Starting phenix.real_space_refine on Sat Mar 7 13:32:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lom_0938/03_2026/6lom_0938.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lom_0938/03_2026/6lom_0938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lom_0938/03_2026/6lom_0938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lom_0938/03_2026/6lom_0938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lom_0938/03_2026/6lom_0938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lom_0938/03_2026/6lom_0938.map" } resolution = 3.73 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= 0.015 sd= 0.071 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 280 5.16 5 C 28760 2.51 5 N 7620 2.21 5 O 8060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.03s 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: 44720 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T Time building chain proxies: 3.40, per 1000 atoms: 0.08 Number of scatterers: 44720 At special positions: 0 Unit cell: (141, 143, 193, 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 280 16.00 O 8060 8.00 N 7620 7.00 C 28760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=80, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 131 " distance=2.02 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 171 " distance=2.05 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 131 " distance=2.02 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 131 " distance=2.02 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 131 " distance=2.02 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 131 " distance=2.02 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 131 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 131 " distance=2.02 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 131 " distance=2.02 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 131 " distance=2.02 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 131 " distance=2.02 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 131 " distance=2.02 Simple disulfide: pdb=" SG CYS L 46 " - pdb=" SG CYS L 131 " distance=2.02 Simple disulfide: pdb=" SG CYS M 46 " - pdb=" SG CYS M 131 " distance=2.02 Simple disulfide: pdb=" SG CYS N 46 " - pdb=" SG CYS N 131 " distance=2.02 Simple disulfide: pdb=" SG CYS O 46 " - pdb=" SG CYS O 131 " distance=2.02 Simple disulfide: pdb=" SG CYS P 46 " - pdb=" SG CYS P 131 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 131 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 131 " distance=2.02 Simple disulfide: pdb=" SG CYS S 46 " - pdb=" SG CYS S 131 " distance=2.02 Simple disulfide: pdb=" SG CYS T 46 " - pdb=" SG CYS T 131 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 176 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 176 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 176 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 176 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 176 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 176 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 176 " distance=2.03 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 176 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 176 " distance=2.03 Simple disulfide: pdb=" SG CYS O 48 " - pdb=" SG CYS O 176 " distance=2.03 Simple disulfide: pdb=" SG CYS P 48 " - pdb=" SG CYS P 176 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 176 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 48 " - pdb=" SG CYS S 176 " distance=2.03 Simple disulfide: pdb=" SG CYS T 48 " - pdb=" SG CYS T 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 174 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 174 " distance=2.03 Simple disulfide: pdb=" SG CYS O 138 " - pdb=" SG CYS O 174 " distance=2.03 Simple disulfide: pdb=" SG CYS P 138 " - pdb=" SG CYS P 174 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 138 " - pdb=" SG CYS Q 174 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 174 " distance=2.03 Simple disulfide: pdb=" SG CYS S 138 " - pdb=" SG CYS S 174 " distance=2.03 Simple disulfide: pdb=" SG CYS T 138 " - pdb=" SG CYS T 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 171 " distance=2.05 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 171 " distance=2.05 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 171 " distance=2.05 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 171 " distance=2.05 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 171 " distance=2.05 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 171 " distance=2.05 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 171 " distance=2.05 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 171 " distance=2.05 Simple disulfide: pdb=" SG CYS J 146 " - pdb=" SG CYS J 171 " distance=2.05 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 171 " distance=2.05 Simple disulfide: pdb=" SG CYS L 146 " - pdb=" SG CYS L 171 " distance=2.05 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 171 " distance=2.05 Simple disulfide: pdb=" SG CYS N 146 " - pdb=" SG CYS N 171 " distance=2.05 Simple disulfide: pdb=" SG CYS O 146 " - pdb=" SG CYS O 171 " distance=2.05 Simple disulfide: pdb=" SG CYS P 146 " - pdb=" SG CYS P 171 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 146 " - pdb=" SG CYS Q 171 " distance=2.05 Simple disulfide: pdb=" SG CYS R 146 " - pdb=" SG CYS R 171 " distance=2.05 Simple disulfide: pdb=" SG CYS S 146 " - pdb=" SG CYS S 171 " distance=2.05 Simple disulfide: pdb=" SG CYS T 146 " - pdb=" SG CYS T 171 " distance=2.05 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: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11240 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 0 sheets defined 74.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 19 Processing helix chain 'A' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Proline residue: A 64 - end of helix removed outlier: 3.718A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS A 174 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 212 Processing helix chain 'A' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'B' and resid 2 through 19 Processing helix chain 'B' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 60 " --> pdb=" O HIS B 56 " (cutoff:3.500A) Proline residue: B 64 - end of helix removed outlier: 3.718A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS B 101 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS B 174 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 212 Processing helix chain 'B' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'C' and resid 2 through 19 Processing helix chain 'C' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) Proline residue: C 64 - end of helix removed outlier: 3.718A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS C 101 " --> pdb=" O TRP C 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS C 174 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 212 Processing helix chain 'C' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP C 238 " --> pdb=" O THR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'D' and resid 2 through 19 Processing helix chain 'D' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA D 30 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 60 " --> pdb=" O HIS D 56 " (cutoff:3.500A) Proline residue: D 64 - end of helix removed outlier: 3.718A pdb=" N ASN D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS D 101 " --> pdb=" O TRP D 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.162A pdb=" N CYS D 174 " --> pdb=" O CYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 212 Processing helix chain 'D' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA E 30 " --> pdb=" O GLY E 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 31 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Proline residue: E 64 - end of helix removed outlier: 3.718A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS E 101 " --> pdb=" O TRP E 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS E 135 " --> pdb=" O CYS E 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.744A pdb=" N ASN E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS E 174 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 212 Processing helix chain 'E' and resid 219 through 255 removed outlier: 4.412A pdb=" N GLN E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 299 through 307 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA F 30 " --> pdb=" O GLY F 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 31 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE F 60 " --> pdb=" O HIS F 56 " (cutoff:3.500A) Proline residue: F 64 - end of helix removed outlier: 3.718A pdb=" N ASN F 76 " --> pdb=" O GLY F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) Proline residue: F 115 - end of helix Processing helix chain 'F' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS F 135 " --> pdb=" O CYS F 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS F 174 " --> pdb=" O CYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 212 Processing helix chain 'F' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 299 through 307 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 25 through 41 removed outlier: 4.007A pdb=" N ALA G 30 " --> pdb=" O GLY G 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 removed outlier: 4.109A pdb=" N ILE G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE G 60 " --> pdb=" O HIS G 56 " (cutoff:3.500A) Proline residue: G 64 - end of helix removed outlier: 3.718A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS G 101 " --> pdb=" O TRP G 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) Proline residue: G 115 - end of helix Processing helix chain 'G' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS G 135 " --> pdb=" O CYS G 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS G 174 " --> pdb=" O CYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 212 Processing helix chain 'G' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN G 235 " --> pdb=" O ASN G 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP G 238 " --> pdb=" O THR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 299 through 307 Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE H 60 " --> pdb=" O HIS H 56 " (cutoff:3.500A) Proline residue: H 64 - end of helix removed outlier: 3.718A pdb=" N ASN H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS H 101 " --> pdb=" O TRP H 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA H 114 " --> pdb=" O GLN H 110 " (cutoff:3.500A) Proline residue: H 115 - end of helix Processing helix chain 'H' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS H 135 " --> pdb=" O CYS H 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'H' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS H 174 " --> pdb=" O CYS H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 212 Processing helix chain 'H' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN H 235 " --> pdb=" O ASN H 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP H 238 " --> pdb=" O THR H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA I 30 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR I 31 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU I 38 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE I 60 " --> pdb=" O HIS I 56 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.718A pdb=" N ASN I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS I 101 " --> pdb=" O TRP I 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Proline residue: I 115 - end of helix Processing helix chain 'I' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS I 135 " --> pdb=" O CYS I 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 147 Processing helix chain 'I' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN I 153 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS I 174 " --> pdb=" O CYS I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 212 Processing helix chain 'I' and resid 219 through 255 removed outlier: 4.412A pdb=" N GLN I 235 " --> pdb=" O ASN I 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP I 238 " --> pdb=" O THR I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 286 Processing helix chain 'I' and resid 299 through 307 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR J 31 " --> pdb=" O ILE J 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU J 38 " --> pdb=" O GLY J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE J 60 " --> pdb=" O HIS J 56 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.718A pdb=" N ASN J 76 " --> pdb=" O GLY J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS J 101 " --> pdb=" O TRP J 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Proline residue: J 115 - end of helix Processing helix chain 'J' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS J 135 " --> pdb=" O CYS J 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS J 138 " --> pdb=" O SER J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 175 removed outlier: 4.160A pdb=" N CYS J 174 " --> pdb=" O CYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 212 Processing helix chain 'J' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN J 235 " --> pdb=" O ASN J 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP J 238 " --> pdb=" O THR J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 286 Processing helix chain 'J' and resid 299 through 307 Processing helix chain 'K' and resid 2 through 19 Processing helix chain 'K' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA K 30 " --> pdb=" O GLY K 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR K 31 " --> pdb=" O ILE K 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU K 38 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE K 60 " --> pdb=" O HIS K 56 " (cutoff:3.500A) Proline residue: K 64 - end of helix removed outlier: 3.718A pdb=" N ASN K 76 " --> pdb=" O GLY K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP K 80 " --> pdb=" O ASN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS K 101 " --> pdb=" O TRP K 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA K 114 " --> pdb=" O GLN K 110 " (cutoff:3.500A) Proline residue: K 115 - end of helix Processing helix chain 'K' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS K 135 " --> pdb=" O CYS K 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS K 138 " --> pdb=" O SER K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 149 through 158 removed outlier: 3.746A pdb=" N ASN K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS K 174 " --> pdb=" O CYS K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 212 Processing helix chain 'K' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN K 235 " --> pdb=" O ASN K 231 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP K 238 " --> pdb=" O THR K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 286 Processing helix chain 'K' and resid 299 through 307 Processing helix chain 'L' and resid 2 through 19 Processing helix chain 'L' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 31 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE L 60 " --> pdb=" O HIS L 56 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.718A pdb=" N ASN L 76 " --> pdb=" O GLY L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS L 101 " --> pdb=" O TRP L 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA L 114 " --> pdb=" O GLN L 110 " (cutoff:3.500A) Proline residue: L 115 - end of helix Processing helix chain 'L' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS L 135 " --> pdb=" O CYS L 131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS L 138 " --> pdb=" O SER L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 147 Processing helix chain 'L' and resid 149 through 158 removed outlier: 3.744A pdb=" N ASN L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS L 174 " --> pdb=" O CYS L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 212 Processing helix chain 'L' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN L 235 " --> pdb=" O ASN L 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP L 238 " --> pdb=" O THR L 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN L 252 " --> pdb=" O LEU L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 286 Processing helix chain 'L' and resid 299 through 307 Processing helix chain 'M' and resid 2 through 19 Processing helix chain 'M' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA M 30 " --> pdb=" O GLY M 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR M 31 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU M 38 " --> pdb=" O GLY M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE M 54 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE M 60 " --> pdb=" O HIS M 56 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.717A pdb=" N ASN M 76 " --> pdb=" O GLY M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS M 101 " --> pdb=" O TRP M 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA M 114 " --> pdb=" O GLN M 110 " (cutoff:3.500A) Proline residue: M 115 - end of helix Processing helix chain 'M' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS M 135 " --> pdb=" O CYS M 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS M 138 " --> pdb=" O SER M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 147 Processing helix chain 'M' and resid 149 through 158 removed outlier: 3.744A pdb=" N ASN M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS M 174 " --> pdb=" O CYS M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 212 Processing helix chain 'M' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN M 235 " --> pdb=" O ASN M 231 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP M 238 " --> pdb=" O THR M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 286 Processing helix chain 'M' and resid 299 through 307 Processing helix chain 'N' and resid 2 through 19 Processing helix chain 'N' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 31 " --> pdb=" O ILE N 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE N 54 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE N 60 " --> pdb=" O HIS N 56 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.718A pdb=" N ASN N 76 " --> pdb=" O GLY N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP N 80 " --> pdb=" O ASN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS N 101 " --> pdb=" O TRP N 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA N 114 " --> pdb=" O GLN N 110 " (cutoff:3.500A) Proline residue: N 115 - end of helix Processing helix chain 'N' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS N 135 " --> pdb=" O CYS N 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS N 138 " --> pdb=" O SER N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 147 Processing helix chain 'N' and resid 149 through 158 removed outlier: 3.746A pdb=" N ASN N 153 " --> pdb=" O SER N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS N 174 " --> pdb=" O CYS N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 212 Processing helix chain 'N' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN N 235 " --> pdb=" O ASN N 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP N 238 " --> pdb=" O THR N 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 281 through 286 Processing helix chain 'N' and resid 299 through 307 Processing helix chain 'O' and resid 2 through 19 Processing helix chain 'O' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR O 31 " --> pdb=" O ILE O 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU O 38 " --> pdb=" O GLY O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE O 54 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE O 60 " --> pdb=" O HIS O 56 " (cutoff:3.500A) Proline residue: O 64 - end of helix removed outlier: 3.718A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS O 101 " --> pdb=" O TRP O 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA O 114 " --> pdb=" O GLN O 110 " (cutoff:3.500A) Proline residue: O 115 - end of helix Processing helix chain 'O' and resid 129 through 138 removed outlier: 4.825A pdb=" N HIS O 135 " --> pdb=" O CYS O 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 147 Processing helix chain 'O' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 175 removed outlier: 4.162A pdb=" N CYS O 174 " --> pdb=" O CYS O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 212 Processing helix chain 'O' and resid 219 through 255 removed outlier: 4.410A pdb=" N GLN O 235 " --> pdb=" O ASN O 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP O 238 " --> pdb=" O THR O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 286 Processing helix chain 'O' and resid 299 through 307 Processing helix chain 'P' and resid 2 through 19 Processing helix chain 'P' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR P 31 " --> pdb=" O ILE P 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE P 54 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE P 60 " --> pdb=" O HIS P 56 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.718A pdb=" N ASN P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP P 80 " --> pdb=" O ASN P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS P 101 " --> pdb=" O TRP P 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA P 114 " --> pdb=" O GLN P 110 " (cutoff:3.500A) Proline residue: P 115 - end of helix Processing helix chain 'P' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS P 135 " --> pdb=" O CYS P 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS P 138 " --> pdb=" O SER P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 147 Processing helix chain 'P' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN P 153 " --> pdb=" O SER P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS P 174 " --> pdb=" O CYS P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 212 Processing helix chain 'P' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN P 235 " --> pdb=" O ASN P 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP P 238 " --> pdb=" O THR P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 286 Processing helix chain 'P' and resid 299 through 307 Processing helix chain 'Q' and resid 2 through 19 Processing helix chain 'Q' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR Q 31 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU Q 38 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE Q 54 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE Q 60 " --> pdb=" O HIS Q 56 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.718A pdb=" N ASN Q 76 " --> pdb=" O GLY Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP Q 80 " --> pdb=" O ASN Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS Q 101 " --> pdb=" O TRP Q 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA Q 114 " --> pdb=" O GLN Q 110 " (cutoff:3.500A) Proline residue: Q 115 - end of helix Processing helix chain 'Q' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS Q 135 " --> pdb=" O CYS Q 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS Q 138 " --> pdb=" O SER Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 147 Processing helix chain 'Q' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN Q 153 " --> pdb=" O SER Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS Q 174 " --> pdb=" O CYS Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 212 Processing helix chain 'Q' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN Q 235 " --> pdb=" O ASN Q 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 286 Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'R' and resid 2 through 19 Processing helix chain 'R' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.109A pdb=" N ILE R 54 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE R 60 " --> pdb=" O HIS R 56 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.718A pdb=" N ASN R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP R 80 " --> pdb=" O ASN R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS R 101 " --> pdb=" O TRP R 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA R 114 " --> pdb=" O GLN R 110 " (cutoff:3.500A) Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 129 through 138 removed outlier: 4.825A pdb=" N HIS R 135 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS R 138 " --> pdb=" O SER R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS R 174 " --> pdb=" O CYS R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 Processing helix chain 'R' and resid 219 through 255 removed outlier: 4.410A pdb=" N GLN R 235 " --> pdb=" O ASN R 231 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN R 252 " --> pdb=" O LEU R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 286 Processing helix chain 'R' and resid 299 through 307 Processing helix chain 'S' and resid 2 through 19 Processing helix chain 'S' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR S 31 " --> pdb=" O ILE S 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU S 38 " --> pdb=" O GLY S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE S 54 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE S 60 " --> pdb=" O HIS S 56 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.718A pdb=" N ASN S 76 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 84 removed outlier: 4.210A pdb=" N TRP S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS S 101 " --> pdb=" O TRP S 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA S 114 " --> pdb=" O GLN S 110 " (cutoff:3.500A) Proline residue: S 115 - end of helix Processing helix chain 'S' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS S 135 " --> pdb=" O CYS S 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS S 138 " --> pdb=" O SER S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 147 Processing helix chain 'S' and resid 149 through 158 removed outlier: 3.746A pdb=" N ASN S 153 " --> pdb=" O SER S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS S 174 " --> pdb=" O CYS S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 212 Processing helix chain 'S' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN S 235 " --> pdb=" O ASN S 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP S 238 " --> pdb=" O THR S 234 " (cutoff:3.500A) Processing helix chain 'S' and resid 281 through 286 Processing helix chain 'S' and resid 299 through 307 Processing helix chain 'T' and resid 2 through 19 Processing helix chain 'T' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA T 30 " --> pdb=" O GLY T 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR T 31 " --> pdb=" O ILE T 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU T 38 " --> pdb=" O GLY T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE T 54 " --> pdb=" O TYR T 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) Proline residue: T 64 - end of helix removed outlier: 3.718A pdb=" N ASN T 76 " --> pdb=" O GLY T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP T 80 " --> pdb=" O ASN T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS T 101 " --> pdb=" O TRP T 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA T 114 " --> pdb=" O GLN T 110 " (cutoff:3.500A) Proline residue: T 115 - end of helix Processing helix chain 'T' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS T 135 " --> pdb=" O CYS T 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS T 138 " --> pdb=" O SER T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 147 Processing helix chain 'T' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN T 153 " --> pdb=" O SER T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS T 174 " --> pdb=" O CYS T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 212 Processing helix chain 'T' and resid 219 through 255 removed outlier: 4.410A pdb=" N GLN T 235 " --> pdb=" O ASN T 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP T 238 " --> pdb=" O THR T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 286 Processing helix chain 'T' and resid 299 through 307 2956 hydrogen bonds defined for protein. 8808 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: 8.29 Time building geometry restraints manager: 4.82 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: 14037 1.34 - 1.47: 12541 1.47 - 1.60: 18942 1.60 - 1.73: 0 1.73 - 1.85: 340 Bond restraints: 45860 Sorted by residual: bond pdb=" C PRO K 172 " pdb=" N PRO K 173 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.08e-02 8.57e+03 7.22e+00 bond pdb=" C PRO R 172 " pdb=" N PRO R 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 7.04e+00 bond pdb=" C PRO S 172 " pdb=" N PRO S 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 7.00e+00 bond pdb=" C PRO A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 6.98e+00 bond pdb=" C PRO O 172 " pdb=" N PRO O 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 6.98e+00 ... (remaining 45855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 58586 2.15 - 4.30: 3174 4.30 - 6.44: 469 6.44 - 8.59: 251 8.59 - 10.74: 40 Bond angle restraints: 62520 Sorted by residual: angle pdb=" N PRO I 172 " pdb=" CA PRO I 172 " pdb=" C PRO I 172 " ideal model delta sigma weight residual 110.70 116.58 -5.88 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO G 172 " pdb=" CA PRO G 172 " pdb=" C PRO G 172 " ideal model delta sigma weight residual 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO F 172 " pdb=" CA PRO F 172 " pdb=" C PRO F 172 " ideal model delta sigma weight residual 110.70 116.56 -5.86 1.22e+00 6.72e-01 2.31e+01 angle pdb=" N PRO E 172 " pdb=" CA PRO E 172 " pdb=" C PRO E 172 " ideal model delta sigma weight residual 110.70 116.56 -5.86 1.22e+00 6.72e-01 2.30e+01 angle pdb=" N PRO J 172 " pdb=" CA PRO J 172 " pdb=" C PRO J 172 " ideal model delta sigma weight residual 110.70 116.55 -5.85 1.22e+00 6.72e-01 2.30e+01 ... (remaining 62515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 23882 14.96 - 29.92: 2198 29.92 - 44.88: 660 44.88 - 59.84: 200 59.84 - 74.80: 60 Dihedral angle restraints: 27000 sinusoidal: 9620 harmonic: 17380 Sorted by residual: dihedral pdb=" CA CYS T 171 " pdb=" C CYS T 171 " pdb=" N PRO T 172 " pdb=" CA PRO T 172 " ideal model delta harmonic sigma weight residual -180.00 -123.73 -56.27 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS M 171 " pdb=" C CYS M 171 " pdb=" N PRO M 172 " pdb=" CA PRO M 172 " ideal model delta harmonic sigma weight residual -180.00 -123.75 -56.25 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS S 171 " pdb=" C CYS S 171 " pdb=" N PRO S 172 " pdb=" CA PRO S 172 " ideal model delta harmonic sigma weight residual -180.00 -123.75 -56.25 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 26997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4020 0.043 - 0.086: 2084 0.086 - 0.129: 750 0.129 - 0.171: 146 0.171 - 0.214: 60 Chirality restraints: 7060 Sorted by residual: chirality pdb=" CA PHE P 44 " pdb=" N PHE P 44 " pdb=" C PHE P 44 " pdb=" CB PHE P 44 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE R 44 " pdb=" N PHE R 44 " pdb=" C PHE R 44 " pdb=" CB PHE R 44 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE N 44 " pdb=" N PHE N 44 " pdb=" C PHE N 44 " pdb=" CB PHE N 44 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 7057 not shown) Planarity restraints: 7940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 311 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO M 312 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO M 312 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 312 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 311 " 0.045 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO F 312 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO F 312 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 312 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 311 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 312 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 312 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 312 " 0.035 5.00e-02 4.00e+02 ... (remaining 7937 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3643 2.73 - 3.27: 46063 3.27 - 3.82: 76275 3.82 - 4.36: 84741 4.36 - 4.90: 144060 Nonbonded interactions: 354782 Sorted by model distance: nonbonded pdb=" OD1 ASN A 304 " pdb=" ND2 ASN B 252 " model vdw 2.191 3.120 nonbonded pdb=" OD1 ASN R 304 " pdb=" ND2 ASN S 252 " model vdw 2.243 3.120 nonbonded pdb=" O ARG C 130 " pdb=" OG SER C 134 " model vdw 2.244 3.040 nonbonded pdb=" O ARG S 130 " pdb=" OG SER S 134 " model vdw 2.244 3.040 nonbonded pdb=" O ARG G 130 " pdb=" OG SER G 134 " model vdw 2.245 3.040 ... (remaining 354777 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 2.380 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: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 31.210 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.130 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:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.007 0.094 45940 Z= 0.349 Angle : 1.175 10.739 62680 Z= 0.631 Chirality : 0.058 0.214 7060 Planarity : 0.009 0.069 7940 Dihedral : 13.554 74.799 15520 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 1.81 % Allowed : 9.50 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 27.27 % Twisted General : 0.71 % 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: -4.24 (0.08), residues: 5820 helix: -2.34 (0.06), residues: 4180 sheet: None (None), residues: 0 loop : -3.63 (0.12), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG T 283 TYR 0.021 0.003 TYR N 128 PHE 0.024 0.003 PHE H 44 TRP 0.024 0.005 TRP C 118 HIS 0.006 0.002 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00734 (45860) covalent geometry : angle 1.16685 (62520) SS BOND : bond 0.01070 ( 80) SS BOND : angle 3.04194 ( 160) hydrogen bonds : bond 0.12208 ( 2956) hydrogen bonds : angle 7.23110 ( 8808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 973 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8452 (tt) cc_final: 0.7843 (tt) REVERT: A 135 HIS cc_start: 0.7544 (t-90) cc_final: 0.7101 (t-90) REVERT: A 187 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 287 ILE cc_start: 0.6863 (mt) cc_final: 0.6582 (pt) REVERT: B 135 HIS cc_start: 0.7629 (t-90) cc_final: 0.7220 (t-90) REVERT: B 187 GLU cc_start: 0.8704 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 82 LEU cc_start: 0.8527 (tt) cc_final: 0.8293 (mt) REVERT: C 98 LYS cc_start: 0.6915 (tttt) cc_final: 0.6657 (tptt) REVERT: C 135 HIS cc_start: 0.7459 (t-90) cc_final: 0.7122 (t-90) REVERT: C 186 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8777 (tp) REVERT: C 187 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8266 (tm-30) REVERT: C 242 LYS cc_start: 0.8309 (ttmt) cc_final: 0.8048 (ttmm) REVERT: D 135 HIS cc_start: 0.7675 (t-90) cc_final: 0.7231 (t-90) REVERT: D 187 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8021 (tm-30) REVERT: D 231 ASN cc_start: 0.8310 (t160) cc_final: 0.8027 (t0) REVERT: D 285 ARG cc_start: 0.7612 (mpt90) cc_final: 0.7296 (ttm110) REVERT: D 286 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8359 (mm) REVERT: E 135 HIS cc_start: 0.7700 (t-90) cc_final: 0.7165 (t-90) REVERT: E 187 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8296 (tm-30) REVERT: E 199 LEU cc_start: 0.8740 (tt) cc_final: 0.8493 (tp) REVERT: E 285 ARG cc_start: 0.7401 (mpt90) cc_final: 0.7141 (ttm110) REVERT: F 82 LEU cc_start: 0.8393 (tt) cc_final: 0.7864 (tt) REVERT: F 98 LYS cc_start: 0.6490 (tttt) cc_final: 0.6285 (tptt) REVERT: F 135 HIS cc_start: 0.7652 (t-90) cc_final: 0.7172 (t-90) REVERT: F 187 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8364 (tm-30) REVERT: F 256 PHE cc_start: 0.8546 (t80) cc_final: 0.8333 (t80) REVERT: G 82 LEU cc_start: 0.8550 (tt) cc_final: 0.8293 (mt) REVERT: G 135 HIS cc_start: 0.7644 (t-90) cc_final: 0.7211 (t-90) REVERT: G 186 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8832 (tp) REVERT: G 187 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8147 (tm-30) REVERT: G 285 ARG cc_start: 0.7431 (mpt90) cc_final: 0.7184 (ttm110) REVERT: H 82 LEU cc_start: 0.8525 (tt) cc_final: 0.8297 (mt) REVERT: H 98 LYS cc_start: 0.6923 (tttt) cc_final: 0.6655 (tptt) REVERT: H 135 HIS cc_start: 0.7477 (t-90) cc_final: 0.7131 (t-90) REVERT: H 186 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8771 (tp) REVERT: H 187 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8276 (tm-30) REVERT: H 242 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7940 (ttmm) REVERT: H 256 PHE cc_start: 0.8588 (t80) cc_final: 0.8384 (t80) REVERT: I 135 HIS cc_start: 0.7688 (t-90) cc_final: 0.7262 (t-90) REVERT: I 187 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8018 (tm-30) REVERT: I 231 ASN cc_start: 0.8318 (t160) cc_final: 0.8025 (t0) REVERT: I 242 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8133 (tttp) REVERT: I 285 ARG cc_start: 0.7630 (mpt90) cc_final: 0.7294 (ttm110) REVERT: J 135 HIS cc_start: 0.7644 (t-90) cc_final: 0.7168 (t-90) REVERT: J 187 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8303 (tm-30) REVERT: J 199 LEU cc_start: 0.8748 (tt) cc_final: 0.8471 (tp) REVERT: J 256 PHE cc_start: 0.8578 (t80) cc_final: 0.8330 (t80) REVERT: J 285 ARG cc_start: 0.7395 (mpt90) cc_final: 0.7140 (ttm110) REVERT: K 82 LEU cc_start: 0.8540 (tt) cc_final: 0.8278 (mt) REVERT: K 135 HIS cc_start: 0.7654 (t-90) cc_final: 0.7131 (t-90) REVERT: K 186 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8814 (tp) REVERT: K 187 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8091 (tm-30) REVERT: K 285 ARG cc_start: 0.7451 (mpt90) cc_final: 0.7129 (ttm110) REVERT: L 82 LEU cc_start: 0.8557 (tt) cc_final: 0.8305 (mt) REVERT: L 98 LYS cc_start: 0.7030 (tttt) cc_final: 0.6755 (tptt) REVERT: L 135 HIS cc_start: 0.7360 (t-90) cc_final: 0.7012 (t-90) REVERT: L 186 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8740 (tp) REVERT: L 187 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8235 (tm-30) REVERT: L 231 ASN cc_start: 0.8216 (t160) cc_final: 0.7978 (t0) REVERT: L 242 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8066 (ttmm) REVERT: L 256 PHE cc_start: 0.8557 (t80) cc_final: 0.8326 (t80) REVERT: M 135 HIS cc_start: 0.7642 (t-90) cc_final: 0.7095 (t-90) REVERT: M 187 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7992 (tm-30) REVERT: M 199 LEU cc_start: 0.8714 (tt) cc_final: 0.8478 (tp) REVERT: M 231 ASN cc_start: 0.8311 (t160) cc_final: 0.8013 (t0) REVERT: M 256 PHE cc_start: 0.8549 (t80) cc_final: 0.8284 (t80) REVERT: M 285 ARG cc_start: 0.7554 (mpt90) cc_final: 0.7188 (ttm110) REVERT: N 135 HIS cc_start: 0.7614 (t-90) cc_final: 0.7130 (t-90) REVERT: N 187 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8290 (tm-30) REVERT: N 199 LEU cc_start: 0.8720 (tt) cc_final: 0.8471 (tp) REVERT: N 285 ARG cc_start: 0.7377 (mpt90) cc_final: 0.7120 (ttm110) REVERT: O 82 LEU cc_start: 0.8444 (tt) cc_final: 0.7884 (tt) REVERT: O 135 HIS cc_start: 0.7565 (t-90) cc_final: 0.7108 (t-90) REVERT: O 187 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8332 (tm-30) REVERT: O 287 ILE cc_start: 0.6825 (mt) cc_final: 0.6597 (pt) REVERT: P 82 LEU cc_start: 0.8556 (tt) cc_final: 0.8303 (mt) REVERT: P 135 HIS cc_start: 0.7676 (t-90) cc_final: 0.7142 (t-90) REVERT: P 186 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8820 (tp) REVERT: P 187 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8099 (tm-30) REVERT: P 285 ARG cc_start: 0.7455 (mpt90) cc_final: 0.7151 (ttm110) REVERT: Q 82 LEU cc_start: 0.8544 (tt) cc_final: 0.8309 (mt) REVERT: Q 98 LYS cc_start: 0.7003 (tttt) cc_final: 0.6723 (tptt) REVERT: Q 135 HIS cc_start: 0.7384 (t-90) cc_final: 0.7034 (t-90) REVERT: Q 186 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (tp) REVERT: Q 187 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8236 (tm-30) REVERT: Q 231 ASN cc_start: 0.8223 (t160) cc_final: 0.8000 (t0) REVERT: Q 242 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8061 (ttmm) REVERT: Q 256 PHE cc_start: 0.8565 (t80) cc_final: 0.8338 (t80) REVERT: R 135 HIS cc_start: 0.7615 (t-90) cc_final: 0.7082 (t-90) REVERT: R 187 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7968 (tm-30) REVERT: R 199 LEU cc_start: 0.8685 (tt) cc_final: 0.8482 (tp) REVERT: R 231 ASN cc_start: 0.8327 (t160) cc_final: 0.8020 (t0) REVERT: R 242 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8112 (tttp) REVERT: R 285 ARG cc_start: 0.7603 (mpt90) cc_final: 0.7268 (ttm110) REVERT: S 98 LYS cc_start: 0.6743 (tttt) cc_final: 0.6439 (tptt) REVERT: S 135 HIS cc_start: 0.7663 (t-90) cc_final: 0.7178 (t-90) REVERT: S 187 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8259 (tm-30) REVERT: S 199 LEU cc_start: 0.8740 (tt) cc_final: 0.8492 (tp) REVERT: S 285 ARG cc_start: 0.7505 (mpt90) cc_final: 0.7184 (ttm110) REVERT: T 82 LEU cc_start: 0.8441 (tt) cc_final: 0.7888 (tt) REVERT: T 135 HIS cc_start: 0.7527 (t-90) cc_final: 0.7129 (t-90) REVERT: T 187 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8321 (tm-30) REVERT: T 287 ILE cc_start: 0.6771 (mt) cc_final: 0.6550 (pt) outliers start: 80 outliers final: 40 residues processed: 1033 average time/residue: 0.2659 time to fit residues: 435.7076 Evaluate side-chains 567 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 519 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 209 ILE Chi-restraints excluded: chain T residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 394 optimal weight: 30.0000 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 0.0270 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 231 ASN A 244 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN B 53 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 231 ASN B 244 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN C 53 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 244 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN D 53 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN D 231 ASN D 244 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN E 53 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 231 ASN E 244 HIS ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN F 231 ASN F 244 HIS ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN G 53 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN G 231 ASN G 244 HIS ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN H 53 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN H 244 HIS ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN I 53 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN I 231 ASN I 244 HIS ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 ASN J 53 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN J 231 ASN J 244 HIS ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN K 53 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 ASN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN K 231 ASN K 244 HIS ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN L 53 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 ASN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 GLN L 231 ASN L 244 HIS ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN M 53 ASN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 GLN M 231 ASN M 244 HIS ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 ASN N 53 ASN ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 231 ASN N 244 HIS ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 306 ASN O 53 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 191 GLN O 231 ASN O 244 HIS ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 ASN P 53 ASN ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 ASN ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 191 GLN P 231 ASN P 244 HIS ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 ASN Q 53 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 148 ASN ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 191 GLN Q 231 ASN Q 244 HIS ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 ASN R 53 ASN ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 191 GLN R 231 ASN R 244 HIS ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 ASN S 53 ASN ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 GLN S 231 ASN S 244 HIS ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 ASN T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 148 ASN ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 191 GLN T 231 ASN T 244 HIS ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 306 ASN Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.212133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166403 restraints weight = 72600.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.170096 restraints weight = 41997.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.172599 restraints weight = 29610.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173910 restraints weight = 23514.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.175017 restraints weight = 20576.354| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 45940 Z= 0.158 Angle : 0.722 11.091 62680 Z= 0.386 Chirality : 0.043 0.173 7060 Planarity : 0.006 0.044 7940 Dihedral : 8.797 56.295 6456 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.79 % Allowed : 17.24 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 18.18 % 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: -2.36 (0.10), residues: 5820 helix: -0.72 (0.07), residues: 4100 sheet: None (None), residues: 0 loop : -3.52 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 254 TYR 0.014 0.002 TYR P 128 PHE 0.022 0.001 PHE C 200 TRP 0.032 0.003 TRP R 195 HIS 0.004 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00328 (45860) covalent geometry : angle 0.71477 (62520) SS BOND : bond 0.00624 ( 80) SS BOND : angle 2.10237 ( 160) hydrogen bonds : bond 0.04043 ( 2956) hydrogen bonds : angle 4.97559 ( 8808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 646 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 231 ASN cc_start: 0.8211 (t0) cc_final: 0.7982 (t0) REVERT: A 296 MET cc_start: 0.5513 (mmp) cc_final: 0.5313 (mmp) REVERT: B 187 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 256 PHE cc_start: 0.8564 (t80) cc_final: 0.8162 (t80) REVERT: C 187 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7216 (tm-30) REVERT: C 242 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7928 (ttmm) REVERT: D 187 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 199 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8629 (mp) REVERT: D 231 ASN cc_start: 0.8328 (t0) cc_final: 0.8124 (t0) REVERT: D 285 ARG cc_start: 0.7715 (mpt90) cc_final: 0.7421 (mtp-110) REVERT: E 61 MET cc_start: 0.7392 (mmm) cc_final: 0.7146 (tpp) REVERT: E 187 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 223 ARG cc_start: 0.8305 (tpp-160) cc_final: 0.7605 (tpp80) REVERT: E 231 ASN cc_start: 0.8324 (t0) cc_final: 0.8113 (t0) REVERT: E 285 ARG cc_start: 0.7418 (mpt90) cc_final: 0.7191 (mtp-110) REVERT: F 187 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7421 (tm-30) REVERT: F 231 ASN cc_start: 0.8195 (t0) cc_final: 0.7986 (t0) REVERT: F 256 PHE cc_start: 0.8597 (t80) cc_final: 0.8360 (t80) REVERT: G 186 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8895 (tp) REVERT: G 187 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7615 (tm-30) REVERT: G 285 ARG cc_start: 0.7352 (mpt90) cc_final: 0.6988 (mtp-110) REVERT: H 187 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7193 (tm-30) REVERT: H 242 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7926 (ttmm) REVERT: H 256 PHE cc_start: 0.8488 (t80) cc_final: 0.8282 (t80) REVERT: I 187 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7577 (tm-30) REVERT: I 231 ASN cc_start: 0.8318 (t0) cc_final: 0.8089 (t0) REVERT: I 285 ARG cc_start: 0.7570 (mpt90) cc_final: 0.7203 (mtp-110) REVERT: J 61 MET cc_start: 0.7375 (mmm) cc_final: 0.6879 (tpp) REVERT: J 123 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: J 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7544 (tm-30) REVERT: J 223 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.7552 (tpp80) REVERT: J 231 ASN cc_start: 0.8328 (t0) cc_final: 0.8116 (t0) REVERT: J 256 PHE cc_start: 0.8620 (t80) cc_final: 0.8398 (t80) REVERT: J 285 ARG cc_start: 0.7388 (mpt90) cc_final: 0.7177 (mtp-110) REVERT: K 186 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8800 (tp) REVERT: K 187 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7622 (tm-30) REVERT: K 195 TRP cc_start: 0.8854 (m100) cc_final: 0.8616 (m100) REVERT: K 285 ARG cc_start: 0.7390 (mpt90) cc_final: 0.6933 (mtp-110) REVERT: L 187 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7304 (tm-30) REVERT: L 231 ASN cc_start: 0.8151 (t0) cc_final: 0.7923 (t0) REVERT: L 242 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7913 (ttmm) REVERT: L 256 PHE cc_start: 0.8504 (t80) cc_final: 0.8286 (t80) REVERT: M 187 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7554 (tm-30) REVERT: M 223 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7970 (tpp-160) REVERT: M 231 ASN cc_start: 0.8312 (t0) cc_final: 0.8092 (t0) REVERT: M 256 PHE cc_start: 0.8530 (t80) cc_final: 0.8263 (t80) REVERT: M 285 ARG cc_start: 0.7599 (mpt90) cc_final: 0.7217 (mtp-110) REVERT: M 307 LYS cc_start: 0.7308 (mttt) cc_final: 0.7036 (mttm) REVERT: N 53 ASN cc_start: 0.8152 (t0) cc_final: 0.7802 (t0) REVERT: N 187 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7496 (tm-30) REVERT: N 223 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.7565 (tpp80) REVERT: N 231 ASN cc_start: 0.8302 (t0) cc_final: 0.8095 (t0) REVERT: N 285 ARG cc_start: 0.7392 (mpt90) cc_final: 0.7170 (mtp-110) REVERT: O 187 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7360 (tm-30) REVERT: O 231 ASN cc_start: 0.8204 (t0) cc_final: 0.7977 (t0) REVERT: P 186 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8876 (tp) REVERT: P 187 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7627 (tm-30) REVERT: P 195 TRP cc_start: 0.8848 (m100) cc_final: 0.8611 (m100) REVERT: P 285 ARG cc_start: 0.7380 (mpt90) cc_final: 0.6942 (mtp-110) REVERT: Q 187 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7241 (tm-30) REVERT: Q 223 ARG cc_start: 0.8157 (tpp-160) cc_final: 0.7940 (tpp-160) REVERT: Q 231 ASN cc_start: 0.8204 (t0) cc_final: 0.7937 (t0) REVERT: Q 242 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7933 (ttmm) REVERT: Q 256 PHE cc_start: 0.8497 (t80) cc_final: 0.8286 (t80) REVERT: R 187 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7536 (tm-30) REVERT: R 231 ASN cc_start: 0.8282 (t0) cc_final: 0.8041 (t0) REVERT: R 242 LYS cc_start: 0.8229 (ttmt) cc_final: 0.8010 (tttp) REVERT: R 285 ARG cc_start: 0.7608 (mpt90) cc_final: 0.7234 (mtp-110) REVERT: S 61 MET cc_start: 0.7440 (mmm) cc_final: 0.6880 (tpp) REVERT: S 98 LYS cc_start: 0.6478 (tttt) cc_final: 0.6116 (tptt) REVERT: S 123 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: S 187 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7505 (tm-30) REVERT: S 223 ARG cc_start: 0.8325 (tpp-160) cc_final: 0.7570 (tpp80) REVERT: S 256 PHE cc_start: 0.8623 (t80) cc_final: 0.8396 (t80) REVERT: S 285 ARG cc_start: 0.7462 (mpt90) cc_final: 0.7206 (mtp-110) REVERT: T 187 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7342 (tm-30) REVERT: T 231 ASN cc_start: 0.8161 (t0) cc_final: 0.7932 (t0) outliers start: 256 outliers final: 124 residues processed: 861 average time/residue: 0.2535 time to fit residues: 353.3501 Evaluate side-chains 608 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 478 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 287 ILE Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 364 optimal weight: 9.9990 chunk 491 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 410 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 430 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 411 optimal weight: 7.9990 chunk 390 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 ASN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 231 ASN ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 231 ASN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.205141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158971 restraints weight = 73732.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.162812 restraints weight = 42699.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.165159 restraints weight = 29608.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.166382 restraints weight = 23818.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.167415 restraints weight = 20965.987| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 45940 Z= 0.181 Angle : 0.701 10.374 62680 Z= 0.378 Chirality : 0.044 0.184 7060 Planarity : 0.005 0.041 7940 Dihedral : 7.943 58.657 6424 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.83 % Allowed : 18.89 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 18.18 % 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: -1.81 (0.11), residues: 5820 helix: -0.18 (0.08), residues: 4220 sheet: None (None), residues: 0 loop : -3.94 (0.12), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 254 TYR 0.015 0.002 TYR D 129 PHE 0.014 0.001 PHE A 44 TRP 0.034 0.002 TRP M 195 HIS 0.004 0.001 HIS T 244 Details of bonding type rmsd covalent geometry : bond 0.00386 (45860) covalent geometry : angle 0.69523 (62520) SS BOND : bond 0.00702 ( 80) SS BOND : angle 1.90995 ( 160) hydrogen bonds : bond 0.04154 ( 2956) hydrogen bonds : angle 4.57391 ( 8808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 302 poor density : 471 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 219 THR cc_start: 0.8170 (t) cc_final: 0.7965 (m) REVERT: B 187 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 195 TRP cc_start: 0.8945 (m100) cc_final: 0.8417 (m100) REVERT: B 254 ARG cc_start: 0.8161 (mmt180) cc_final: 0.7939 (mmt-90) REVERT: C 187 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 242 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8045 (ttmm) REVERT: D 187 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7677 (tm-30) REVERT: D 195 TRP cc_start: 0.8992 (m100) cc_final: 0.8756 (m100) REVERT: D 285 ARG cc_start: 0.7841 (mpt90) cc_final: 0.7534 (mtp-110) REVERT: D 296 MET cc_start: 0.6095 (mmp) cc_final: 0.5563 (tpt) REVERT: E 187 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7759 (tm-30) REVERT: E 199 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8615 (mp) REVERT: F 187 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7652 (tm-30) REVERT: F 296 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.5337 (tpt) REVERT: G 187 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7641 (tm-30) REVERT: G 285 ARG cc_start: 0.7457 (mpt90) cc_final: 0.6974 (mtp-110) REVERT: H 187 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7507 (tm-30) REVERT: H 242 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8034 (ttmm) REVERT: I 187 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7682 (tm-30) REVERT: I 195 TRP cc_start: 0.8961 (m100) cc_final: 0.8729 (m100) REVERT: I 285 ARG cc_start: 0.7713 (mpt90) cc_final: 0.7284 (mtp-110) REVERT: J 187 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7749 (tm-30) REVERT: J 199 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (mp) REVERT: K 61 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7088 (tpp) REVERT: K 187 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7608 (tm-30) REVERT: K 195 TRP cc_start: 0.8878 (m100) cc_final: 0.8335 (m100) REVERT: K 285 ARG cc_start: 0.7496 (mpt90) cc_final: 0.6962 (mtp-110) REVERT: L 187 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7513 (tm-30) REVERT: L 242 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7994 (ttmm) REVERT: L 250 GLU cc_start: 0.7806 (tp30) cc_final: 0.7354 (mm-30) REVERT: M 187 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7601 (tm-30) REVERT: M 285 ARG cc_start: 0.7846 (mpt90) cc_final: 0.7439 (mtp-110) REVERT: N 61 MET cc_start: 0.7679 (mmm) cc_final: 0.7034 (tpp) REVERT: N 123 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: N 187 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7752 (tm-30) REVERT: N 199 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8616 (mp) REVERT: O 187 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7588 (tm-30) REVERT: P 123 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: P 187 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7626 (tm-30) REVERT: P 195 TRP cc_start: 0.8879 (m100) cc_final: 0.8340 (m100) REVERT: P 285 ARG cc_start: 0.7499 (mpt90) cc_final: 0.6983 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7505 (tm-30) REVERT: Q 242 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8013 (ttmm) REVERT: R 187 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7624 (tm-30) REVERT: R 195 TRP cc_start: 0.8994 (m100) cc_final: 0.8779 (m100) REVERT: R 242 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8127 (tttp) REVERT: R 285 ARG cc_start: 0.7748 (mpt90) cc_final: 0.7319 (mtp-110) REVERT: S 187 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7733 (tm-30) REVERT: S 195 TRP cc_start: 0.9052 (m100) cc_final: 0.8347 (m100) REVERT: S 199 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8480 (mp) REVERT: T 187 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7546 (tm-30) outliers start: 302 outliers final: 182 residues processed: 710 average time/residue: 0.2467 time to fit residues: 285.6528 Evaluate side-chains 629 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 439 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain L residue 46 CYS Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 46 CYS Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain Q residue 46 CYS Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 492 optimal weight: 1.9990 chunk 264 optimal weight: 30.0000 chunk 574 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 558 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 HIS ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 231 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 HIS ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 HIS ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 231 ASN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.205507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158275 restraints weight = 74129.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161948 restraints weight = 43067.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.164474 restraints weight = 30576.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165755 restraints weight = 24533.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166856 restraints weight = 21625.374| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45940 Z= 0.198 Angle : 0.694 9.958 62680 Z= 0.374 Chirality : 0.044 0.223 7060 Planarity : 0.005 0.045 7940 Dihedral : 7.396 57.396 6418 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 9.77 % Allowed : 17.13 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.55 % 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: -1.39 (0.11), residues: 5820 helix: 0.14 (0.08), residues: 4220 sheet: None (None), residues: 0 loop : -3.82 (0.12), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 254 TYR 0.016 0.002 TYR B 129 PHE 0.023 0.001 PHE O 200 TRP 0.037 0.002 TRP M 195 HIS 0.006 0.002 HIS T 244 Details of bonding type rmsd covalent geometry : bond 0.00432 (45860) covalent geometry : angle 0.68792 (62520) SS BOND : bond 0.00663 ( 80) SS BOND : angle 1.88427 ( 160) hydrogen bonds : bond 0.04121 ( 2956) hydrogen bonds : angle 4.44584 ( 8808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 432 poor density : 484 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 187 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 189 GLU cc_start: 0.8421 (tp30) cc_final: 0.7936 (tp30) REVERT: A 281 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: B 187 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 195 TRP cc_start: 0.8950 (m100) cc_final: 0.8407 (m100) REVERT: C 187 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 250 GLU cc_start: 0.7945 (tp30) cc_final: 0.7386 (mm-30) REVERT: D 187 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 195 TRP cc_start: 0.9017 (m100) cc_final: 0.8813 (m100) REVERT: D 285 ARG cc_start: 0.7874 (mpt90) cc_final: 0.7590 (mtp-110) REVERT: E 169 LYS cc_start: 0.7027 (mttt) cc_final: 0.6813 (mtpp) REVERT: E 187 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7816 (tm-30) REVERT: E 189 GLU cc_start: 0.8491 (tp30) cc_final: 0.8287 (tp30) REVERT: E 199 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8633 (mp) REVERT: F 187 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7685 (tm-30) REVERT: F 189 GLU cc_start: 0.8424 (tp30) cc_final: 0.7906 (tp30) REVERT: F 281 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: G 187 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7702 (tm-30) REVERT: G 195 TRP cc_start: 0.8967 (m100) cc_final: 0.8366 (m100) REVERT: G 285 ARG cc_start: 0.7587 (mpt90) cc_final: 0.7112 (mtp-110) REVERT: G 297 TYR cc_start: 0.5228 (OUTLIER) cc_final: 0.4589 (p90) REVERT: H 187 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7590 (tm-30) REVERT: H 242 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8158 (tttp) REVERT: H 250 GLU cc_start: 0.7977 (tp30) cc_final: 0.7553 (mm-30) REVERT: I 187 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7751 (tm-30) REVERT: I 195 TRP cc_start: 0.9028 (m100) cc_final: 0.8817 (m100) REVERT: I 285 ARG cc_start: 0.7866 (mpt90) cc_final: 0.7599 (ttm110) REVERT: J 187 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7832 (tm-30) REVERT: J 189 GLU cc_start: 0.8522 (tp30) cc_final: 0.8319 (tp30) REVERT: J 195 TRP cc_start: 0.9060 (m100) cc_final: 0.8306 (m100) REVERT: J 199 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8550 (mp) REVERT: K 61 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7194 (tpp) REVERT: K 187 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7642 (tm-30) REVERT: K 195 TRP cc_start: 0.8878 (m100) cc_final: 0.8270 (m100) REVERT: K 285 ARG cc_start: 0.7489 (mpt90) cc_final: 0.7091 (mtp-110) REVERT: K 297 TYR cc_start: 0.5243 (OUTLIER) cc_final: 0.4702 (p90) REVERT: L 187 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7659 (tm-30) REVERT: L 242 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8031 (ttmm) REVERT: L 250 GLU cc_start: 0.7849 (tp30) cc_final: 0.7426 (mm-30) REVERT: M 187 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7699 (tm-30) REVERT: M 195 TRP cc_start: 0.9058 (m100) cc_final: 0.8849 (m100) REVERT: M 285 ARG cc_start: 0.7898 (mpt90) cc_final: 0.7613 (mtp-110) REVERT: N 53 ASN cc_start: 0.8277 (t0) cc_final: 0.8054 (t0) REVERT: N 61 MET cc_start: 0.7557 (mmm) cc_final: 0.7357 (tpp) REVERT: N 169 LYS cc_start: 0.7107 (mttt) cc_final: 0.6871 (mtpp) REVERT: N 187 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7811 (tm-30) REVERT: N 189 GLU cc_start: 0.8494 (tp30) cc_final: 0.8258 (tp30) REVERT: N 199 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8637 (mp) REVERT: N 231 ASN cc_start: 0.8380 (t0) cc_final: 0.8030 (t0) REVERT: O 187 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7668 (tm-30) REVERT: O 189 GLU cc_start: 0.8420 (tp30) cc_final: 0.7893 (tp30) REVERT: O 281 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: P 187 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7664 (tm-30) REVERT: P 195 TRP cc_start: 0.8877 (m100) cc_final: 0.8272 (m100) REVERT: P 285 ARG cc_start: 0.7587 (mpt90) cc_final: 0.7091 (mtp-110) REVERT: P 297 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.4540 (p90) REVERT: Q 187 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7636 (tm-30) REVERT: Q 242 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8179 (tttp) REVERT: R 187 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7705 (tm-30) REVERT: R 195 TRP cc_start: 0.9036 (m100) cc_final: 0.8832 (m100) REVERT: R 242 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8178 (tttp) REVERT: R 285 ARG cc_start: 0.7891 (mpt90) cc_final: 0.7547 (mtp-110) REVERT: S 187 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7784 (tm-30) REVERT: S 189 GLU cc_start: 0.8492 (tp30) cc_final: 0.7985 (tp30) REVERT: S 195 TRP cc_start: 0.9043 (m100) cc_final: 0.8332 (m100) REVERT: S 199 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8528 (mp) REVERT: T 187 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7655 (tm-30) REVERT: T 189 GLU cc_start: 0.8415 (tp30) cc_final: 0.7883 (tp30) REVERT: T 281 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7586 (m-80) outliers start: 432 outliers final: 255 residues processed: 820 average time/residue: 0.2468 time to fit residues: 331.9580 Evaluate side-chains 708 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 441 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain L residue 46 CYS Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 46 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 104 TRP Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain Q residue 46 CYS Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 296 MET Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 116 optimal weight: 120.0000 chunk 185 optimal weight: 0.9990 chunk 481 optimal weight: 3.9990 chunk 386 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 chunk 434 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 chunk 468 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 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 = 0.4531 r_free = 0.4531 target = 0.202626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156262 restraints weight = 74201.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160065 restraints weight = 41710.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.162576 restraints weight = 28980.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164305 restraints weight = 23069.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165098 restraints weight = 19841.099| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 45940 Z= 0.165 Angle : 0.666 8.952 62680 Z= 0.356 Chirality : 0.044 0.233 7060 Planarity : 0.005 0.044 7940 Dihedral : 7.111 59.820 6418 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 7.94 % Allowed : 17.47 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % 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: -0.96 (0.11), residues: 5820 helix: 0.44 (0.08), residues: 4200 sheet: None (None), residues: 0 loop : -3.55 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.011 0.001 TYR S 129 PHE 0.021 0.001 PHE F 200 TRP 0.025 0.002 TRP M 195 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00357 (45860) covalent geometry : angle 0.65876 (62520) SS BOND : bond 0.00643 ( 80) SS BOND : angle 2.02756 ( 160) hydrogen bonds : bond 0.03895 ( 2956) hydrogen bonds : angle 4.39342 ( 8808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 494 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 189 GLU cc_start: 0.8429 (tp30) cc_final: 0.7962 (tp30) REVERT: B 187 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 297 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.4776 (p90) REVERT: C 187 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 250 GLU cc_start: 0.7919 (tp30) cc_final: 0.7517 (mm-30) REVERT: D 187 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 195 TRP cc_start: 0.8994 (m100) cc_final: 0.8687 (m100) REVERT: D 281 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: D 285 ARG cc_start: 0.7830 (mpt90) cc_final: 0.7599 (mtp-110) REVERT: D 286 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8597 (mm) REVERT: D 297 TYR cc_start: 0.5339 (OUTLIER) cc_final: 0.3711 (p90) REVERT: E 187 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7852 (tm-30) REVERT: E 189 GLU cc_start: 0.8456 (tp30) cc_final: 0.7972 (tp30) REVERT: E 195 TRP cc_start: 0.9041 (m100) cc_final: 0.8311 (m100) REVERT: E 199 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8561 (mp) REVERT: F 187 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7658 (tm-30) REVERT: F 189 GLU cc_start: 0.8352 (tp30) cc_final: 0.8001 (tp30) REVERT: F 281 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: G 187 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7620 (tm-30) REVERT: G 195 TRP cc_start: 0.8939 (m100) cc_final: 0.8337 (m100) REVERT: G 285 ARG cc_start: 0.7500 (mpt90) cc_final: 0.7154 (mtp-110) REVERT: H 187 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7585 (tm-30) REVERT: H 242 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8020 (ttmm) REVERT: H 250 GLU cc_start: 0.7891 (tp30) cc_final: 0.7503 (mm-30) REVERT: I 187 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7715 (tm-30) REVERT: I 195 TRP cc_start: 0.8978 (m100) cc_final: 0.8724 (m100) REVERT: I 281 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: I 285 ARG cc_start: 0.7717 (mpt90) cc_final: 0.7317 (mtp-110) REVERT: I 297 TYR cc_start: 0.5344 (OUTLIER) cc_final: 0.3859 (p90) REVERT: J 123 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: J 187 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7768 (tm-30) REVERT: J 189 GLU cc_start: 0.8504 (tp30) cc_final: 0.7991 (tp30) REVERT: J 195 TRP cc_start: 0.9048 (m100) cc_final: 0.8336 (m100) REVERT: J 199 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8533 (mp) REVERT: K 187 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7562 (tm-30) REVERT: K 195 TRP cc_start: 0.8922 (m100) cc_final: 0.8341 (m100) REVERT: K 285 ARG cc_start: 0.7528 (mpt90) cc_final: 0.7131 (mtp-110) REVERT: L 187 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7639 (tm-30) REVERT: L 242 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8038 (ttmm) REVERT: L 250 GLU cc_start: 0.7777 (tp30) cc_final: 0.7424 (mm-30) REVERT: M 187 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7664 (tm-30) REVERT: M 195 TRP cc_start: 0.9011 (m100) cc_final: 0.8677 (m100) REVERT: M 281 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: M 285 ARG cc_start: 0.7769 (mpt90) cc_final: 0.7346 (mtp-110) REVERT: M 297 TYR cc_start: 0.5372 (OUTLIER) cc_final: 0.3845 (p90) REVERT: N 53 ASN cc_start: 0.8125 (t0) cc_final: 0.7911 (t0) REVERT: N 187 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7835 (tm-30) REVERT: N 189 GLU cc_start: 0.8443 (tp30) cc_final: 0.7987 (tp30) REVERT: N 195 TRP cc_start: 0.9030 (m100) cc_final: 0.8282 (m100) REVERT: N 199 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8574 (mp) REVERT: N 231 ASN cc_start: 0.8406 (t0) cc_final: 0.8083 (t0) REVERT: O 187 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7690 (tm-30) REVERT: O 189 GLU cc_start: 0.8311 (tp30) cc_final: 0.7938 (tp30) REVERT: O 231 ASN cc_start: 0.8225 (t0) cc_final: 0.8021 (t0) REVERT: O 281 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: P 187 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7602 (tm-30) REVERT: P 195 TRP cc_start: 0.8918 (m100) cc_final: 0.8331 (m100) REVERT: P 285 ARG cc_start: 0.7526 (mpt90) cc_final: 0.7142 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7573 (tm-30) REVERT: Q 242 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8025 (ttmm) REVERT: R 187 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7673 (tm-30) REVERT: R 195 TRP cc_start: 0.8963 (m100) cc_final: 0.8719 (m100) REVERT: R 242 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8161 (tttp) REVERT: R 281 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: R 285 ARG cc_start: 0.7726 (mpt90) cc_final: 0.7280 (mtp-110) REVERT: R 297 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.4135 (p90) REVERT: S 53 ASN cc_start: 0.8319 (t0) cc_final: 0.8059 (t0) REVERT: S 61 MET cc_start: 0.7371 (tpp) cc_final: 0.6797 (tpp) REVERT: S 123 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: S 187 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7800 (tm-30) REVERT: S 189 GLU cc_start: 0.8471 (tp30) cc_final: 0.7983 (tp30) REVERT: T 187 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7691 (tm-30) REVERT: T 189 GLU cc_start: 0.8326 (tp30) cc_final: 0.7897 (tp30) REVERT: T 281 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: T 300 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8456 (tp) outliers start: 351 outliers final: 243 residues processed: 741 average time/residue: 0.2324 time to fit residues: 286.0187 Evaluate side-chains 736 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 474 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 296 MET Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 46 CYS Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 296 MET Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 296 MET Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 46 CYS Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 296 MET Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Chi-restraints excluded: chain T residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 334 optimal weight: 8.9990 chunk 433 optimal weight: 1.9990 chunk 512 optimal weight: 6.9990 chunk 562 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 482 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.200708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153975 restraints weight = 75272.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157707 restraints weight = 42558.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.160313 restraints weight = 29872.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.161665 restraints weight = 23697.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162701 restraints weight = 20801.355| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45940 Z= 0.169 Angle : 0.671 9.453 62680 Z= 0.358 Chirality : 0.044 0.241 7060 Planarity : 0.005 0.047 7940 Dihedral : 6.578 59.770 6400 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 8.69 % Allowed : 16.54 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.11), residues: 5820 helix: 0.61 (0.08), residues: 4220 sheet: None (None), residues: 0 loop : -3.48 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 91 TYR 0.015 0.001 TYR B 50 PHE 0.016 0.001 PHE F 200 TRP 0.026 0.001 TRP F 195 HIS 0.005 0.001 HIS H 244 Details of bonding type rmsd covalent geometry : bond 0.00368 (45860) covalent geometry : angle 0.66176 (62520) SS BOND : bond 0.00751 ( 80) SS BOND : angle 2.34093 ( 160) hydrogen bonds : bond 0.03876 ( 2956) hydrogen bonds : angle 4.34049 ( 8808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 384 poor density : 493 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 189 GLU cc_start: 0.8313 (tp30) cc_final: 0.7837 (tp30) REVERT: A 281 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 187 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 250 GLU cc_start: 0.8108 (tp30) cc_final: 0.7784 (tt0) REVERT: B 297 TYR cc_start: 0.5395 (OUTLIER) cc_final: 0.4864 (p90) REVERT: C 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 250 GLU cc_start: 0.7901 (tp30) cc_final: 0.7398 (mm-30) REVERT: D 187 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 195 TRP cc_start: 0.8998 (m100) cc_final: 0.8686 (m100) REVERT: D 231 ASN cc_start: 0.8404 (t0) cc_final: 0.8159 (t0) REVERT: D 281 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: D 285 ARG cc_start: 0.7823 (mpt90) cc_final: 0.7497 (mtp-110) REVERT: D 286 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (mm) REVERT: D 297 TYR cc_start: 0.5458 (OUTLIER) cc_final: 0.3900 (p90) REVERT: E 53 ASN cc_start: 0.8349 (t0) cc_final: 0.8116 (t0) REVERT: E 187 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 189 GLU cc_start: 0.8486 (tp30) cc_final: 0.8048 (tp30) REVERT: E 195 TRP cc_start: 0.9052 (m100) cc_final: 0.8325 (m100) REVERT: E 199 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8555 (mp) REVERT: E 250 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: F 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7727 (tm-30) REVERT: F 189 GLU cc_start: 0.8346 (tp30) cc_final: 0.7958 (tp30) REVERT: F 281 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: G 187 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 195 TRP cc_start: 0.8946 (m100) cc_final: 0.8350 (m100) REVERT: G 285 ARG cc_start: 0.7570 (mpt90) cc_final: 0.7210 (mtp-110) REVERT: G 297 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4672 (p90) REVERT: H 187 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7762 (tm-30) REVERT: H 242 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8025 (ttmm) REVERT: H 250 GLU cc_start: 0.7875 (tp30) cc_final: 0.7459 (mm-30) REVERT: I 187 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7756 (tm-30) REVERT: I 195 TRP cc_start: 0.8990 (m100) cc_final: 0.8654 (m100) REVERT: I 231 ASN cc_start: 0.8415 (t0) cc_final: 0.8146 (t0) REVERT: I 281 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: I 285 ARG cc_start: 0.7728 (mpt90) cc_final: 0.7305 (mtp-110) REVERT: I 297 TYR cc_start: 0.5509 (OUTLIER) cc_final: 0.4066 (p90) REVERT: J 61 MET cc_start: 0.7505 (tpp) cc_final: 0.7134 (tpp) REVERT: J 123 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7258 (m-10) REVERT: J 187 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7843 (tm-30) REVERT: J 189 GLU cc_start: 0.8507 (tp30) cc_final: 0.7980 (tp30) REVERT: J 195 TRP cc_start: 0.9057 (m100) cc_final: 0.8359 (m100) REVERT: J 199 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (mp) REVERT: K 187 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7608 (tm-30) REVERT: K 285 ARG cc_start: 0.7564 (mpt90) cc_final: 0.7202 (mtp-110) REVERT: K 297 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.4770 (p90) REVERT: L 187 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7782 (tm-30) REVERT: L 242 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8016 (ttmm) REVERT: L 250 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: M 53 ASN cc_start: 0.8345 (t0) cc_final: 0.7995 (t0) REVERT: M 187 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7696 (tm-30) REVERT: M 195 TRP cc_start: 0.9060 (m100) cc_final: 0.8767 (m100) REVERT: M 231 ASN cc_start: 0.8390 (t0) cc_final: 0.8130 (t0) REVERT: M 281 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: M 285 ARG cc_start: 0.7770 (mpt90) cc_final: 0.7328 (mtp-110) REVERT: M 297 TYR cc_start: 0.5562 (OUTLIER) cc_final: 0.4090 (p90) REVERT: N 187 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7829 (tm-30) REVERT: N 189 GLU cc_start: 0.8492 (tp30) cc_final: 0.8059 (tp30) REVERT: N 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8322 (m100) REVERT: N 199 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8581 (mp) REVERT: N 231 ASN cc_start: 0.8403 (t0) cc_final: 0.8084 (t0) REVERT: N 250 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: O 187 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7728 (tm-30) REVERT: O 189 GLU cc_start: 0.8366 (tp30) cc_final: 0.7991 (tp30) REVERT: P 187 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7617 (tm-30) REVERT: P 285 ARG cc_start: 0.7594 (mpt90) cc_final: 0.7206 (mtp-110) REVERT: P 297 TYR cc_start: 0.5299 (OUTLIER) cc_final: 0.4759 (p90) REVERT: Q 187 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7773 (tm-30) REVERT: Q 242 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8033 (ttmm) REVERT: Q 250 GLU cc_start: 0.7843 (tp30) cc_final: 0.7334 (mm-30) REVERT: R 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7744 (tm-30) REVERT: R 195 TRP cc_start: 0.8983 (m100) cc_final: 0.8658 (m100) REVERT: R 231 ASN cc_start: 0.8382 (t0) cc_final: 0.8131 (t0) REVERT: R 242 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8204 (tttp) REVERT: R 281 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: R 285 ARG cc_start: 0.7717 (mpt90) cc_final: 0.7335 (mtp-110) REVERT: R 297 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.4160 (p90) REVERT: S 53 ASN cc_start: 0.8325 (t0) cc_final: 0.8084 (t0) REVERT: S 61 MET cc_start: 0.7372 (tpp) cc_final: 0.7086 (tpp) REVERT: S 123 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7303 (m-10) REVERT: S 187 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7823 (tm-30) REVERT: S 189 GLU cc_start: 0.8524 (tp30) cc_final: 0.8002 (tp30) REVERT: S 199 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8603 (mp) REVERT: T 187 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7720 (tm-30) REVERT: T 189 GLU cc_start: 0.8352 (tp30) cc_final: 0.7982 (tp30) REVERT: T 281 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: T 300 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8376 (tp) outliers start: 384 outliers final: 276 residues processed: 776 average time/residue: 0.2326 time to fit residues: 303.6044 Evaluate side-chains 757 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 302 poor density : 455 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 296 MET Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 250 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 296 MET Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 296 MET Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 296 MET Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 104 TRP Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain S residue 307 LYS Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Chi-restraints excluded: chain T residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 499 optimal weight: 5.9990 chunk 116 optimal weight: 120.0000 chunk 388 optimal weight: 0.8980 chunk 570 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 426 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 389 optimal weight: 0.9990 chunk 554 optimal weight: 50.0000 chunk 172 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.202655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155748 restraints weight = 74809.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159335 restraints weight = 43714.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161817 restraints weight = 31276.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163051 restraints weight = 25089.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164017 restraints weight = 22228.047| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45940 Z= 0.197 Angle : 0.716 10.610 62680 Z= 0.380 Chirality : 0.045 0.223 7060 Planarity : 0.005 0.050 7940 Dihedral : 6.418 59.879 6398 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 8.55 % Allowed : 17.15 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.67 (0.11), residues: 5820 helix: 0.53 (0.08), residues: 4340 sheet: None (None), residues: 0 loop : -3.38 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 254 TYR 0.015 0.002 TYR R 129 PHE 0.014 0.001 PHE F 200 TRP 0.026 0.001 TRP F 195 HIS 0.006 0.001 HIS Q 244 Details of bonding type rmsd covalent geometry : bond 0.00432 (45860) covalent geometry : angle 0.70609 (62520) SS BOND : bond 0.01154 ( 80) SS BOND : angle 2.46746 ( 160) hydrogen bonds : bond 0.04066 ( 2956) hydrogen bonds : angle 4.43930 ( 8808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 378 poor density : 485 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 187 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 189 GLU cc_start: 0.8441 (tp30) cc_final: 0.7887 (tp30) REVERT: A 281 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: B 52 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 187 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 250 GLU cc_start: 0.8142 (tp30) cc_final: 0.7832 (tt0) REVERT: B 297 TYR cc_start: 0.5584 (OUTLIER) cc_final: 0.5067 (p90) REVERT: C 187 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7806 (tm-30) REVERT: D 187 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 195 TRP cc_start: 0.9027 (m100) cc_final: 0.8668 (m100) REVERT: D 250 GLU cc_start: 0.8028 (tp30) cc_final: 0.7704 (tt0) REVERT: D 281 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: D 285 ARG cc_start: 0.7839 (mpt90) cc_final: 0.7365 (mtp-110) REVERT: D 286 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8717 (mm) REVERT: D 297 TYR cc_start: 0.5471 (OUTLIER) cc_final: 0.3921 (p90) REVERT: E 53 ASN cc_start: 0.8401 (t0) cc_final: 0.8163 (t0) REVERT: E 187 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 189 GLU cc_start: 0.8513 (tp30) cc_final: 0.7998 (tp30) REVERT: E 195 TRP cc_start: 0.9091 (m100) cc_final: 0.8359 (m100) REVERT: E 199 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8525 (mp) REVERT: E 231 ASN cc_start: 0.8377 (t0) cc_final: 0.8050 (t0) REVERT: E 250 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: F 187 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7737 (tm-30) REVERT: F 189 GLU cc_start: 0.8373 (tp30) cc_final: 0.7984 (tp30) REVERT: F 281 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: G 187 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7799 (tm-30) REVERT: G 285 ARG cc_start: 0.7643 (mpt90) cc_final: 0.7329 (mtp-110) REVERT: G 297 TYR cc_start: 0.5391 (OUTLIER) cc_final: 0.4872 (p90) REVERT: H 53 ASN cc_start: 0.8573 (t0) cc_final: 0.8368 (t0) REVERT: H 187 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7819 (tm-30) REVERT: H 242 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8163 (tttp) REVERT: H 250 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: I 187 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7769 (tm-30) REVERT: I 195 TRP cc_start: 0.9026 (m100) cc_final: 0.8656 (m100) REVERT: I 250 GLU cc_start: 0.8136 (tp30) cc_final: 0.7834 (tt0) REVERT: I 281 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: I 285 ARG cc_start: 0.7793 (mpt90) cc_final: 0.7216 (mtp-110) REVERT: I 297 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.4117 (p90) REVERT: J 53 ASN cc_start: 0.8469 (t0) cc_final: 0.8205 (t0) REVERT: J 61 MET cc_start: 0.7508 (tpp) cc_final: 0.7104 (tpp) REVERT: J 123 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: J 187 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7865 (tm-30) REVERT: J 189 GLU cc_start: 0.8525 (tp30) cc_final: 0.7955 (tp30) REVERT: K 187 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7777 (tm-30) REVERT: K 285 ARG cc_start: 0.7576 (mpt90) cc_final: 0.7196 (mtp-110) REVERT: K 297 TYR cc_start: 0.5463 (OUTLIER) cc_final: 0.4849 (p90) REVERT: L 131 CYS cc_start: 0.6528 (t) cc_final: 0.6294 (t) REVERT: L 187 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7798 (tm-30) REVERT: L 231 ASN cc_start: 0.8301 (t0) cc_final: 0.7998 (t0) REVERT: L 242 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8139 (tttp) REVERT: M 53 ASN cc_start: 0.8387 (t0) cc_final: 0.7978 (t0) REVERT: M 187 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7792 (tm-30) REVERT: M 195 TRP cc_start: 0.9076 (m100) cc_final: 0.8723 (m100) REVERT: M 231 ASN cc_start: 0.8376 (t0) cc_final: 0.8115 (t0) REVERT: M 250 GLU cc_start: 0.8121 (tp30) cc_final: 0.7842 (tt0) REVERT: M 281 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: M 285 ARG cc_start: 0.7823 (mpt90) cc_final: 0.7233 (mtp-110) REVERT: M 297 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.4136 (p90) REVERT: N 123 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: N 187 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7849 (tm-30) REVERT: N 189 GLU cc_start: 0.8502 (tp30) cc_final: 0.7973 (tp30) REVERT: N 195 TRP cc_start: 0.9087 (m100) cc_final: 0.8365 (m100) REVERT: N 199 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8535 (mp) REVERT: N 250 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: O 187 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7725 (tm-30) REVERT: O 189 GLU cc_start: 0.8373 (tp30) cc_final: 0.7971 (tp30) REVERT: O 281 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: P 187 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7793 (tm-30) REVERT: P 285 ARG cc_start: 0.7659 (mpt90) cc_final: 0.7301 (mtp-110) REVERT: P 297 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.4911 (p90) REVERT: Q 53 ASN cc_start: 0.8470 (t0) cc_final: 0.8268 (t0) REVERT: Q 131 CYS cc_start: 0.6516 (t) cc_final: 0.6276 (t) REVERT: Q 187 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7816 (tm-30) REVERT: Q 231 ASN cc_start: 0.8300 (t0) cc_final: 0.8008 (t0) REVERT: Q 242 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8174 (tttp) REVERT: R 187 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7768 (tm-30) REVERT: R 195 TRP cc_start: 0.9027 (m100) cc_final: 0.8680 (m100) REVERT: R 242 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8233 (tttp) REVERT: R 250 GLU cc_start: 0.8065 (tp30) cc_final: 0.7751 (tt0) REVERT: R 281 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: R 285 ARG cc_start: 0.7806 (mpt90) cc_final: 0.7413 (mtp-110) REVERT: R 297 TYR cc_start: 0.5602 (OUTLIER) cc_final: 0.4177 (p90) REVERT: S 53 ASN cc_start: 0.8412 (t0) cc_final: 0.8153 (t0) REVERT: S 123 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: S 187 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7823 (tm-30) REVERT: S 189 GLU cc_start: 0.8460 (tp30) cc_final: 0.7930 (tp30) REVERT: T 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7725 (tm-30) REVERT: T 189 GLU cc_start: 0.8382 (tp30) cc_final: 0.7976 (tp30) REVERT: T 281 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7755 (m-80) outliers start: 378 outliers final: 307 residues processed: 753 average time/residue: 0.2296 time to fit residues: 289.6350 Evaluate side-chains 800 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 333 poor density : 467 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 296 MET Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 296 MET Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 104 TRP Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 104 TRP Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 104 TRP Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 296 MET Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 104 TRP Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 146 CYS Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 550 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 348 optimal weight: 120.0000 chunk 183 optimal weight: 8.9990 chunk 340 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 501 optimal weight: 6.9990 chunk 358 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 76 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 153 ASN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 ASN ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.203500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158171 restraints weight = 75874.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.161950 restraints weight = 42579.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.164597 restraints weight = 29347.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165936 restraints weight = 23186.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.167319 restraints weight = 20375.974| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45940 Z= 0.142 Angle : 0.668 10.636 62680 Z= 0.353 Chirality : 0.043 0.211 7060 Planarity : 0.004 0.045 7940 Dihedral : 6.111 58.070 6396 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 6.76 % Allowed : 18.76 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.11), residues: 5820 helix: 0.83 (0.08), residues: 4300 sheet: None (None), residues: 0 loop : -3.51 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 254 TYR 0.014 0.001 TYR N 50 PHE 0.015 0.001 PHE F 200 TRP 0.027 0.002 TRP F 195 HIS 0.003 0.001 HIS R 135 Details of bonding type rmsd covalent geometry : bond 0.00304 (45860) covalent geometry : angle 0.65633 (62520) SS BOND : bond 0.00918 ( 80) SS BOND : angle 2.58378 ( 160) hydrogen bonds : bond 0.03620 ( 2956) hydrogen bonds : angle 4.36583 ( 8808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 510 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 189 GLU cc_start: 0.8409 (tp30) cc_final: 0.8053 (tp30) REVERT: A 281 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: A 286 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (tm) REVERT: B 52 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 187 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 250 GLU cc_start: 0.8004 (tp30) cc_final: 0.7704 (tt0) REVERT: C 187 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 187 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 195 TRP cc_start: 0.9013 (m100) cc_final: 0.8714 (m100) REVERT: D 231 ASN cc_start: 0.8272 (t0) cc_final: 0.8066 (t0) REVERT: D 281 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: D 285 ARG cc_start: 0.7659 (mpt90) cc_final: 0.7317 (mtp-110) REVERT: D 286 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8435 (mm) REVERT: D 297 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.3921 (p90) REVERT: E 53 ASN cc_start: 0.8163 (t0) cc_final: 0.7922 (t0) REVERT: E 187 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7849 (tm-30) REVERT: E 189 GLU cc_start: 0.8518 (tp30) cc_final: 0.8086 (tp30) REVERT: E 195 TRP cc_start: 0.9050 (m100) cc_final: 0.8459 (m100) REVERT: E 231 ASN cc_start: 0.8328 (t0) cc_final: 0.8048 (t0) REVERT: E 250 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: F 187 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7627 (tm-30) REVERT: F 189 GLU cc_start: 0.8301 (tp30) cc_final: 0.8018 (tp30) REVERT: G 187 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7727 (tm-30) REVERT: H 187 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7709 (tm-30) REVERT: H 242 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8014 (ttmm) REVERT: H 250 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: I 187 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7776 (tm-30) REVERT: I 195 TRP cc_start: 0.9007 (m100) cc_final: 0.8709 (m100) REVERT: I 231 ASN cc_start: 0.8350 (t0) cc_final: 0.8139 (t0) REVERT: I 250 GLU cc_start: 0.8011 (tp30) cc_final: 0.7732 (tt0) REVERT: I 281 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: I 285 ARG cc_start: 0.7681 (mpt90) cc_final: 0.7094 (mtp-110) REVERT: I 297 TYR cc_start: 0.5531 (OUTLIER) cc_final: 0.4124 (p90) REVERT: J 61 MET cc_start: 0.7350 (tpp) cc_final: 0.7037 (tpp) REVERT: J 123 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: J 187 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7739 (tm-30) REVERT: J 189 GLU cc_start: 0.8512 (tp30) cc_final: 0.8058 (tp30) REVERT: J 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8359 (m100) REVERT: J 250 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: K 187 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7698 (tm-30) REVERT: K 285 ARG cc_start: 0.7442 (mpt90) cc_final: 0.7206 (mtp-110) REVERT: L 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7746 (tm-30) REVERT: L 231 ASN cc_start: 0.8147 (t0) cc_final: 0.7899 (t0) REVERT: L 242 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8000 (ttmm) REVERT: L 250 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7450 (mm-30) REVERT: M 53 ASN cc_start: 0.8109 (t0) cc_final: 0.7754 (t0) REVERT: M 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7752 (tm-30) REVERT: M 195 TRP cc_start: 0.9049 (m100) cc_final: 0.8690 (m100) REVERT: M 281 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: M 285 ARG cc_start: 0.7680 (mpt90) cc_final: 0.7145 (mtp-110) REVERT: M 297 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.3981 (p90) REVERT: N 123 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: N 130 ARG cc_start: 0.8331 (ptt90) cc_final: 0.8118 (ptt90) REVERT: N 187 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7761 (tm-30) REVERT: N 189 GLU cc_start: 0.8510 (tp30) cc_final: 0.8084 (tp30) REVERT: N 250 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: O 187 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7564 (tm-30) REVERT: O 189 GLU cc_start: 0.8287 (tp30) cc_final: 0.8027 (tp30) REVERT: O 281 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: P 187 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7726 (tm-30) REVERT: P 285 ARG cc_start: 0.7428 (mpt90) cc_final: 0.7183 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7742 (tm-30) REVERT: Q 242 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7994 (ttmm) REVERT: Q 250 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7536 (mm-30) REVERT: R 187 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7669 (tm-30) REVERT: R 195 TRP cc_start: 0.9009 (m100) cc_final: 0.8710 (m100) REVERT: R 242 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8183 (tttp) REVERT: R 281 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: R 285 ARG cc_start: 0.7667 (mpt90) cc_final: 0.7334 (mtp-110) REVERT: R 297 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4166 (p90) REVERT: S 53 ASN cc_start: 0.8165 (t0) cc_final: 0.7902 (t0) REVERT: S 123 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: S 187 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7706 (tm-30) REVERT: S 189 GLU cc_start: 0.8480 (tp30) cc_final: 0.8042 (tp30) REVERT: S 195 TRP cc_start: 0.9047 (m100) cc_final: 0.8351 (m100) REVERT: S 296 MET cc_start: 0.6005 (mmp) cc_final: 0.5736 (mmm) REVERT: T 187 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7632 (tm-30) REVERT: T 189 GLU cc_start: 0.8262 (tp30) cc_final: 0.8000 (tp30) outliers start: 299 outliers final: 230 residues processed: 722 average time/residue: 0.2239 time to fit residues: 274.1272 Evaluate side-chains 695 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 445 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 296 MET Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 250 GLU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 296 MET Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 296 MET Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 122 optimal weight: 0.4980 chunk 254 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 427 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 472 optimal weight: 10.0000 chunk 357 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 153 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 ASN N 153 ASN ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 ASN ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Q 153 ASN ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 ASN ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.202897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.157235 restraints weight = 75659.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160990 restraints weight = 42764.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.163589 restraints weight = 29732.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164913 restraints weight = 23631.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.166114 restraints weight = 20711.995| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45940 Z= 0.151 Angle : 0.694 13.087 62680 Z= 0.362 Chirality : 0.044 0.220 7060 Planarity : 0.004 0.041 7940 Dihedral : 5.911 59.295 6388 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.54 % Allowed : 19.73 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.11), residues: 5820 helix: 0.93 (0.08), residues: 4320 sheet: None (None), residues: 0 loop : -3.50 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 285 TYR 0.030 0.002 TYR B 170 PHE 0.015 0.001 PHE G 123 TRP 0.028 0.001 TRP A 195 HIS 0.004 0.001 HIS N 135 Details of bonding type rmsd covalent geometry : bond 0.00328 (45860) covalent geometry : angle 0.68212 (62520) SS BOND : bond 0.00962 ( 80) SS BOND : angle 2.66389 ( 160) hydrogen bonds : bond 0.03659 ( 2956) hydrogen bonds : angle 4.28666 ( 8808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 468 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 189 GLU cc_start: 0.8386 (tp30) cc_final: 0.8031 (tp30) REVERT: A 195 TRP cc_start: 0.9085 (m100) cc_final: 0.8614 (m100) REVERT: A 281 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 187 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 250 GLU cc_start: 0.8032 (tp30) cc_final: 0.7715 (tt0) REVERT: C 187 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 187 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7668 (tm-30) REVERT: D 195 TRP cc_start: 0.9032 (m100) cc_final: 0.8697 (m100) REVERT: D 231 ASN cc_start: 0.8321 (t0) cc_final: 0.8107 (t0) REVERT: D 250 GLU cc_start: 0.7910 (tp30) cc_final: 0.7614 (tt0) REVERT: D 281 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: D 285 ARG cc_start: 0.7596 (mpt90) cc_final: 0.7191 (mtp-110) REVERT: D 286 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8474 (mm) REVERT: E 53 ASN cc_start: 0.8222 (t0) cc_final: 0.8014 (t0) REVERT: E 123 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: E 187 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7770 (tm-30) REVERT: E 189 GLU cc_start: 0.8539 (tp30) cc_final: 0.8060 (tp30) REVERT: E 195 TRP cc_start: 0.9045 (m100) cc_final: 0.8307 (m100) REVERT: E 231 ASN cc_start: 0.8335 (t0) cc_final: 0.8035 (t0) REVERT: E 250 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: E 305 ASP cc_start: 0.7781 (t0) cc_final: 0.7578 (t0) REVERT: F 187 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7640 (tm-30) REVERT: F 189 GLU cc_start: 0.8288 (tp30) cc_final: 0.7972 (tp30) REVERT: F 195 TRP cc_start: 0.9078 (m100) cc_final: 0.8599 (m100) REVERT: G 187 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7765 (tm-30) REVERT: H 187 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7695 (tm-30) REVERT: H 242 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7965 (ttmm) REVERT: I 187 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7693 (tm-30) REVERT: I 195 TRP cc_start: 0.9025 (m100) cc_final: 0.8695 (m100) REVERT: I 231 ASN cc_start: 0.8381 (t0) cc_final: 0.8140 (t0) REVERT: I 250 GLU cc_start: 0.8066 (tp30) cc_final: 0.7767 (tt0) REVERT: I 281 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: I 285 ARG cc_start: 0.7750 (mpt90) cc_final: 0.7135 (mtp-110) REVERT: I 297 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.4064 (p90) REVERT: J 61 MET cc_start: 0.7383 (tpp) cc_final: 0.7039 (tpp) REVERT: J 123 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7289 (m-10) REVERT: J 187 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7765 (tm-30) REVERT: J 189 GLU cc_start: 0.8527 (tp30) cc_final: 0.8059 (tp30) REVERT: J 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8280 (m100) REVERT: J 199 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8515 (mp) REVERT: J 250 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: J 305 ASP cc_start: 0.7811 (t0) cc_final: 0.7356 (m-30) REVERT: K 187 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7749 (tm-30) REVERT: L 187 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7769 (tm-30) REVERT: L 231 ASN cc_start: 0.8146 (t0) cc_final: 0.7862 (t0) REVERT: L 242 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7979 (ttmm) REVERT: L 250 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7481 (mm-30) REVERT: M 187 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7765 (tm-30) REVERT: M 195 TRP cc_start: 0.9071 (m100) cc_final: 0.8678 (m100) REVERT: M 250 GLU cc_start: 0.8001 (tp30) cc_final: 0.7717 (tt0) REVERT: M 281 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: M 285 ARG cc_start: 0.7828 (mpt90) cc_final: 0.7271 (mtp-110) REVERT: N 123 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: N 187 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7725 (tm-30) REVERT: N 189 GLU cc_start: 0.8526 (tp30) cc_final: 0.8067 (tp30) REVERT: N 195 TRP cc_start: 0.9050 (m100) cc_final: 0.8346 (m100) REVERT: N 250 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: O 187 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7607 (tm-30) REVERT: O 189 GLU cc_start: 0.8287 (tp30) cc_final: 0.7981 (tp30) REVERT: O 195 TRP cc_start: 0.9078 (m100) cc_final: 0.8589 (m100) REVERT: O 281 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: P 187 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7762 (tm-30) REVERT: Q 187 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7755 (tm-30) REVERT: Q 242 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8014 (ttmm) REVERT: R 187 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7685 (tm-30) REVERT: R 195 TRP cc_start: 0.9025 (m100) cc_final: 0.8683 (m100) REVERT: R 242 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8149 (tttp) REVERT: R 250 GLU cc_start: 0.7887 (tp30) cc_final: 0.7583 (tt0) REVERT: R 281 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: R 285 ARG cc_start: 0.7779 (mpt90) cc_final: 0.7410 (mtp-110) REVERT: S 53 ASN cc_start: 0.8314 (t0) cc_final: 0.8048 (t0) REVERT: S 123 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: S 187 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7733 (tm-30) REVERT: S 189 GLU cc_start: 0.8523 (tp30) cc_final: 0.8060 (tp30) REVERT: S 195 TRP cc_start: 0.9046 (m100) cc_final: 0.8360 (m100) REVERT: T 187 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7663 (tm-30) REVERT: T 189 GLU cc_start: 0.8300 (tp30) cc_final: 0.7977 (tp30) REVERT: T 195 TRP cc_start: 0.9072 (m100) cc_final: 0.8568 (m100) REVERT: T 281 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7523 (m-80) outliers start: 289 outliers final: 249 residues processed: 672 average time/residue: 0.2222 time to fit residues: 252.3007 Evaluate side-chains 702 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 436 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 296 MET Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 296 MET Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 296 MET Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 307 LYS Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 53 optimal weight: 5.9990 chunk 544 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 478 optimal weight: 30.0000 chunk 465 optimal weight: 50.0000 chunk 176 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 539 optimal weight: 0.0870 chunk 430 optimal weight: 3.9990 chunk 119 optimal weight: 30.0000 chunk 545 optimal weight: 4.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 153 ASN ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 153 ASN ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.200796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155457 restraints weight = 76346.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.159152 restraints weight = 42624.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161759 restraints weight = 29476.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163066 restraints weight = 23279.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.164206 restraints weight = 20380.020| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45940 Z= 0.167 Angle : 0.708 18.845 62680 Z= 0.366 Chirality : 0.044 0.278 7060 Planarity : 0.004 0.042 7940 Dihedral : 5.954 59.844 6388 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.31 % Allowed : 20.09 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.20 (0.11), residues: 5820 helix: 1.09 (0.08), residues: 4200 sheet: None (None), residues: 0 loop : -3.56 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 254 TYR 0.021 0.001 TYR N 170 PHE 0.015 0.001 PHE G 123 TRP 0.028 0.001 TRP A 195 HIS 0.005 0.001 HIS T 135 Details of bonding type rmsd covalent geometry : bond 0.00368 (45860) covalent geometry : angle 0.69699 (62520) SS BOND : bond 0.00925 ( 80) SS BOND : angle 2.52697 ( 160) hydrogen bonds : bond 0.03755 ( 2956) hydrogen bonds : angle 4.28447 ( 8808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 436 time to evaluate : 1.627 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 187 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 189 GLU cc_start: 0.8371 (tp30) cc_final: 0.7978 (tp30) REVERT: A 195 TRP cc_start: 0.9095 (m100) cc_final: 0.8601 (m100) REVERT: A 281 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: B 187 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 195 TRP cc_start: 0.8945 (m100) cc_final: 0.8434 (m100) REVERT: B 250 GLU cc_start: 0.8065 (tp30) cc_final: 0.7748 (tt0) REVERT: C 187 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7788 (tm-30) REVERT: D 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 195 TRP cc_start: 0.9046 (m100) cc_final: 0.8721 (m100) REVERT: D 250 GLU cc_start: 0.7978 (tp30) cc_final: 0.7665 (tt0) REVERT: D 281 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: D 285 ARG cc_start: 0.7760 (mpt90) cc_final: 0.7269 (mtp-110) REVERT: D 286 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8589 (mm) REVERT: E 53 ASN cc_start: 0.8247 (t0) cc_final: 0.8038 (t0) REVERT: E 123 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: E 187 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7796 (tm-30) REVERT: E 189 GLU cc_start: 0.8564 (tp30) cc_final: 0.8077 (tp30) REVERT: E 195 TRP cc_start: 0.9056 (m100) cc_final: 0.8329 (m100) REVERT: E 231 ASN cc_start: 0.8320 (t0) cc_final: 0.8021 (t0) REVERT: E 250 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: F 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7671 (tm-30) REVERT: F 189 GLU cc_start: 0.8298 (tp30) cc_final: 0.7982 (tp30) REVERT: F 195 TRP cc_start: 0.9086 (m100) cc_final: 0.8600 (m100) REVERT: F 281 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: G 187 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7782 (tm-30) REVERT: G 195 TRP cc_start: 0.8946 (m100) cc_final: 0.8369 (m100) REVERT: G 287 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6057 (pt) REVERT: H 187 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7753 (tm-30) REVERT: I 187 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7732 (tm-30) REVERT: I 195 TRP cc_start: 0.9036 (m100) cc_final: 0.8719 (m100) REVERT: I 250 GLU cc_start: 0.8077 (tp30) cc_final: 0.7774 (tt0) REVERT: I 281 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: I 285 ARG cc_start: 0.7800 (mpt90) cc_final: 0.7172 (mtp-110) REVERT: I 297 TYR cc_start: 0.5452 (OUTLIER) cc_final: 0.3897 (p90) REVERT: J 53 ASN cc_start: 0.8345 (t0) cc_final: 0.8073 (t0) REVERT: J 61 MET cc_start: 0.7465 (tpp) cc_final: 0.7018 (tpp) REVERT: J 123 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: J 187 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7778 (tm-30) REVERT: J 189 GLU cc_start: 0.8520 (tp30) cc_final: 0.8038 (tp30) REVERT: J 195 TRP cc_start: 0.9032 (m100) cc_final: 0.8359 (m100) REVERT: J 250 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: J 305 ASP cc_start: 0.7835 (t0) cc_final: 0.7386 (m-30) REVERT: K 187 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7762 (tm-30) REVERT: K 195 TRP cc_start: 0.8944 (m100) cc_final: 0.8403 (m100) REVERT: L 187 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7811 (tm-30) REVERT: L 242 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8034 (ttmm) REVERT: L 250 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7538 (mm-30) REVERT: M 187 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7793 (tm-30) REVERT: M 195 TRP cc_start: 0.9089 (m100) cc_final: 0.8690 (m100) REVERT: M 250 GLU cc_start: 0.8041 (tp30) cc_final: 0.7724 (tt0) REVERT: M 281 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: M 285 ARG cc_start: 0.7809 (mpt90) cc_final: 0.7306 (mtp-110) REVERT: M 297 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.3851 (p90) REVERT: N 123 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: N 187 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7749 (tm-30) REVERT: N 189 GLU cc_start: 0.8541 (tp30) cc_final: 0.8078 (tp30) REVERT: N 195 TRP cc_start: 0.9048 (m100) cc_final: 0.8366 (m100) REVERT: N 250 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: N 305 ASP cc_start: 0.7825 (t0) cc_final: 0.7373 (m-30) REVERT: O 187 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7626 (tm-30) REVERT: O 189 GLU cc_start: 0.8310 (tp30) cc_final: 0.8002 (tp30) REVERT: O 195 TRP cc_start: 0.9092 (m100) cc_final: 0.8613 (m100) REVERT: O 281 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: P 187 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7782 (tm-30) REVERT: P 195 TRP cc_start: 0.8935 (m100) cc_final: 0.8375 (m100) REVERT: Q 187 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7803 (tm-30) REVERT: Q 242 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8024 (ttmm) REVERT: R 187 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7706 (tm-30) REVERT: R 195 TRP cc_start: 0.9042 (m100) cc_final: 0.8712 (m100) REVERT: R 242 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8234 (tttp) REVERT: R 250 GLU cc_start: 0.7988 (tp30) cc_final: 0.7679 (tt0) REVERT: R 281 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: R 285 ARG cc_start: 0.7790 (mpt90) cc_final: 0.7464 (mtp-110) REVERT: R 297 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.3900 (p90) REVERT: S 53 ASN cc_start: 0.8299 (t0) cc_final: 0.8067 (t0) REVERT: S 123 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: S 187 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7738 (tm-30) REVERT: S 189 GLU cc_start: 0.8543 (tp30) cc_final: 0.8078 (tp30) REVERT: S 195 TRP cc_start: 0.9019 (m100) cc_final: 0.8343 (m100) REVERT: S 231 ASN cc_start: 0.8305 (t0) cc_final: 0.8072 (t0) REVERT: T 187 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7648 (tm-30) REVERT: T 189 GLU cc_start: 0.8309 (tp30) cc_final: 0.7993 (tp30) REVERT: T 195 TRP cc_start: 0.9077 (m100) cc_final: 0.8594 (m100) REVERT: T 281 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7674 (m-80) outliers start: 279 outliers final: 245 residues processed: 640 average time/residue: 0.2223 time to fit residues: 240.7516 Evaluate side-chains 692 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 427 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 296 MET Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 296 MET Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 296 MET Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 307 LYS Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 540 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 290 optimal weight: 120.0000 chunk 571 optimal weight: 5.9990 chunk 549 optimal weight: 6.9990 chunk 545 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 chunk 521 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 ASN ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 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 = 0.4510 r_free = 0.4510 target = 0.198353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152376 restraints weight = 77252.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156204 restraints weight = 43200.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.158804 restraints weight = 29940.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.160097 restraints weight = 23754.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161113 restraints weight = 20810.840| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45940 Z= 0.167 Angle : 0.704 18.004 62680 Z= 0.364 Chirality : 0.044 0.308 7060 Planarity : 0.004 0.043 7940 Dihedral : 5.922 59.830 6388 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.49 % Allowed : 19.91 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.17 (0.11), residues: 5820 helix: 1.11 (0.08), residues: 4200 sheet: None (None), residues: 0 loop : -3.54 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 254 TYR 0.019 0.001 TYR G 170 PHE 0.015 0.001 PHE G 123 TRP 0.027 0.002 TRP C 195 HIS 0.005 0.001 HIS H 244 Details of bonding type rmsd covalent geometry : bond 0.00370 (45860) covalent geometry : angle 0.69352 (62520) SS BOND : bond 0.00843 ( 80) SS BOND : angle 2.44339 ( 160) hydrogen bonds : bond 0.03775 ( 2956) hydrogen bonds : angle 4.26728 ( 8808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8035.63 seconds wall clock time: 139 minutes 50.63 seconds (8390.63 seconds total)