 (t0) cc_final: 0.7747 (t0) REVERT: G 158 TYR cc_start: 0.7986 (t80) cc_final: 0.7509 (t80) REVERT: H 88 LYS cc_start: 0.8702 (tptp) cc_final: 0.8264 (tptt) REVERT: H 159 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7598 (t80) REVERT: H 218 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6685 (mt-10) REVERT: I 216 GLU cc_start: 0.7327 (tt0) cc_final: 0.7079 (tt0) REVERT: a 28 ARG cc_start: 0.6571 (mmt180) cc_final: 0.5962 (mmt180) REVERT: d 31 ASN cc_start: 0.7865 (t0) cc_final: 0.7607 (t0) REVERT: h 49 GLN cc_start: 0.7445 (mm110) cc_final: 0.7203 (mm-40) outliers start: 55 outliers final: 31 residues processed: 385 average time/residue: 0.1554 time to fit residues: 88.7518 Evaluate side-chains 368 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 336 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 159 PHE Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 102 GLN ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111245 restraints weight = 28857.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114491 restraints weight = 15195.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116534 restraints weight = 9617.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117825 restraints weight = 7036.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118609 restraints weight = 5709.642| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20646 Z= 0.131 Angle : 0.548 7.713 28017 Z= 0.299 Chirality : 0.042 0.156 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.710 24.968 2835 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 1.73 % Allowed : 19.03 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.79 (0.18), residues: 2583 helix: 0.52 (0.19), residues: 810 sheet: -0.60 (0.23), residues: 657 loop : -1.17 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 157 TYR 0.017 0.001 TYR I 54 PHE 0.024 0.002 PHE b 32 TRP 0.012 0.002 TRP F 252 HIS 0.002 0.001 HIS H 270 Details of bonding type rmsd covalent geometry : bond 0.00305 (20646) covalent geometry : angle 0.54783 (28017) hydrogen bonds : bond 0.02958 ( 713) hydrogen bonds : angle 4.56282 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 344 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7848 (t0) cc_final: 0.7613 (t0) REVERT: A 102 GLN cc_start: 0.8008 (tp40) cc_final: 0.7680 (pm20) REVERT: A 180 ASN cc_start: 0.8537 (t0) cc_final: 0.8246 (t0) REVERT: A 218 GLU cc_start: 0.7214 (tt0) cc_final: 0.6885 (mt-10) REVERT: B 164 ASP cc_start: 0.8440 (p0) cc_final: 0.8181 (p0) REVERT: D 88 LYS cc_start: 0.8756 (tptp) cc_final: 0.8350 (tptt) REVERT: D 216 GLU cc_start: 0.7358 (tt0) cc_final: 0.7075 (tt0) REVERT: G 38 ASP cc_start: 0.7968 (t0) cc_final: 0.7738 (t0) REVERT: G 158 TYR cc_start: 0.8055 (t80) cc_final: 0.7692 (t80) REVERT: G 270 HIS cc_start: 0.7233 (m-70) cc_final: 0.7032 (m-70) REVERT: H 88 LYS cc_start: 0.8673 (tptp) cc_final: 0.8226 (tptt) REVERT: H 218 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6685 (mt-10) REVERT: I 59 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7374 (mt-10) REVERT: I 216 GLU cc_start: 0.7246 (tt0) cc_final: 0.6933 (tt0) REVERT: a 28 ARG cc_start: 0.6582 (mmt180) cc_final: 0.5929 (mmt180) REVERT: e 28 ARG cc_start: 0.7112 (mmt180) cc_final: 0.6796 (mmt-90) outliers start: 38 outliers final: 29 residues processed: 375 average time/residue: 0.1542 time to fit residues: 87.1070 Evaluate side-chains 352 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 131 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 31 ASN ** g 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111509 restraints weight = 28830.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114695 restraints weight = 15141.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116723 restraints weight = 9638.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117993 restraints weight = 7050.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118763 restraints weight = 5742.833| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20646 Z= 0.134 Angle : 0.553 7.011 28017 Z= 0.302 Chirality : 0.042 0.163 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.714 25.023 2835 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.87 % Allowed : 20.04 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.18), residues: 2583 helix: 0.70 (0.19), residues: 810 sheet: -0.35 (0.25), residues: 567 loop : -1.00 (0.20), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 157 TYR 0.019 0.001 TYR I 54 PHE 0.024 0.002 PHE b 32 TRP 0.012 0.001 TRP F 252 HIS 0.002 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00313 (20646) covalent geometry : angle 0.55258 (28017) hydrogen bonds : bond 0.02942 ( 713) hydrogen bonds : angle 4.49822 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 331 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7998 (tp40) cc_final: 0.7669 (pm20) REVERT: A 180 ASN cc_start: 0.8486 (t0) cc_final: 0.8223 (t0) REVERT: A 218 GLU cc_start: 0.7153 (tt0) cc_final: 0.6863 (mt-10) REVERT: B 164 ASP cc_start: 0.8397 (p0) cc_final: 0.8167 (p0) REVERT: B 221 TYR cc_start: 0.8802 (t80) cc_final: 0.8477 (t80) REVERT: D 88 LYS cc_start: 0.8741 (tptp) cc_final: 0.8347 (tptt) REVERT: G 38 ASP cc_start: 0.8025 (t0) cc_final: 0.7802 (t0) REVERT: G 158 TYR cc_start: 0.8068 (t80) cc_final: 0.7669 (t80) REVERT: H 88 LYS cc_start: 0.8661 (tptp) cc_final: 0.8219 (tptt) REVERT: H 218 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6609 (mt-10) REVERT: I 216 GLU cc_start: 0.7242 (tt0) cc_final: 0.6925 (tt0) REVERT: a 28 ARG cc_start: 0.6568 (mmt180) cc_final: 0.5921 (mmt180) outliers start: 41 outliers final: 31 residues processed: 361 average time/residue: 0.1532 time to fit residues: 82.8210 Evaluate side-chains 350 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 319 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain b residue 31 ASN Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 74 optimal weight: 0.0170 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117085 restraints weight = 28152.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120192 restraints weight = 14900.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122131 restraints weight = 9513.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123281 restraints weight = 6988.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124121 restraints weight = 5724.605| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20646 Z= 0.142 Angle : 0.557 6.771 28017 Z= 0.304 Chirality : 0.043 0.158 3168 Planarity : 0.003 0.035 3699 Dihedral : 4.735 25.199 2835 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 1.68 % Allowed : 20.49 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.44 (0.18), residues: 2583 helix: 0.79 (0.20), residues: 810 sheet: -0.33 (0.25), residues: 567 loop : -0.97 (0.20), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 157 TYR 0.025 0.001 TYR D 54 PHE 0.024 0.002 PHE b 32 TRP 0.013 0.002 TRP F 252 HIS 0.004 0.001 HIS G 270 Details of bonding type rmsd covalent geometry : bond 0.00332 (20646) covalent geometry : angle 0.55725 (28017) hydrogen bonds : bond 0.02971 ( 713) hydrogen bonds : angle 4.44299 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 323 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7963 (tp40) cc_final: 0.7739 (pm20) REVERT: A 180 ASN cc_start: 0.8500 (t0) cc_final: 0.8252 (t0) REVERT: A 218 GLU cc_start: 0.7088 (tt0) cc_final: 0.6856 (mt-10) REVERT: B 164 ASP cc_start: 0.8377 (p0) cc_final: 0.8159 (p0) REVERT: C 82 MET cc_start: 0.8151 (mtm) cc_final: 0.7873 (mtp) REVERT: D 88 LYS cc_start: 0.8740 (tptp) cc_final: 0.8332 (tptt) REVERT: E 97 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: G 38 ASP cc_start: 0.7979 (t0) cc_final: 0.7776 (t0) REVERT: G 158 TYR cc_start: 0.8083 (t80) cc_final: 0.7768 (t80) REVERT: H 88 LYS cc_start: 0.8655 (tptp) cc_final: 0.8218 (tptt) REVERT: a 28 ARG cc_start: 0.6641 (mmt180) cc_final: 0.5947 (mmt180) REVERT: d 52 TYR cc_start: 0.7493 (m-80) cc_final: 0.7289 (m-10) REVERT: e 28 ARG cc_start: 0.6463 (mmt180) cc_final: 0.5778 (mmt-90) REVERT: g 52 TYR cc_start: 0.7626 (m-80) cc_final: 0.7292 (m-10) outliers start: 37 outliers final: 29 residues processed: 351 average time/residue: 0.1538 time to fit residues: 81.1898 Evaluate side-chains 348 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 318 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 270 HIS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 234 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111053 restraints weight = 29067.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114238 restraints weight = 15295.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116247 restraints weight = 9727.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117478 restraints weight = 7132.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118246 restraints weight = 5818.004| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20646 Z= 0.147 Angle : 0.563 6.668 28017 Z= 0.308 Chirality : 0.043 0.153 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.764 25.400 2835 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.50 % Allowed : 20.90 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.42 (0.18), residues: 2583 helix: 0.83 (0.20), residues: 810 sheet: -0.34 (0.25), residues: 567 loop : -0.95 (0.20), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 213 TYR 0.025 0.001 TYR D 54 PHE 0.023 0.002 PHE b 32 TRP 0.013 0.002 TRP F 252 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00342 (20646) covalent geometry : angle 0.56283 (28017) hydrogen bonds : bond 0.02958 ( 713) hydrogen bonds : angle 4.41966 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7977 (tp40) cc_final: 0.7714 (pm20) REVERT: A 180 ASN cc_start: 0.8513 (t0) cc_final: 0.8229 (t0) REVERT: A 218 GLU cc_start: 0.7137 (tt0) cc_final: 0.6848 (mt-10) REVERT: B 164 ASP cc_start: 0.8411 (p0) cc_final: 0.8178 (p0) REVERT: D 88 LYS cc_start: 0.8764 (tptp) cc_final: 0.8351 (tptt) REVERT: E 97 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: G 38 ASP cc_start: 0.8000 (t0) cc_final: 0.7778 (t0) REVERT: G 158 TYR cc_start: 0.8104 (t80) cc_final: 0.7721 (t80) REVERT: H 88 LYS cc_start: 0.8668 (tptp) cc_final: 0.8229 (tptt) REVERT: I 216 GLU cc_start: 0.7033 (tt0) cc_final: 0.6823 (tt0) REVERT: a 28 ARG cc_start: 0.6668 (mmt180) cc_final: 0.5942 (mmt180) REVERT: d 52 TYR cc_start: 0.7582 (m-80) cc_final: 0.7352 (m-10) REVERT: e 28 ARG cc_start: 0.6510 (mmt180) cc_final: 0.5772 (mmt-90) REVERT: g 52 TYR cc_start: 0.7700 (m-80) cc_final: 0.7346 (m-10) outliers start: 33 outliers final: 28 residues processed: 353 average time/residue: 0.1574 time to fit residues: 83.2253 Evaluate side-chains 349 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 77 optimal weight: 0.0970 chunk 216 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120134 restraints weight = 28317.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123248 restraints weight = 14891.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125183 restraints weight = 9446.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126392 restraints weight = 6935.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127105 restraints weight = 5634.193| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20646 Z= 0.113 Angle : 0.548 6.617 28017 Z= 0.300 Chirality : 0.042 0.150 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.669 24.572 2835 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.46 % Allowed : 21.04 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.43 (0.18), residues: 2583 helix: 0.96 (0.20), residues: 810 sheet: -0.46 (0.23), residues: 657 loop : -1.05 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 28 TYR 0.023 0.001 TYR D 54 PHE 0.029 0.001 PHE G 159 TRP 0.009 0.001 TRP D 252 HIS 0.006 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00259 (20646) covalent geometry : angle 0.54797 (28017) hydrogen bonds : bond 0.02763 ( 713) hydrogen bonds : angle 4.31974 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.03 seconds wall clock time: 52 minutes 50.10 seconds (3170.10 seconds total)