Starting phenix.real_space_refine on Thu Dec 26 09:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lom_0938/12_2024/6lom_0938.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lom_0938/12_2024/6lom_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lom_0938/12_2024/6lom_0938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lom_0938/12_2024/6lom_0938.map" model { file = "/net/cci-nas-00/data/ceres_data/6lom_0938/12_2024/6lom_0938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lom_0938/12_2024/6lom_0938.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 11.03, per 1000 atoms: 0.25 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=4, 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 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: 12.27 Conformation dependent library (CDL) restraints added in 5.6 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: 4.02 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: 17.41 Time building geometry restraints manager: 13.68 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: 23825 14.96 - 29.92: 2179 29.92 - 44.88: 584 44.88 - 59.84: 143 59.84 - 74.80: 41 Dihedral angle restraints: 26772 sinusoidal: 9392 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 26769 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: 2.02 - 2.60: 515 2.60 - 3.17: 38375 3.17 - 3.75: 73479 3.75 - 4.32: 92073 4.32 - 4.90: 150568 Nonbonded interactions: 355010 Sorted by model distance: nonbonded pdb=" SG CYS H 46 " pdb=" SG CYS H 131 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS C 46 " pdb=" SG CYS C 131 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS D 46 " pdb=" SG CYS D 131 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS J 46 " pdb=" SG CYS J 131 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS S 46 " pdb=" SG CYS S 131 " model vdw 2.023 3.760 ... (remaining 355005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 1.430 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: 1.860 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 79.840 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.190 ------------------------------------------------------------------------------- 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 45860 Z= 0.472 Angle : 1.167 10.739 62520 Z= 0.628 Chirality : 0.058 0.214 7060 Planarity : 0.009 0.069 7940 Dihedral : 13.554 74.799 15520 Min Nonbonded Distance : 2.023 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.005 TRP C 118 HIS 0.006 0.002 HIS B 135 PHE 0.024 0.003 PHE H 44 TYR 0.021 0.003 TYR N 128 ARG 0.024 0.002 ARG T 283 *********************** 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 : 5.409 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: 0.7102 (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: 0.6583 (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: 0.7979 (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: 0.6655 (tptt) REVERT: C 135 HIS cc_start: 0.7459 (t-90) cc_final: 0.7121 (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: 0.8308 (ttmt) cc_final: 0.8053 (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: 0.8022 (tm-30) REVERT: D 231 ASN cc_start: 0.8310 (t160) cc_final: 0.8028 (t0) REVERT: D 256 PHE cc_start: 0.8502 (t80) cc_final: 0.8265 (t80) 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: 0.8356 (mm) REVERT: E 135 HIS cc_start: 0.7700 (t-90) cc_final: 0.7164 (t-90) REVERT: E 187 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8295 (tm-30) REVERT: E 199 LEU cc_start: 0.8740 (tt) cc_final: 0.8494 (tp) REVERT: E 285 ARG cc_start: 0.7401 (mpt90) cc_final: 0.7137 (ttm110) REVERT: F 82 LEU cc_start: 0.8393 (tt) cc_final: 0.7863 (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: 0.7173 (t-90) REVERT: F 187 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8364 (tm-30) 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: 0.7212 (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: 0.8148 (tm-30) REVERT: G 285 ARG cc_start: 0.7431 (mpt90) cc_final: 0.7183 (ttm110) REVERT: H 82 LEU cc_start: 0.8524 (tt) cc_final: 0.8298 (mt) REVERT: H 98 LYS cc_start: 0.6923 (tttt) cc_final: 0.6652 (tptt) REVERT: H 135 HIS cc_start: 0.7477 (t-90) cc_final: 0.7132 (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: 0.7941 (ttmm) REVERT: H 256 PHE cc_start: 0.8587 (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: 0.8028 (t0) REVERT: I 242 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8132 (tttp) REVERT: I 256 PHE cc_start: 0.8508 (t80) cc_final: 0.8295 (t80) REVERT: I 285 ARG cc_start: 0.7630 (mpt90) cc_final: 0.7296 (ttm110) REVERT: J 135 HIS cc_start: 0.7644 (t-90) cc_final: 0.7169 (t-90) REVERT: J 187 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8302 (tm-30) REVERT: J 199 LEU cc_start: 0.8748 (tt) cc_final: 0.8471 (tp) REVERT: J 285 ARG cc_start: 0.7395 (mpt90) cc_final: 0.7139 (ttm110) REVERT: K 82 LEU cc_start: 0.8540 (tt) cc_final: 0.8279 (mt) REVERT: K 135 HIS cc_start: 0.7654 (t-90) cc_final: 0.7130 (t-90) REVERT: K 186 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8813 (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: 0.7133 (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: 0.6753 (tptt) REVERT: L 135 HIS cc_start: 0.7360 (t-90) cc_final: 0.7013 (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: 0.8234 (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: 0.8065 (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: 0.8479 (tp) REVERT: M 231 ASN cc_start: 0.8311 (t160) cc_final: 0.8014 (t0) REVERT: M 256 PHE cc_start: 0.8549 (t80) cc_final: 0.8223 (t80) REVERT: M 285 ARG cc_start: 0.7554 (mpt90) cc_final: 0.7187 (ttm110) REVERT: N 135 HIS cc_start: 0.7614 (t-90) cc_final: 0.7129 (t-90) REVERT: N 187 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8291 (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: 0.6587 (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: 0.7143 (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: 0.7150 (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: 0.6721 (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: 0.7998 (t0) REVERT: Q 242 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8063 (ttmm) REVERT: Q 256 PHE cc_start: 0.8565 (t80) cc_final: 0.8336 (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: 0.8481 (tp) REVERT: R 231 ASN cc_start: 0.8327 (t160) cc_final: 0.8021 (t0) REVERT: R 242 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8113 (tttp) REVERT: R 256 PHE cc_start: 0.8493 (t80) cc_final: 0.8242 (t80) REVERT: R 285 ARG cc_start: 0.7602 (mpt90) cc_final: 0.7270 (ttm110) REVERT: S 98 LYS cc_start: 0.6742 (tttt) cc_final: 0.6440 (tptt) REVERT: S 135 HIS cc_start: 0.7663 (t-90) cc_final: 0.7182 (t-90) REVERT: S 187 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8261 (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: 0.7889 (tt) REVERT: T 135 HIS cc_start: 0.7527 (t-90) cc_final: 0.7128 (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: 0.6548 (pt) outliers start: 80 outliers final: 40 residues processed: 1033 average time/residue: 0.6389 time to fit residues: 1041.5037 Evaluate side-chains 568 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 520 time to evaluate : 5.498 ------------------------------------------------------------------------------- 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 489 optimal weight: 1.9990 chunk 439 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 454 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 526 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 84 HIS 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 84 HIS 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 84 HIS 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 84 HIS 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: 122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 45860 Z= 0.321 Angle : 0.789 14.000 62520 Z= 0.424 Chirality : 0.046 0.172 7060 Planarity : 0.006 0.051 7940 Dihedral : 8.862 58.753 6456 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 7.47 % Allowed : 15.18 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 5820 helix: -0.91 (0.07), residues: 4140 sheet: None (None), residues: 0 loop : -3.30 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP R 195 HIS 0.004 0.001 HIS S 244 PHE 0.020 0.002 PHE C 200 TYR 0.018 0.002 TYR D 128 ARG 0.007 0.001 ARG B 254 *********************** 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 905 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 330 poor density : 575 time to evaluate : 5.181 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: symmetry clash REVERT: A 135 HIS cc_start: 0.7455 (t-90) cc_final: 0.7054 (t-90) REVERT: A 187 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 123 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: B 135 HIS cc_start: 0.7742 (t-90) cc_final: 0.7419 (t-90) REVERT: B 187 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 252 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8209 (t160) REVERT: C 135 HIS cc_start: 0.7461 (t-90) cc_final: 0.7127 (t-90) REVERT: C 186 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8811 (tp) REVERT: C 187 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 135 HIS cc_start: 0.7636 (t-90) cc_final: 0.7263 (t-90) REVERT: D 187 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7567 (tm-30) REVERT: D 285 ARG cc_start: 0.7846 (mpt90) cc_final: 0.7486 (mtp-110) REVERT: E 187 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7788 (tm-30) REVERT: F 135 HIS cc_start: 0.7544 (t-90) cc_final: 0.7137 (t-90) REVERT: F 187 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7756 (tm-30) REVERT: G 123 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7672 (m-10) REVERT: G 135 HIS cc_start: 0.7714 (t-90) cc_final: 0.7353 (t-90) REVERT: G 187 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7729 (tm-30) REVERT: G 195 TRP cc_start: 0.8855 (m100) cc_final: 0.8635 (m100) REVERT: G 252 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8298 (t160) REVERT: G 285 ARG cc_start: 0.7451 (mpt90) cc_final: 0.7048 (ttm110) REVERT: H 135 HIS cc_start: 0.7453 (t-90) cc_final: 0.7108 (t-90) REVERT: H 186 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8803 (tp) REVERT: H 187 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7652 (tm-30) REVERT: H 242 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8115 (tttp) REVERT: I 135 HIS cc_start: 0.7615 (t-90) cc_final: 0.7243 (t-90) REVERT: I 187 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7756 (tm-30) REVERT: I 285 ARG cc_start: 0.7828 (mpt90) cc_final: 0.7398 (mtp-110) REVERT: J 187 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7791 (tm-30) REVERT: K 123 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: K 135 HIS cc_start: 0.7731 (t-90) cc_final: 0.7362 (t-90) REVERT: K 187 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7735 (tm-30) REVERT: K 195 TRP cc_start: 0.8917 (m100) cc_final: 0.8609 (m100) REVERT: K 285 ARG cc_start: 0.7492 (mpt90) cc_final: 0.7188 (ttm110) REVERT: L 135 HIS cc_start: 0.7439 (t-90) cc_final: 0.7075 (t-90) REVERT: L 186 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8818 (tp) REVERT: L 187 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7625 (tm-30) REVERT: L 195 TRP cc_start: 0.8911 (m100) cc_final: 0.8661 (m100) REVERT: M 135 HIS cc_start: 0.7630 (t-90) cc_final: 0.7268 (t-90) REVERT: M 187 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7750 (tm-30) REVERT: M 285 ARG cc_start: 0.7844 (mpt90) cc_final: 0.7391 (mtp-110) REVERT: N 187 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7780 (tm-30) REVERT: N 285 ARG cc_start: 0.7613 (mpt90) cc_final: 0.7409 (mtp-110) REVERT: O 135 HIS cc_start: 0.7467 (t-90) cc_final: 0.7053 (t-90) REVERT: O 187 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7730 (tm-30) REVERT: P 123 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: P 135 HIS cc_start: 0.7731 (t-90) cc_final: 0.7361 (t-90) REVERT: P 187 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7718 (tm-30) REVERT: P 195 TRP cc_start: 0.8926 (m100) cc_final: 0.8625 (m100) REVERT: P 252 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8329 (t160) REVERT: P 285 ARG cc_start: 0.7444 (mpt90) cc_final: 0.7137 (ttm110) REVERT: Q 135 HIS cc_start: 0.7447 (t-90) cc_final: 0.7093 (t-90) REVERT: Q 186 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8805 (tp) REVERT: Q 187 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7643 (tm-30) REVERT: Q 195 TRP cc_start: 0.8903 (m100) cc_final: 0.8657 (m100) REVERT: R 135 HIS cc_start: 0.7497 (t-90) cc_final: 0.7177 (t-90) REVERT: R 187 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7727 (tm-30) REVERT: R 285 ARG cc_start: 0.7793 (mpt90) cc_final: 0.7306 (mtp-110) REVERT: S 61 MET cc_start: 0.7679 (mmm) cc_final: 0.7165 (tpp) REVERT: S 98 LYS cc_start: 0.6645 (tttt) cc_final: 0.6194 (tptt) REVERT: S 123 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: S 187 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7767 (tm-30) REVERT: S 285 ARG cc_start: 0.7561 (mpt90) cc_final: 0.7290 (mtp-110) REVERT: T 135 HIS cc_start: 0.7489 (t-90) cc_final: 0.7070 (t-90) REVERT: T 187 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7714 (tm-30) outliers start: 330 outliers final: 167 residues processed: 845 average time/residue: 0.6008 time to fit residues: 822.1348 Evaluate side-chains 654 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 475 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP 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 209 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 140 ILE 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 252 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 TRP 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 186 LEU Chi-restraints excluded: chain C residue 201 SER 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 123 PHE Chi-restraints excluded: chain D residue 140 ILE 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 58 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 252 ASN 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 58 LEU Chi-restraints excluded: chain H residue 104 TRP 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 186 LEU Chi-restraints excluded: chain H residue 201 SER 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 123 PHE Chi-restraints excluded: chain I residue 140 ILE 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 104 TRP 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 201 SER Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 123 PHE Chi-restraints excluded: chain K residue 140 ILE 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 209 ILE 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 58 LEU Chi-restraints excluded: chain L residue 104 TRP 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 186 LEU Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 209 ILE 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 68 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE 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 58 LEU Chi-restraints excluded: chain N residue 104 TRP Chi-restraints excluded: chain N residue 140 ILE 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 219 THR Chi-restraints excluded: chain O residue 104 TRP Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain P residue 104 TRP Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 252 ASN 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 Q residue 58 LEU Chi-restraints excluded: chain Q residue 104 TRP 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 186 LEU Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 209 ILE 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 68 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 140 ILE 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 217 LYS Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain S residue 58 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 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 219 THR Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 209 ILE Chi-restraints excluded: chain T residue 214 MET 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 292 optimal weight: 40.0000 chunk 163 optimal weight: 4.9990 chunk 438 optimal weight: 20.0000 chunk 358 optimal weight: 3.9990 chunk 145 optimal weight: 120.0000 chunk 527 optimal weight: 3.9990 chunk 570 optimal weight: 2.9990 chunk 469 optimal weight: 6.9990 chunk 523 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 423 optimal weight: 40.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 301 GLN ** 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 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 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** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** 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** ** 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 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 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 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 301 GLN ** 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 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 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 45860 Z= 0.296 Angle : 0.716 11.254 62520 Z= 0.383 Chirality : 0.045 0.177 7060 Planarity : 0.005 0.050 7940 Dihedral : 8.023 59.994 6446 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 7.08 % Allowed : 17.26 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5820 helix: -0.22 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -3.27 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 195 HIS 0.007 0.002 HIS N 84 PHE 0.018 0.001 PHE B 200 TYR 0.016 0.002 TYR S 129 ARG 0.008 0.001 ARG B 254 *********************** 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 853 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 313 poor density : 540 time to evaluate : 5.632 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: 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: 0.8162 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 189 GLU cc_start: 0.8430 (tp30) cc_final: 0.7945 (tp30) REVERT: A 231 ASN cc_start: 0.8292 (t0) cc_final: 0.8059 (t0) REVERT: A 281 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: A 286 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8543 (tm) REVERT: B 187 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 195 TRP cc_start: 0.8962 (m100) cc_final: 0.8435 (m100) REVERT: C 187 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7602 (tm-30) REVERT: D 187 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 195 TRP cc_start: 0.9003 (m100) cc_final: 0.8800 (m100) REVERT: D 281 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: D 285 ARG cc_start: 0.7870 (mpt90) cc_final: 0.7615 (mtp-110) REVERT: D 286 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8526 (mm) REVERT: E 187 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 189 GLU cc_start: 0.8486 (tp30) cc_final: 0.8256 (tp30) REVERT: E 286 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8566 (mm) REVERT: E 301 GLN cc_start: 0.8094 (tp40) cc_final: 0.7622 (mt0) REVERT: F 53 ASN cc_start: 0.8438 (t0) cc_final: 0.8201 (t0) REVERT: F 187 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7710 (tm-30) REVERT: F 199 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (mp) REVERT: F 231 ASN cc_start: 0.8280 (t0) cc_final: 0.8043 (t0) REVERT: F 281 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: F 301 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7345 (mm110) REVERT: G 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7708 (tm-30) REVERT: G 231 ASN cc_start: 0.8310 (t0) cc_final: 0.8032 (t0) REVERT: G 285 ARG cc_start: 0.7447 (mpt90) cc_final: 0.7104 (mtp-110) REVERT: H 187 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7615 (tm-30) REVERT: H 242 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8117 (tttp) REVERT: I 187 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7697 (tm-30) REVERT: I 285 ARG cc_start: 0.7844 (mpt90) cc_final: 0.7424 (mtp-110) REVERT: J 187 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7876 (tm-30) REVERT: J 189 GLU cc_start: 0.8489 (tp30) cc_final: 0.7937 (tp30) REVERT: J 195 TRP cc_start: 0.9036 (m100) cc_final: 0.8533 (m100) REVERT: K 187 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7652 (tm-30) REVERT: K 231 ASN cc_start: 0.8301 (t0) cc_final: 0.8021 (t0) REVERT: K 285 ARG cc_start: 0.7490 (mpt90) cc_final: 0.7107 (mtp-110) REVERT: K 286 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8453 (tm) REVERT: L 187 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7609 (tm-30) REVERT: M 187 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7707 (tm-30) REVERT: M 281 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: M 285 ARG cc_start: 0.7875 (mpt90) cc_final: 0.7448 (mtp-110) REVERT: M 307 LYS cc_start: 0.7823 (mttt) cc_final: 0.7532 (mttm) REVERT: N 53 ASN cc_start: 0.8558 (t0) cc_final: 0.8117 (t0) REVERT: N 61 MET cc_start: 0.7682 (mmm) cc_final: 0.7146 (tpp) REVERT: N 123 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: N 187 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7778 (tm-30) REVERT: N 189 GLU cc_start: 0.8495 (tp30) cc_final: 0.8238 (tp30) REVERT: N 285 ARG cc_start: 0.7708 (mpt90) cc_final: 0.7438 (mtp-110) REVERT: N 286 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8574 (mm) REVERT: O 53 ASN cc_start: 0.8414 (t0) cc_final: 0.8184 (t0) REVERT: O 187 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7682 (tm-30) REVERT: O 231 ASN cc_start: 0.8300 (t0) cc_final: 0.8078 (t0) REVERT: O 281 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: P 123 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: P 187 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7706 (tm-30) REVERT: P 231 ASN cc_start: 0.8266 (t0) cc_final: 0.7975 (t0) REVERT: P 250 GLU cc_start: 0.7773 (tp30) cc_final: 0.7555 (tp30) REVERT: P 285 ARG cc_start: 0.7499 (mpt90) cc_final: 0.7132 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7633 (tm-30) REVERT: R 187 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7662 (tm-30) REVERT: R 195 TRP cc_start: 0.9023 (m100) cc_final: 0.8814 (m100) REVERT: R 285 ARG cc_start: 0.7838 (mpt90) cc_final: 0.7384 (mtp-110) REVERT: S 98 LYS cc_start: 0.6301 (tttt) cc_final: 0.6004 (tptt) REVERT: S 123 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: S 187 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7831 (tm-30) REVERT: S 189 GLU cc_start: 0.8502 (tp30) cc_final: 0.7927 (tp30) REVERT: S 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8557 (m100) REVERT: T 53 ASN cc_start: 0.8441 (t0) cc_final: 0.8232 (t0) REVERT: T 187 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7668 (tm-30) REVERT: T 231 ASN cc_start: 0.8272 (t0) cc_final: 0.8039 (t0) REVERT: T 281 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7645 (m-80) outliers start: 313 outliers final: 202 residues processed: 783 average time/residue: 0.6211 time to fit residues: 781.7775 Evaluate side-chains 739 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 522 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 113 VAL 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 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 140 ILE 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 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ILE 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 162 ASN Chi-restraints excluded: chain C residue 171 CYS 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 D residue 58 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 171 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 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 201 SER 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 113 VAL 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 199 LEU 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 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 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN 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 252 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU 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 162 ASN Chi-restraints excluded: chain H residue 171 CYS 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 H residue 296 MET 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 171 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 296 MET Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 104 TRP 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 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 286 LEU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 140 ILE 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 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 162 ASN Chi-restraints excluded: chain L residue 171 CYS 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 232 VAL 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 171 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 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 104 TRP 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 171 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 281 PHE Chi-restraints excluded: chain N residue 286 LEU 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 181 THR Chi-restraints excluded: chain O residue 201 SER 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 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 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 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 162 ASN Chi-restraints excluded: chain Q residue 171 CYS 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 232 VAL 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 171 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 R residue 296 MET Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 104 TRP Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 171 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 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 58 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 171 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 521 optimal weight: 1.9990 chunk 396 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 58 optimal weight: 110.0000 chunk 251 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 529 optimal weight: 7.9990 chunk 560 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 501 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** 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 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 301 GLN ** 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 252 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** ** H 304 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** 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** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 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** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 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** ** O 301 GLN ** 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 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 45860 Z= 0.312 Angle : 0.696 10.886 62520 Z= 0.373 Chirality : 0.045 0.207 7060 Planarity : 0.006 0.055 7940 Dihedral : 7.462 59.335 6418 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 9.39 % Allowed : 15.07 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.11), residues: 5820 helix: -0.13 (0.08), residues: 4340 sheet: None (None), residues: 0 loop : -3.68 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 195 HIS 0.007 0.002 HIS T 244 PHE 0.024 0.001 PHE O 200 TYR 0.019 0.002 TYR L 129 ARG 0.007 0.001 ARG L 254 *********************** 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 965 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 415 poor density : 550 time to evaluate : 5.209 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: 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: 0.8208 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 189 GLU cc_start: 0.8437 (tp30) cc_final: 0.7975 (tp30) REVERT: A 281 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: B 187 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 195 TRP cc_start: 0.8991 (m100) cc_final: 0.8445 (m100) REVERT: B 231 ASN cc_start: 0.8278 (t0) cc_final: 0.8024 (t0) REVERT: B 297 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.4893 (p90) REVERT: C 187 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 53 ASN cc_start: 0.8530 (t0) cc_final: 0.8222 (t0) REVERT: D 187 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 195 TRP cc_start: 0.9066 (m100) cc_final: 0.8752 (m100) REVERT: D 231 ASN cc_start: 0.8383 (t0) cc_final: 0.8119 (t0) REVERT: D 281 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: D 285 ARG cc_start: 0.7875 (mpt90) cc_final: 0.7662 (mtp-110) REVERT: D 297 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.4261 (p90) REVERT: E 53 ASN cc_start: 0.8607 (t0) cc_final: 0.8210 (t0) REVERT: E 61 MET cc_start: 0.7194 (tpp) cc_final: 0.6966 (tpp) REVERT: E 123 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: E 187 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7860 (tm-30) REVERT: E 189 GLU cc_start: 0.8514 (tp30) cc_final: 0.8216 (tp30) REVERT: E 195 TRP cc_start: 0.9103 (m100) cc_final: 0.8462 (m100) REVERT: E 231 ASN cc_start: 0.8385 (t0) cc_final: 0.8043 (t0) REVERT: E 250 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: E 286 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8580 (mm) REVERT: E 296 MET cc_start: 0.6165 (mmp) cc_final: 0.5815 (mtt) REVERT: E 301 GLN cc_start: 0.7864 (tp40) cc_final: 0.7276 (mt0) REVERT: F 53 ASN cc_start: 0.8478 (t0) cc_final: 0.8243 (t0) REVERT: F 187 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7805 (tm-30) REVERT: F 189 GLU cc_start: 0.8471 (tp30) cc_final: 0.7934 (tp30) REVERT: F 199 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8654 (mp) REVERT: F 231 ASN cc_start: 0.8311 (t0) cc_final: 0.8093 (t0) REVERT: F 281 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: G 187 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7797 (tm-30) REVERT: G 195 TRP cc_start: 0.8998 (m100) cc_final: 0.8324 (m100) REVERT: G 231 ASN cc_start: 0.8275 (t0) cc_final: 0.8024 (t0) REVERT: G 247 GLN cc_start: 0.6845 (mt0) cc_final: 0.6638 (pt0) REVERT: G 285 ARG cc_start: 0.7572 (mpt90) cc_final: 0.7107 (mtp-110) REVERT: G 297 TYR cc_start: 0.5555 (OUTLIER) cc_final: 0.4816 (p90) REVERT: H 187 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7693 (tm-30) REVERT: H 242 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8113 (tttp) REVERT: I 53 ASN cc_start: 0.8555 (t0) cc_final: 0.8230 (t0) REVERT: I 187 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7737 (tm-30) REVERT: I 195 TRP cc_start: 0.9043 (m100) cc_final: 0.8836 (m100) REVERT: I 231 ASN cc_start: 0.8381 (t0) cc_final: 0.8122 (t0) REVERT: I 250 GLU cc_start: 0.8066 (tp30) cc_final: 0.7771 (tt0) REVERT: I 281 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: I 285 ARG cc_start: 0.7868 (mpt90) cc_final: 0.7506 (mtp-110) REVERT: I 297 TYR cc_start: 0.5645 (OUTLIER) cc_final: 0.4343 (p90) REVERT: J 53 ASN cc_start: 0.8573 (t0) cc_final: 0.8164 (t0) REVERT: J 123 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: J 187 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7835 (tm-30) REVERT: J 189 GLU cc_start: 0.8522 (tp30) cc_final: 0.8222 (tp30) REVERT: J 195 TRP cc_start: 0.9040 (m100) cc_final: 0.8509 (m100) REVERT: J 231 ASN cc_start: 0.8397 (t0) cc_final: 0.8027 (t0) REVERT: J 286 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8581 (mm) REVERT: K 187 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7719 (tm-30) REVERT: K 195 TRP cc_start: 0.9007 (m100) cc_final: 0.8335 (m100) REVERT: K 231 ASN cc_start: 0.8252 (t0) cc_final: 0.7964 (t0) REVERT: K 285 ARG cc_start: 0.7576 (mpt90) cc_final: 0.7166 (mtp-110) REVERT: K 297 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.5188 (p90) REVERT: L 187 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7681 (tm-30) REVERT: L 250 GLU cc_start: 0.7923 (tp30) cc_final: 0.7540 (mm-30) REVERT: M 53 ASN cc_start: 0.8548 (t0) cc_final: 0.8224 (t0) REVERT: M 187 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7708 (tm-30) REVERT: M 195 TRP cc_start: 0.9042 (m100) cc_final: 0.8838 (m100) REVERT: M 231 ASN cc_start: 0.8380 (t0) cc_final: 0.8122 (t0) REVERT: M 281 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: M 285 ARG cc_start: 0.7895 (mpt90) cc_final: 0.7586 (mtp-110) REVERT: M 307 LYS cc_start: 0.7825 (mttt) cc_final: 0.7582 (mttm) REVERT: N 53 ASN cc_start: 0.8542 (t0) cc_final: 0.8166 (t0) REVERT: N 130 ARG cc_start: 0.8523 (ptt90) cc_final: 0.8299 (ptm-80) REVERT: N 187 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7845 (tm-30) REVERT: N 189 GLU cc_start: 0.8522 (tp30) cc_final: 0.8254 (tp30) REVERT: N 231 ASN cc_start: 0.8362 (t0) cc_final: 0.7999 (t0) REVERT: N 286 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8575 (mm) REVERT: O 53 ASN cc_start: 0.8487 (t0) cc_final: 0.8263 (t0) REVERT: O 187 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7764 (tm-30) REVERT: O 189 GLU cc_start: 0.8413 (tp30) cc_final: 0.7888 (tp30) REVERT: O 281 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: P 187 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7733 (tm-30) REVERT: P 195 TRP cc_start: 0.9027 (m100) cc_final: 0.8370 (m100) REVERT: P 231 ASN cc_start: 0.8240 (t0) cc_final: 0.7984 (t0) REVERT: P 250 GLU cc_start: 0.7731 (tp30) cc_final: 0.7521 (tp30) REVERT: P 285 ARG cc_start: 0.7596 (mpt90) cc_final: 0.7120 (mtp-110) REVERT: P 297 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.4948 (p90) REVERT: Q 187 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7701 (tm-30) REVERT: R 53 ASN cc_start: 0.8544 (t0) cc_final: 0.8221 (t0) REVERT: R 187 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7743 (tm-30) REVERT: R 195 TRP cc_start: 0.9086 (m100) cc_final: 0.8783 (m100) REVERT: R 231 ASN cc_start: 0.8374 (t0) cc_final: 0.8101 (t0) REVERT: R 281 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: R 285 ARG cc_start: 0.7870 (mpt90) cc_final: 0.7467 (mtp-110) REVERT: R 297 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.4278 (p90) REVERT: S 53 ASN cc_start: 0.8602 (t0) cc_final: 0.8198 (t0) REVERT: S 98 LYS cc_start: 0.6422 (tttt) cc_final: 0.6083 (tptt) REVERT: S 123 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: S 187 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7821 (tm-30) REVERT: S 189 GLU cc_start: 0.8515 (tp30) cc_final: 0.8213 (tp30) REVERT: S 195 TRP cc_start: 0.9050 (m100) cc_final: 0.8507 (m100) REVERT: S 231 ASN cc_start: 0.8381 (t0) cc_final: 0.8017 (t0) REVERT: T 53 ASN cc_start: 0.8499 (t0) cc_final: 0.8270 (t0) REVERT: T 187 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7763 (tm-30) REVERT: T 189 GLU cc_start: 0.8407 (tp30) cc_final: 0.7876 (tp30) REVERT: T 231 ASN cc_start: 0.8311 (t0) cc_final: 0.8101 (t0) REVERT: T 281 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7802 (m-80) outliers start: 415 outliers final: 273 residues processed: 856 average time/residue: 0.5854 time to fit residues: 822.0816 Evaluate side-chains 823 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 527 time to evaluate : 5.647 ------------------------------------------------------------------------------- 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 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 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 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 233 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain C residue 58 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 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 232 VAL 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 104 TRP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 162 ASN 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 297 TYR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 108 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 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 201 SER 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 280 LEU 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 297 TYR Chi-restraints excluded: chain E residue 302 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 181 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 201 SER 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 104 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 140 ILE 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 280 LEU 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 G residue 302 LEU Chi-restraints excluded: chain H residue 58 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 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 232 VAL 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 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 108 LEU Chi-restraints excluded: chain I residue 140 ILE 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 280 LEU 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 52 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 108 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 181 THR Chi-restraints excluded: chain J residue 186 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 280 LEU 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 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 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 280 LEU 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 108 LEU 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 199 LEU Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 232 VAL 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 297 TYR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN 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 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 302 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 104 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN 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 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 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 108 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 199 LEU 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 287 ILE 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 113 VAL 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 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 280 LEU 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 58 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 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 232 VAL 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 52 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 104 TRP Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 140 ILE 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 233 GLU Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 104 TRP Chi-restraints excluded: chain S residue 108 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 181 THR Chi-restraints excluded: chain S residue 186 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 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 108 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 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 287 ILE 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 466 optimal weight: 0.3980 chunk 318 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 417 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 478 optimal weight: 20.0000 chunk 387 optimal weight: 3.9990 chunk 0 optimal weight: 120.0000 chunk 286 optimal weight: 0.9980 chunk 503 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 76 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 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 53 ASN G 76 ASN ** G 95 HIS ** 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 ** H 95 HIS ** 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 ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** J 95 HIS ** 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 ** K 95 HIS ** 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 95 HIS ** 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** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** N 95 HIS ** 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 53 ASN P 76 ASN ** P 95 HIS ** 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 95 HIS ** 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 76 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN ** S 95 HIS ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45860 Z= 0.170 Angle : 0.606 8.528 62520 Z= 0.322 Chirality : 0.043 0.229 7060 Planarity : 0.005 0.044 7940 Dihedral : 7.016 57.672 6418 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.58 % Allowed : 16.54 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5820 helix: 0.40 (0.08), residues: 4320 sheet: None (None), residues: 0 loop : -3.36 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 195 HIS 0.004 0.001 HIS G 251 PHE 0.021 0.001 PHE M 200 TYR 0.011 0.001 TYR C 132 ARG 0.009 0.001 ARG B 254 *********************** 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 869 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 534 time to evaluate : 5.786 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 187 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 254 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.8020 (mmt180) REVERT: B 297 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4676 (p90) REVERT: C 187 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7665 (tm-30) REVERT: D 53 ASN cc_start: 0.8276 (t0) cc_final: 0.8056 (t0) REVERT: D 135 HIS cc_start: 0.7132 (t-90) cc_final: 0.6931 (t-90) REVERT: D 187 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7700 (tm-30) REVERT: D 195 TRP cc_start: 0.8996 (m100) cc_final: 0.8663 (m100) REVERT: D 231 ASN cc_start: 0.8169 (t0) cc_final: 0.7948 (t0) REVERT: D 286 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8448 (tm) REVERT: E 53 ASN cc_start: 0.8359 (t0) cc_final: 0.7983 (t0) REVERT: E 162 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7620 (t0) REVERT: E 173 PRO cc_start: 0.8835 (Cg_exo) cc_final: 0.8407 (Cg_endo) REVERT: E 187 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7722 (tm-30) REVERT: E 231 ASN cc_start: 0.8210 (t0) cc_final: 0.7953 (t0) REVERT: F 187 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7636 (tm-30) REVERT: F 189 GLU cc_start: 0.8381 (tp30) cc_final: 0.7910 (tp30) REVERT: F 286 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8530 (tm) REVERT: G 162 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7422 (t0) REVERT: G 173 PRO cc_start: 0.8774 (Cg_exo) cc_final: 0.8362 (Cg_endo) REVERT: G 187 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7646 (tm-30) REVERT: G 285 ARG cc_start: 0.7368 (mpt90) cc_final: 0.7012 (mtp-110) REVERT: G 297 TYR cc_start: 0.5146 (OUTLIER) cc_final: 0.4597 (p90) REVERT: H 187 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7666 (tm-30) REVERT: H 242 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7903 (ttmm) REVERT: I 53 ASN cc_start: 0.8262 (t0) cc_final: 0.8050 (t0) REVERT: I 187 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7681 (tm-30) REVERT: I 195 TRP cc_start: 0.9052 (m100) cc_final: 0.8758 (m100) REVERT: I 231 ASN cc_start: 0.8170 (t0) cc_final: 0.7952 (t0) REVERT: I 281 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: I 285 ARG cc_start: 0.7668 (mpt90) cc_final: 0.7268 (mtp-110) REVERT: J 53 ASN cc_start: 0.8344 (t0) cc_final: 0.7857 (t0) REVERT: J 61 MET cc_start: 0.7365 (tpp) cc_final: 0.6981 (tpp) REVERT: J 123 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: J 162 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7716 (t0) REVERT: J 173 PRO cc_start: 0.8941 (Cg_exo) cc_final: 0.8482 (Cg_endo) REVERT: J 187 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7736 (tm-30) REVERT: J 231 ASN cc_start: 0.8265 (t0) cc_final: 0.8020 (t0) REVERT: J 250 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: K 94 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.7027 (ptt-90) REVERT: K 187 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7598 (tm-30) REVERT: K 285 ARG cc_start: 0.7342 (mpt90) cc_final: 0.7103 (mtp-110) REVERT: K 286 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8317 (tm) REVERT: L 187 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7685 (tm-30) REVERT: M 53 ASN cc_start: 0.8250 (t0) cc_final: 0.8047 (t0) REVERT: M 135 HIS cc_start: 0.7120 (t-90) cc_final: 0.6917 (t-90) REVERT: M 187 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7583 (tm-30) REVERT: M 195 TRP cc_start: 0.9041 (m100) cc_final: 0.8719 (m100) REVERT: M 231 ASN cc_start: 0.8177 (t0) cc_final: 0.7948 (t0) REVERT: M 285 ARG cc_start: 0.7672 (mpt90) cc_final: 0.7289 (mtp-110) REVERT: N 53 ASN cc_start: 0.8288 (t0) cc_final: 0.7925 (t0) REVERT: N 123 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: N 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7679 (tm-30) REVERT: N 195 TRP cc_start: 0.9035 (m100) cc_final: 0.8462 (m100) REVERT: N 231 ASN cc_start: 0.8227 (t0) cc_final: 0.7985 (t0) REVERT: N 250 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: O 130 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8199 (ptt90) REVERT: O 187 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7658 (tm-30) REVERT: O 189 GLU cc_start: 0.8360 (tp30) cc_final: 0.7867 (tp30) REVERT: O 250 GLU cc_start: 0.7730 (tp30) cc_final: 0.7338 (mm-30) REVERT: P 94 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6967 (ptt-90) REVERT: P 162 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7568 (t0) REVERT: P 173 PRO cc_start: 0.8766 (Cg_exo) cc_final: 0.8348 (Cg_endo) REVERT: P 187 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7615 (tm-30) REVERT: P 250 GLU cc_start: 0.7597 (tp30) cc_final: 0.7173 (mm-30) REVERT: P 254 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.7996 (mmt180) REVERT: P 285 ARG cc_start: 0.7410 (mpt90) cc_final: 0.7009 (mtp-110) REVERT: P 297 TYR cc_start: 0.5190 (OUTLIER) cc_final: 0.4624 (p90) REVERT: Q 187 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7667 (tm-30) REVERT: Q 232 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8273 (t) REVERT: R 53 ASN cc_start: 0.8273 (t0) cc_final: 0.8062 (t0) REVERT: R 187 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7669 (tm-30) REVERT: R 195 TRP cc_start: 0.9002 (m100) cc_final: 0.8677 (m100) REVERT: R 231 ASN cc_start: 0.8189 (t0) cc_final: 0.7952 (t0) REVERT: R 281 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: R 285 ARG cc_start: 0.7669 (mpt90) cc_final: 0.7260 (mtp-110) REVERT: S 53 ASN cc_start: 0.8371 (t0) cc_final: 0.7980 (t0) REVERT: S 61 MET cc_start: 0.7483 (tpp) cc_final: 0.7223 (tpp) REVERT: S 98 LYS cc_start: 0.6380 (tttt) cc_final: 0.5982 (tptt) REVERT: S 187 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7669 (tm-30) REVERT: S 231 ASN cc_start: 0.8253 (t0) cc_final: 0.8026 (t0) REVERT: T 130 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.8186 (ptt90) REVERT: T 187 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7655 (tm-30) REVERT: T 189 GLU cc_start: 0.8346 (tp30) cc_final: 0.7864 (tp30) outliers start: 335 outliers final: 210 residues processed: 773 average time/residue: 0.6239 time to fit residues: 779.5172 Evaluate side-chains 727 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 498 time to evaluate : 5.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 113 VAL 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 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU 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 140 ILE Chi-restraints excluded: chain B residue 181 THR 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 296 MET Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 108 LEU 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 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 219 THR 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 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 181 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN 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 233 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 F residue 52 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 181 THR 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 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 181 THR 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 108 LEU 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 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 219 THR 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 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 162 ASN 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 302 LEU 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 162 ASN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 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 284 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU 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 302 LEU Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 108 LEU 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 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 219 THR 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 297 TYR Chi-restraints excluded: chain M residue 58 LEU 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 181 THR Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 286 LEU 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 52 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 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain N residue 297 TYR 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 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 233 GLU Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 287 ILE 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 94 ARG Chi-restraints excluded: chain P residue 113 VAL 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 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU 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 108 LEU 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 162 ASN 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 232 VAL 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 58 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 181 THR 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 302 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 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 287 ILE Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain T residue 113 VAL 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 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 188 optimal weight: 20.0000 chunk 504 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 561 optimal weight: 6.9990 chunk 465 optimal weight: 30.0000 chunk 259 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 294 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** 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 95 HIS ** 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 HIS ** 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 95 HIS ** 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 95 HIS ** 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 ** Q 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45860 Z= 0.184 Angle : 0.609 8.677 62520 Z= 0.321 Chirality : 0.043 0.226 7060 Planarity : 0.005 0.043 7940 Dihedral : 6.708 59.682 6414 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 7.38 % Allowed : 16.81 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 5820 helix: 0.89 (0.08), residues: 4160 sheet: None (None), residues: 0 loop : -3.43 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP O 195 HIS 0.005 0.001 HIS J 135 PHE 0.016 0.001 PHE M 200 TYR 0.013 0.001 TYR E 229 ARG 0.007 0.000 ARG B 254 *********************** 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 828 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 326 poor density : 502 time to evaluate : 5.648 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: A 130 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.8066 (ptt90) REVERT: A 187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 189 GLU cc_start: 0.8362 (tp30) cc_final: 0.7985 (tp30) REVERT: A 280 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7190 (tt) REVERT: A 281 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: B 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 286 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (tm) REVERT: B 287 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6423 (pt) REVERT: B 297 TYR cc_start: 0.5322 (OUTLIER) cc_final: 0.4792 (p90) REVERT: C 187 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 187 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7650 (tm-30) REVERT: D 195 TRP cc_start: 0.8968 (m100) cc_final: 0.8668 (m100) REVERT: D 231 ASN cc_start: 0.8215 (t0) cc_final: 0.7996 (t0) REVERT: D 250 GLU cc_start: 0.7765 (tp30) cc_final: 0.7483 (tt0) REVERT: D 280 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7130 (tt) REVERT: D 281 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: E 53 ASN cc_start: 0.8375 (t0) cc_final: 0.7899 (t0) REVERT: E 162 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7663 (t0) REVERT: E 173 PRO cc_start: 0.8872 (Cg_exo) cc_final: 0.8389 (Cg_endo) REVERT: E 187 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7724 (tm-30) REVERT: E 189 GLU cc_start: 0.8501 (tp30) cc_final: 0.7968 (tp30) REVERT: E 195 TRP cc_start: 0.9037 (m100) cc_final: 0.8364 (m100) REVERT: E 231 ASN cc_start: 0.8180 (t0) cc_final: 0.7969 (t0) REVERT: E 250 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: E 305 ASP cc_start: 0.7728 (t0) cc_final: 0.7512 (t0) REVERT: F 187 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7652 (tm-30) REVERT: F 189 GLU cc_start: 0.8369 (tp30) cc_final: 0.7999 (tp30) REVERT: F 199 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8658 (mp) REVERT: F 281 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: G 162 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7561 (t0) REVERT: G 173 PRO cc_start: 0.8779 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: G 187 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7641 (tm-30) REVERT: G 250 GLU cc_start: 0.7693 (tp30) cc_final: 0.7471 (tt0) REVERT: G 285 ARG cc_start: 0.7510 (mpt90) cc_final: 0.7126 (mtp-110) REVERT: G 296 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5713 (mmm) REVERT: G 297 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.4869 (p90) REVERT: H 187 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7646 (tm-30) REVERT: H 242 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7910 (ttmm) REVERT: I 53 ASN cc_start: 0.8378 (t0) cc_final: 0.8128 (t0) REVERT: I 187 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7616 (tm-30) REVERT: I 195 TRP cc_start: 0.9050 (m100) cc_final: 0.8760 (m100) REVERT: I 231 ASN cc_start: 0.8240 (t0) cc_final: 0.8013 (t0) REVERT: I 250 GLU cc_start: 0.7905 (tp30) cc_final: 0.7660 (tt0) REVERT: I 281 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: I 285 ARG cc_start: 0.7729 (mpt90) cc_final: 0.7281 (mtp-110) REVERT: J 53 ASN cc_start: 0.8404 (t0) cc_final: 0.7955 (t0) REVERT: J 61 MET cc_start: 0.7351 (tpp) cc_final: 0.6850 (tpp) REVERT: J 123 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: J 162 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7728 (t0) REVERT: J 173 PRO cc_start: 0.8858 (Cg_exo) cc_final: 0.8385 (Cg_endo) REVERT: J 187 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7765 (tm-30) REVERT: J 189 GLU cc_start: 0.8574 (tp30) cc_final: 0.8026 (tp30) REVERT: J 195 TRP cc_start: 0.8990 (m100) cc_final: 0.8355 (m100) REVERT: J 231 ASN cc_start: 0.8254 (t0) cc_final: 0.8004 (t0) REVERT: J 250 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: K 82 LEU cc_start: 0.8828 (tt) cc_final: 0.8608 (tt) REVERT: K 187 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7634 (tm-30) REVERT: L 187 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7661 (tm-30) REVERT: M 53 ASN cc_start: 0.8331 (t0) cc_final: 0.8119 (t0) REVERT: M 187 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7609 (tm-30) REVERT: M 195 TRP cc_start: 0.9047 (m100) cc_final: 0.8746 (m100) REVERT: M 231 ASN cc_start: 0.8220 (t0) cc_final: 0.8002 (t0) REVERT: M 285 ARG cc_start: 0.7763 (mpt90) cc_final: 0.7408 (mtp-110) REVERT: N 53 ASN cc_start: 0.8320 (t0) cc_final: 0.7881 (t0) REVERT: N 61 MET cc_start: 0.7524 (tpp) cc_final: 0.7131 (tpp) REVERT: N 123 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: N 187 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7677 (tm-30) REVERT: N 189 GLU cc_start: 0.8509 (tp30) cc_final: 0.7951 (tp30) REVERT: N 195 TRP cc_start: 0.9040 (m100) cc_final: 0.8508 (m100) REVERT: N 231 ASN cc_start: 0.8228 (t0) cc_final: 0.7980 (t0) REVERT: N 250 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: O 187 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7643 (tm-30) REVERT: O 189 GLU cc_start: 0.8390 (tp30) cc_final: 0.7934 (tp30) REVERT: O 250 GLU cc_start: 0.7781 (tp30) cc_final: 0.7300 (mm-30) REVERT: O 281 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: P 162 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7631 (t0) REVERT: P 173 PRO cc_start: 0.8793 (Cg_exo) cc_final: 0.8349 (Cg_endo) REVERT: P 187 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7647 (tm-30) REVERT: P 250 GLU cc_start: 0.7621 (tp30) cc_final: 0.7405 (mm-30) REVERT: P 285 ARG cc_start: 0.7526 (mpt90) cc_final: 0.7130 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7648 (tm-30) REVERT: R 53 ASN cc_start: 0.8364 (t0) cc_final: 0.8115 (t0) REVERT: R 187 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7637 (tm-30) REVERT: R 195 TRP cc_start: 0.9006 (m100) cc_final: 0.8735 (m100) REVERT: R 231 ASN cc_start: 0.8235 (t0) cc_final: 0.8005 (t0) REVERT: R 250 GLU cc_start: 0.7747 (tp30) cc_final: 0.7472 (tt0) REVERT: R 281 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: R 285 ARG cc_start: 0.7736 (mpt90) cc_final: 0.7267 (mtp-110) REVERT: S 53 ASN cc_start: 0.8365 (t0) cc_final: 0.7886 (t0) REVERT: S 98 LYS cc_start: 0.6333 (tttt) cc_final: 0.5910 (tptt) REVERT: S 187 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7675 (tm-30) REVERT: S 189 GLU cc_start: 0.8509 (tp30) cc_final: 0.7993 (tp30) REVERT: S 195 TRP cc_start: 0.8989 (m100) cc_final: 0.8328 (m100) REVERT: S 231 ASN cc_start: 0.8246 (t0) cc_final: 0.7999 (t0) REVERT: T 187 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7643 (tm-30) REVERT: T 189 GLU cc_start: 0.8375 (tp30) cc_final: 0.7929 (tp30) REVERT: T 281 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7523 (m-80) outliers start: 326 outliers final: 241 residues processed: 731 average time/residue: 0.6470 time to fit residues: 787.0915 Evaluate side-chains 750 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 485 time to evaluate : 5.364 ------------------------------------------------------------------------------- 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 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 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 280 LEU 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 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 287 ILE 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 219 THR 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 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 162 ASN 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 219 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 PHE 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 52 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 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 201 SER 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 F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 201 SER 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 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 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 219 THR Chi-restraints excluded: chain H residue 232 VAL 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 297 TYR Chi-restraints excluded: chain I residue 52 LEU 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 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 219 THR 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 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 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 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 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 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 140 ILE 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 296 MET Chi-restraints excluded: chain K residue 302 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 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 219 THR 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 M residue 58 LEU 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 181 THR 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 280 LEU 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 52 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 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 287 ILE Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 140 ILE 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 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER 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 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 214 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 232 VAL 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 52 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 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 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 52 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 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 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 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 541 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 319 optimal weight: 120.0000 chunk 409 optimal weight: 20.0000 chunk 317 optimal weight: 7.9990 chunk 472 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 559 optimal weight: 5.9990 chunk 349 optimal weight: 30.0000 chunk 340 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 HIS ** 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 HIS ** 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 95 HIS ** 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 95 HIS ** 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 45860 Z= 0.230 Angle : 0.642 11.334 62520 Z= 0.336 Chirality : 0.044 0.216 7060 Planarity : 0.005 0.040 7940 Dihedral : 6.567 59.784 6412 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 7.44 % Allowed : 16.99 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5820 helix: 1.00 (0.08), residues: 4160 sheet: None (None), residues: 0 loop : -3.36 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP T 195 HIS 0.005 0.002 HIS F 244 PHE 0.019 0.001 PHE S 123 TYR 0.013 0.001 TYR D 129 ARG 0.009 0.001 ARG B 254 *********************** 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 818 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 329 poor density : 489 time to evaluate : 5.889 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: 0.8256 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 189 GLU cc_start: 0.8485 (tp30) cc_final: 0.7944 (tp30) REVERT: A 280 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7265 (tt) REVERT: A 281 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: B 187 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 286 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8226 (tm) REVERT: B 297 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.4808 (p90) REVERT: C 187 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7689 (tm-30) REVERT: D 187 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7716 (tm-30) REVERT: D 195 TRP cc_start: 0.9005 (m100) cc_final: 0.8684 (m100) REVERT: D 250 GLU cc_start: 0.7871 (tp30) cc_final: 0.7568 (tt0) REVERT: D 280 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7183 (tt) REVERT: D 286 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8465 (tm) REVERT: E 53 ASN cc_start: 0.8434 (t0) cc_final: 0.8016 (t0) REVERT: E 123 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: E 162 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7543 (t0) REVERT: E 173 PRO cc_start: 0.8895 (Cg_exo) cc_final: 0.8432 (Cg_endo) REVERT: E 187 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7794 (tm-30) REVERT: E 189 GLU cc_start: 0.8486 (tp30) cc_final: 0.7886 (tp30) REVERT: E 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8360 (m100) REVERT: E 231 ASN cc_start: 0.8264 (t0) cc_final: 0.8013 (t0) REVERT: E 250 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: E 305 ASP cc_start: 0.7744 (t0) cc_final: 0.7538 (t0) REVERT: F 187 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7674 (tm-30) REVERT: F 189 GLU cc_start: 0.8398 (tp30) cc_final: 0.7928 (tp30) REVERT: F 281 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: G 162 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7576 (t0) REVERT: G 173 PRO cc_start: 0.8783 (Cg_exo) cc_final: 0.8323 (Cg_endo) REVERT: G 187 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7681 (tm-30) REVERT: G 250 GLU cc_start: 0.7838 (tp30) cc_final: 0.7600 (tt0) REVERT: G 285 ARG cc_start: 0.7583 (mpt90) cc_final: 0.7158 (mtp-110) REVERT: G 297 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.4776 (p90) REVERT: H 187 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7706 (tm-30) REVERT: H 242 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8097 (tttp) REVERT: I 53 ASN cc_start: 0.8419 (t0) cc_final: 0.8199 (t0) REVERT: I 187 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7647 (tm-30) REVERT: I 195 TRP cc_start: 0.9064 (m100) cc_final: 0.8730 (m100) REVERT: I 231 ASN cc_start: 0.8263 (t0) cc_final: 0.8014 (t0) REVERT: I 250 GLU cc_start: 0.7957 (tp30) cc_final: 0.7691 (tt0) REVERT: I 281 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: I 285 ARG cc_start: 0.7772 (mpt90) cc_final: 0.7285 (mtp-110) REVERT: J 53 ASN cc_start: 0.8439 (t0) cc_final: 0.8019 (t0) REVERT: J 61 MET cc_start: 0.7385 (tpp) cc_final: 0.6915 (tpp) REVERT: J 123 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: J 162 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7645 (t0) REVERT: J 173 PRO cc_start: 0.8914 (Cg_exo) cc_final: 0.8481 (Cg_endo) REVERT: J 187 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7825 (tm-30) REVERT: J 189 GLU cc_start: 0.8560 (tp30) cc_final: 0.7961 (tp30) REVERT: J 195 TRP cc_start: 0.9059 (m100) cc_final: 0.8424 (m100) REVERT: J 231 ASN cc_start: 0.8311 (t0) cc_final: 0.8034 (t0) REVERT: J 250 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: K 82 LEU cc_start: 0.8821 (tt) cc_final: 0.8607 (tt) REVERT: K 187 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7761 (tm-30) REVERT: L 187 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7701 (tm-30) REVERT: M 53 ASN cc_start: 0.8419 (t0) cc_final: 0.8208 (t0) REVERT: M 135 HIS cc_start: 0.7019 (t-90) cc_final: 0.6752 (t-90) REVERT: M 187 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7616 (tm-30) REVERT: M 195 TRP cc_start: 0.9068 (m100) cc_final: 0.8729 (m100) REVERT: M 231 ASN cc_start: 0.8246 (t0) cc_final: 0.8009 (t0) REVERT: M 250 GLU cc_start: 0.7913 (tp30) cc_final: 0.7608 (tt0) REVERT: M 280 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7187 (tt) REVERT: M 281 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: M 285 ARG cc_start: 0.7799 (mpt90) cc_final: 0.7313 (mtp-110) REVERT: N 53 ASN cc_start: 0.8320 (t0) cc_final: 0.7961 (t0) REVERT: N 61 MET cc_start: 0.7613 (tpp) cc_final: 0.7290 (tpp) REVERT: N 123 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: N 187 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7760 (tm-30) REVERT: N 189 GLU cc_start: 0.8506 (tp30) cc_final: 0.8240 (tp30) REVERT: N 231 ASN cc_start: 0.8278 (t0) cc_final: 0.8010 (t0) REVERT: N 250 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: O 187 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7690 (tm-30) REVERT: O 189 GLU cc_start: 0.8406 (tp30) cc_final: 0.7928 (tp30) REVERT: O 250 GLU cc_start: 0.7860 (tp30) cc_final: 0.7427 (mm-30) REVERT: O 281 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: P 162 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7583 (t0) REVERT: P 173 PRO cc_start: 0.8750 (Cg_exo) cc_final: 0.8302 (Cg_endo) REVERT: P 187 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7769 (tm-30) REVERT: P 285 ARG cc_start: 0.7588 (mpt90) cc_final: 0.7156 (mtp-110) REVERT: P 297 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.4614 (p90) REVERT: Q 187 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7715 (tm-30) REVERT: R 53 ASN cc_start: 0.8385 (t0) cc_final: 0.8159 (t0) REVERT: R 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7686 (tm-30) REVERT: R 195 TRP cc_start: 0.9021 (m100) cc_final: 0.8716 (m100) REVERT: R 231 ASN cc_start: 0.8258 (t0) cc_final: 0.8019 (t0) REVERT: R 250 GLU cc_start: 0.7843 (tp30) cc_final: 0.7572 (tt0) REVERT: R 281 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: R 285 ARG cc_start: 0.7771 (mpt90) cc_final: 0.7268 (mtp-110) REVERT: S 53 ASN cc_start: 0.8358 (t0) cc_final: 0.7947 (t0) REVERT: S 187 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7772 (tm-30) REVERT: S 189 GLU cc_start: 0.8486 (tp30) cc_final: 0.7908 (tp30) REVERT: S 195 TRP cc_start: 0.9053 (m100) cc_final: 0.8362 (m100) REVERT: S 231 ASN cc_start: 0.8302 (t0) cc_final: 0.8025 (t0) REVERT: S 250 GLU cc_start: 0.7817 (tt0) cc_final: 0.7595 (tt0) REVERT: T 187 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7684 (tm-30) REVERT: T 189 GLU cc_start: 0.8392 (tp30) cc_final: 0.7921 (tp30) REVERT: T 281 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7670 (m-80) outliers start: 329 outliers final: 263 residues processed: 718 average time/residue: 0.6106 time to fit residues: 731.4161 Evaluate side-chains 763 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 475 time to evaluate : 5.342 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 280 LEU 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 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 287 ILE 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 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 232 VAL 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 52 LEU 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 181 THR Chi-restraints excluded: chain D residue 193 TYR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 280 LEU 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 52 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 162 ASN 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 201 SER 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 297 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE 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 140 ILE Chi-restraints excluded: chain G residue 162 ASN 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 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 113 VAL 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 232 VAL 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 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 162 ASN 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 219 THR 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 82 LEU Chi-restraints excluded: chain J residue 113 VAL 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 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 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 140 ILE 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 287 ILE Chi-restraints excluded: chain K residue 296 MET 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 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 232 VAL 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 297 TYR 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 162 ASN 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 280 LEU 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 52 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 162 ASN 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 287 ILE 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 113 VAL Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 140 ILE 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 104 TRP 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 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 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 214 MET Chi-restraints excluded: chain Q residue 232 VAL 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 52 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 162 ASN 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 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 52 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 113 VAL 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 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 113 VAL 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 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 345 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 380 optimal weight: 40.0000 chunk 276 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 439 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 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 153 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45860 Z= 0.180 Angle : 0.609 10.528 62520 Z= 0.316 Chirality : 0.042 0.204 7060 Planarity : 0.005 0.043 7940 Dihedral : 6.091 59.023 6396 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.52 % Allowed : 18.01 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5820 helix: 1.17 (0.08), residues: 4160 sheet: None (None), residues: 0 loop : -3.33 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 195 HIS 0.004 0.001 HIS A 135 PHE 0.015 0.001 PHE A 44 TYR 0.013 0.001 TYR E 50 ARG 0.008 0.000 ARG B 254 *********************** 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 771 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 483 time to evaluate : 5.313 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: 0.8227 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 189 GLU cc_start: 0.8423 (tp30) cc_final: 0.7896 (tp30) REVERT: A 281 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 187 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 286 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8256 (tm) REVERT: B 297 TYR cc_start: 0.5434 (OUTLIER) cc_final: 0.4885 (p90) REVERT: C 187 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7635 (tm-30) REVERT: D 140 ILE cc_start: 0.4937 (OUTLIER) cc_final: 0.4692 (pp) REVERT: D 187 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 195 TRP cc_start: 0.9014 (m100) cc_final: 0.8690 (m100) REVERT: D 231 ASN cc_start: 0.8260 (t0) cc_final: 0.8021 (t0) REVERT: D 250 GLU cc_start: 0.7819 (tp30) cc_final: 0.7522 (tt0) REVERT: E 53 ASN cc_start: 0.8335 (t0) cc_final: 0.7991 (t0) REVERT: E 162 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7550 (t0) REVERT: E 173 PRO cc_start: 0.8893 (Cg_exo) cc_final: 0.8421 (Cg_endo) REVERT: E 187 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 189 GLU cc_start: 0.8487 (tp30) cc_final: 0.7929 (tp30) REVERT: E 195 TRP cc_start: 0.9027 (m100) cc_final: 0.8371 (m100) REVERT: E 231 ASN cc_start: 0.8190 (t0) cc_final: 0.7959 (t0) REVERT: E 250 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: F 187 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7632 (tm-30) REVERT: F 189 GLU cc_start: 0.8393 (tp30) cc_final: 0.8062 (tp30) REVERT: F 281 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: G 162 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7540 (t0) REVERT: G 173 PRO cc_start: 0.8755 (Cg_exo) cc_final: 0.8302 (Cg_endo) REVERT: G 187 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7668 (tm-30) REVERT: G 250 GLU cc_start: 0.7699 (tp30) cc_final: 0.7491 (tt0) REVERT: G 285 ARG cc_start: 0.7470 (mpt90) cc_final: 0.7100 (mtp-110) REVERT: G 296 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.5972 (mmm) REVERT: G 297 TYR cc_start: 0.5267 (OUTLIER) cc_final: 0.4809 (p90) REVERT: H 187 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7634 (tm-30) REVERT: H 242 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7898 (ttmm) REVERT: I 53 ASN cc_start: 0.8387 (t0) cc_final: 0.8171 (t0) REVERT: I 187 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7656 (tm-30) REVERT: I 195 TRP cc_start: 0.9038 (m100) cc_final: 0.8703 (m100) REVERT: I 231 ASN cc_start: 0.8266 (t0) cc_final: 0.8032 (t0) REVERT: I 250 GLU cc_start: 0.7892 (tp30) cc_final: 0.7608 (tt0) REVERT: I 281 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: I 285 ARG cc_start: 0.7792 (mpt90) cc_final: 0.7365 (mtp-110) REVERT: J 53 ASN cc_start: 0.8334 (t0) cc_final: 0.7964 (t0) REVERT: J 61 MET cc_start: 0.7280 (tpp) cc_final: 0.6834 (tpp) REVERT: J 123 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: J 162 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7682 (t0) REVERT: J 173 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8467 (Cg_endo) REVERT: J 187 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7791 (tm-30) REVERT: J 189 GLU cc_start: 0.8539 (tp30) cc_final: 0.7962 (tp30) REVERT: J 195 TRP cc_start: 0.8982 (m100) cc_final: 0.8378 (m100) REVERT: J 231 ASN cc_start: 0.8265 (t0) cc_final: 0.7997 (t0) REVERT: J 250 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: K 82 LEU cc_start: 0.8768 (tt) cc_final: 0.8540 (tt) REVERT: K 187 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7675 (tm-30) REVERT: L 187 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7657 (tm-30) REVERT: M 187 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7612 (tm-30) REVERT: M 195 TRP cc_start: 0.9042 (m100) cc_final: 0.8669 (m100) REVERT: M 231 ASN cc_start: 0.8266 (t0) cc_final: 0.8053 (t0) REVERT: M 250 GLU cc_start: 0.7885 (tp30) cc_final: 0.7585 (tt0) REVERT: M 281 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: M 285 ARG cc_start: 0.7703 (mpt90) cc_final: 0.7217 (mtp-110) REVERT: N 53 ASN cc_start: 0.8221 (t0) cc_final: 0.7918 (t0) REVERT: N 61 MET cc_start: 0.7464 (tpp) cc_final: 0.6956 (tpp) REVERT: N 123 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7059 (m-10) REVERT: N 187 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7730 (tm-30) REVERT: N 189 GLU cc_start: 0.8513 (tp30) cc_final: 0.7919 (tp30) REVERT: N 195 TRP cc_start: 0.9026 (m100) cc_final: 0.8374 (m100) REVERT: N 231 ASN cc_start: 0.8236 (t0) cc_final: 0.7998 (t0) REVERT: N 250 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: O 187 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7643 (tm-30) REVERT: O 189 GLU cc_start: 0.8363 (tp30) cc_final: 0.8000 (tp30) REVERT: O 250 GLU cc_start: 0.7771 (tp30) cc_final: 0.7336 (mm-30) REVERT: O 281 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: P 162 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7573 (t0) REVERT: P 173 PRO cc_start: 0.8744 (Cg_exo) cc_final: 0.8280 (Cg_endo) REVERT: P 187 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7689 (tm-30) REVERT: P 250 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7314 (mm-30) REVERT: P 285 ARG cc_start: 0.7534 (mpt90) cc_final: 0.7218 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7664 (tm-30) REVERT: R 187 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7679 (tm-30) REVERT: R 195 TRP cc_start: 0.9039 (m100) cc_final: 0.8741 (m100) REVERT: R 231 ASN cc_start: 0.8260 (t0) cc_final: 0.8019 (t0) REVERT: R 250 GLU cc_start: 0.7799 (tp30) cc_final: 0.7509 (tt0) REVERT: R 281 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: R 285 ARG cc_start: 0.7814 (mpt90) cc_final: 0.7411 (mtp-110) REVERT: S 53 ASN cc_start: 0.8264 (t0) cc_final: 0.7940 (t0) REVERT: S 187 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7741 (tm-30) REVERT: S 189 GLU cc_start: 0.8531 (tp30) cc_final: 0.7982 (tp30) REVERT: S 195 TRP cc_start: 0.8975 (m100) cc_final: 0.8308 (m100) REVERT: S 231 ASN cc_start: 0.8287 (t0) cc_final: 0.8013 (t0) REVERT: S 250 GLU cc_start: 0.7799 (tt0) cc_final: 0.7566 (tt0) REVERT: T 187 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7646 (tm-30) REVERT: T 189 GLU cc_start: 0.8347 (tp30) cc_final: 0.7993 (tp30) REVERT: T 281 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7601 (m-80) outliers start: 288 outliers final: 250 residues processed: 687 average time/residue: 0.5601 time to fit residues: 640.4754 Evaluate side-chains 725 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 454 time to evaluate : 5.441 ------------------------------------------------------------------------------- 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 124 LEU 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 219 THR 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 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 287 ILE 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 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 219 THR 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 52 LEU 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 181 THR Chi-restraints excluded: chain D residue 193 TYR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 233 GLU 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 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN 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 201 SER 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 F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE 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 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN 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 297 TYR 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 219 THR 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 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 162 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 193 TYR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 219 THR 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 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 113 VAL 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 181 THR Chi-restraints excluded: chain J residue 186 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 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 140 ILE 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 219 THR 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 58 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 214 MET Chi-restraints excluded: chain L residue 219 THR 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 297 TYR 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 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 181 THR 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 280 LEU 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 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 287 ILE 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 113 VAL Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE 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 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 140 ILE Chi-restraints excluded: chain P residue 162 ASN 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 219 THR 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 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 214 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 232 VAL 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 58 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 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 286 LEU 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 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 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 113 VAL 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 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 508 optimal weight: 10.0000 chunk 535 optimal weight: 0.5980 chunk 488 optimal weight: 1.9990 chunk 520 optimal weight: 0.1980 chunk 313 optimal weight: 2.9990 chunk 226 optimal weight: 0.3980 chunk 409 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 470 optimal weight: 2.9990 chunk 492 optimal weight: 1.9990 chunk 519 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 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** F 76 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN O 76 ASN ** O 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45860 Z= 0.163 Angle : 0.618 18.855 62520 Z= 0.315 Chirality : 0.042 0.204 7060 Planarity : 0.004 0.042 7940 Dihedral : 5.989 59.140 6394 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.29 % Allowed : 18.53 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 5820 helix: 1.23 (0.08), residues: 4220 sheet: None (None), residues: 0 loop : -3.31 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 195 HIS 0.004 0.001 HIS B 135 PHE 0.014 0.001 PHE S 123 TYR 0.015 0.001 TYR M 50 ARG 0.010 0.001 ARG B 254 *********************** 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 754 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 476 time to evaluate : 5.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 189 GLU cc_start: 0.8425 (tp30) cc_final: 0.7899 (tp30) REVERT: A 195 TRP cc_start: 0.9022 (m100) cc_final: 0.8582 (m100) REVERT: A 281 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: B 187 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 187 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7577 (tm-30) REVERT: D 187 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7693 (tm-30) REVERT: D 195 TRP cc_start: 0.8990 (m100) cc_final: 0.8714 (m100) REVERT: D 250 GLU cc_start: 0.7754 (tp30) cc_final: 0.7487 (tt0) REVERT: E 53 ASN cc_start: 0.8315 (t0) cc_final: 0.7991 (t0) REVERT: E 123 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6990 (m-10) REVERT: E 162 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7833 (t0) REVERT: E 187 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7771 (tm-30) REVERT: E 189 GLU cc_start: 0.8509 (tp30) cc_final: 0.7927 (tp30) REVERT: E 195 TRP cc_start: 0.8972 (m100) cc_final: 0.8327 (m100) REVERT: E 231 ASN cc_start: 0.8132 (t0) cc_final: 0.7919 (t0) REVERT: E 250 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: F 187 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7589 (tm-30) REVERT: F 189 GLU cc_start: 0.8334 (tp30) cc_final: 0.8018 (tp30) REVERT: F 195 TRP cc_start: 0.9058 (m100) cc_final: 0.8606 (m100) REVERT: F 281 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: G 162 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7523 (t0) REVERT: G 173 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.8214 (Cg_endo) REVERT: G 187 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7647 (tm-30) REVERT: G 285 ARG cc_start: 0.7513 (mpt90) cc_final: 0.7230 (mtp-110) REVERT: G 296 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6108 (mmm) REVERT: G 297 TYR cc_start: 0.5205 (OUTLIER) cc_final: 0.4760 (p90) REVERT: H 187 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7626 (tm-30) REVERT: H 242 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7893 (ttmm) REVERT: I 187 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7655 (tm-30) REVERT: I 195 TRP cc_start: 0.9022 (m100) cc_final: 0.8667 (m100) REVERT: I 250 GLU cc_start: 0.7861 (tp30) cc_final: 0.7618 (tt0) REVERT: I 281 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: I 285 ARG cc_start: 0.7783 (mpt90) cc_final: 0.7392 (mtp-110) REVERT: J 53 ASN cc_start: 0.8270 (t0) cc_final: 0.7930 (t0) REVERT: J 61 MET cc_start: 0.7219 (tpp) cc_final: 0.6871 (tpp) REVERT: J 123 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: J 162 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7646 (t0) REVERT: J 173 PRO cc_start: 0.8852 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: J 187 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7825 (tm-30) REVERT: J 189 GLU cc_start: 0.8501 (tp30) cc_final: 0.7932 (tp30) REVERT: J 195 TRP cc_start: 0.8968 (m100) cc_final: 0.8366 (m100) REVERT: J 231 ASN cc_start: 0.8220 (t0) cc_final: 0.7983 (t0) REVERT: J 250 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: K 82 LEU cc_start: 0.8756 (tt) cc_final: 0.8539 (tt) REVERT: K 187 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7612 (tm-30) REVERT: L 187 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7644 (tm-30) REVERT: M 52 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8058 (mp) REVERT: M 187 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7642 (tm-30) REVERT: M 195 TRP cc_start: 0.9019 (m100) cc_final: 0.8668 (m100) REVERT: M 231 ASN cc_start: 0.8233 (t0) cc_final: 0.8028 (t0) REVERT: M 250 GLU cc_start: 0.7855 (tp30) cc_final: 0.7512 (tt0) REVERT: M 281 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: M 285 ARG cc_start: 0.7659 (mpt90) cc_final: 0.7236 (mtp-110) REVERT: N 53 ASN cc_start: 0.8223 (t0) cc_final: 0.7932 (t0) REVERT: N 61 MET cc_start: 0.7335 (tpp) cc_final: 0.6902 (tpp) REVERT: N 123 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7098 (m-10) REVERT: N 187 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7716 (tm-30) REVERT: N 189 GLU cc_start: 0.8514 (tp30) cc_final: 0.7931 (tp30) REVERT: N 195 TRP cc_start: 0.9025 (m100) cc_final: 0.8394 (m100) REVERT: N 231 ASN cc_start: 0.8184 (t0) cc_final: 0.7942 (t0) REVERT: N 250 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: O 187 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7628 (tm-30) REVERT: O 189 GLU cc_start: 0.8380 (tp30) cc_final: 0.8054 (tp30) REVERT: O 195 TRP cc_start: 0.9058 (m100) cc_final: 0.8598 (m100) REVERT: O 250 GLU cc_start: 0.7723 (tp30) cc_final: 0.7276 (mm-30) REVERT: O 281 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: P 162 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7558 (t0) REVERT: P 173 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8225 (Cg_endo) REVERT: P 187 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7598 (tm-30) REVERT: P 250 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7155 (mm-30) REVERT: P 254 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.7986 (mmt180) REVERT: P 285 ARG cc_start: 0.7541 (mpt90) cc_final: 0.7269 (mtp-110) REVERT: Q 187 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7653 (tm-30) REVERT: R 187 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7650 (tm-30) REVERT: R 195 TRP cc_start: 0.9005 (m100) cc_final: 0.8751 (m100) REVERT: R 231 ASN cc_start: 0.8225 (t0) cc_final: 0.8024 (t0) REVERT: R 250 GLU cc_start: 0.7736 (tp30) cc_final: 0.7470 (tt0) REVERT: R 281 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: R 285 ARG cc_start: 0.7784 (mpt90) cc_final: 0.7372 (mtp-110) REVERT: S 53 ASN cc_start: 0.8250 (t0) cc_final: 0.7936 (t0) REVERT: S 187 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7643 (tm-30) REVERT: S 189 GLU cc_start: 0.8519 (tp30) cc_final: 0.7970 (tp30) REVERT: S 195 TRP cc_start: 0.8977 (m100) cc_final: 0.8336 (m100) REVERT: S 231 ASN cc_start: 0.8205 (t0) cc_final: 0.7968 (t0) REVERT: T 187 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7624 (tm-30) REVERT: T 189 GLU cc_start: 0.8368 (tp30) cc_final: 0.8069 (tp30) REVERT: T 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8598 (m100) REVERT: T 281 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7443 (m-80) outliers start: 278 outliers final: 235 residues processed: 671 average time/residue: 0.5556 time to fit residues: 629.3936 Evaluate side-chains 711 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 456 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 THR 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 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 296 MET 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 219 THR 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 162 ASN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 193 TYR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 233 GLU 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 82 LEU Chi-restraints excluded: chain E residue 113 VAL 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 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 SER 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 F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE 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 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN 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 219 THR Chi-restraints excluded: chain G residue 233 GLU 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 108 LEU 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 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 219 THR Chi-restraints excluded: chain H residue 232 VAL 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 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 162 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 193 TYR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 219 THR 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 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 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 162 ASN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 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 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain K residue 140 ILE 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 219 THR 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 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 219 THR 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 297 TYR Chi-restraints excluded: chain M residue 52 LEU 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 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 280 LEU 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 52 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 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 52 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 140 ILE 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 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 140 ILE Chi-restraints excluded: chain P residue 162 ASN 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 219 THR 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 302 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 214 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 232 VAL 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 58 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 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 286 LEU 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 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 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 297 TYR 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 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE 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 342 optimal weight: 1.9990 chunk 550 optimal weight: 0.7980 chunk 336 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 382 optimal weight: 8.9990 chunk 577 optimal weight: 3.9990 chunk 531 optimal weight: 0.0770 chunk 460 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 355 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 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 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 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 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 95 HIS ** 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 95 HIS ** 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 45860 Z= 0.228 Angle : 0.656 18.800 62520 Z= 0.334 Chirality : 0.043 0.271 7060 Planarity : 0.005 0.043 7940 Dihedral : 6.005 59.966 6394 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 6.18 % Allowed : 19.00 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), residues: 5820 helix: 1.24 (0.08), residues: 4200 sheet: None (None), residues: 0 loop : -3.23 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 195 HIS 0.005 0.002 HIS E 244 PHE 0.015 0.001 PHE S 123 TYR 0.027 0.001 TYR K 229 ARG 0.009 0.001 ARG B 254 ********************** 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 742 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 469 time to evaluate : 4.918 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: A 135 HIS cc_start: 0.6627 (t-90) cc_final: 0.6404 (t-90) REVERT: A 187 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 189 GLU cc_start: 0.8420 (tp30) cc_final: 0.7867 (tp30) REVERT: A 195 TRP cc_start: 0.9066 (m100) cc_final: 0.8591 (m100) REVERT: A 281 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: B 187 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 287 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.5958 (pt) REVERT: C 187 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 187 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 195 TRP cc_start: 0.9039 (m100) cc_final: 0.8673 (m100) REVERT: D 250 GLU cc_start: 0.7851 (tp30) cc_final: 0.7569 (tt0) REVERT: E 53 ASN cc_start: 0.8452 (t0) cc_final: 0.8132 (t0) REVERT: E 123 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: E 162 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7780 (t0) REVERT: E 169 LYS cc_start: 0.7207 (mttt) cc_final: 0.6956 (mmmt) REVERT: E 187 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 189 GLU cc_start: 0.8481 (tp30) cc_final: 0.7838 (tp30) REVERT: E 195 TRP cc_start: 0.8998 (m100) cc_final: 0.8361 (m100) REVERT: E 231 ASN cc_start: 0.8235 (t0) cc_final: 0.7986 (t0) REVERT: E 250 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: E 305 ASP cc_start: 0.7617 (t0) cc_final: 0.7278 (m-30) REVERT: F 169 LYS cc_start: 0.7171 (mttt) cc_final: 0.6969 (mmmt) REVERT: F 187 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7657 (tm-30) REVERT: F 189 GLU cc_start: 0.8383 (tp30) cc_final: 0.8012 (tp30) REVERT: F 195 TRP cc_start: 0.9099 (m100) cc_final: 0.8600 (m100) REVERT: F 281 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: G 82 LEU cc_start: 0.8858 (tt) cc_final: 0.8502 (tp) REVERT: G 162 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7870 (t0) REVERT: G 187 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7711 (tm-30) REVERT: G 285 ARG cc_start: 0.7620 (mpt90) cc_final: 0.7286 (mtp-110) REVERT: G 296 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6051 (mmm) REVERT: G 297 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.5019 (p90) REVERT: H 187 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7681 (tm-30) REVERT: H 242 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8095 (tttp) REVERT: I 187 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7702 (tm-30) REVERT: I 195 TRP cc_start: 0.9054 (m100) cc_final: 0.8684 (m100) REVERT: I 250 GLU cc_start: 0.7953 (tp30) cc_final: 0.7706 (tt0) REVERT: I 281 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: I 285 ARG cc_start: 0.7920 (mpt90) cc_final: 0.7581 (mtp-110) REVERT: J 53 ASN cc_start: 0.8354 (t0) cc_final: 0.8002 (t0) REVERT: J 61 MET cc_start: 0.7381 (tpp) cc_final: 0.6812 (tpp) REVERT: J 123 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: J 162 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7833 (t0) REVERT: J 169 LYS cc_start: 0.7318 (mttt) cc_final: 0.7077 (mmmt) REVERT: J 187 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7837 (tm-30) REVERT: J 189 GLU cc_start: 0.8534 (tp30) cc_final: 0.7930 (tp30) REVERT: J 195 TRP cc_start: 0.9000 (m100) cc_final: 0.8423 (m100) REVERT: J 231 ASN cc_start: 0.8285 (t0) cc_final: 0.8027 (t0) REVERT: J 250 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: K 82 LEU cc_start: 0.8771 (tt) cc_final: 0.8555 (tt) REVERT: K 187 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7716 (tm-30) REVERT: L 187 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7715 (tm-30) REVERT: M 187 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7666 (tm-30) REVERT: M 195 TRP cc_start: 0.9057 (m100) cc_final: 0.8680 (m100) REVERT: M 250 GLU cc_start: 0.7924 (tp30) cc_final: 0.7587 (tt0) REVERT: M 280 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7180 (tt) REVERT: M 281 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: M 285 ARG cc_start: 0.7853 (mpt90) cc_final: 0.7388 (mtp-110) REVERT: N 53 ASN cc_start: 0.8274 (t0) cc_final: 0.7972 (t0) REVERT: N 61 MET cc_start: 0.7428 (tpp) cc_final: 0.6837 (tpp) REVERT: N 123 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7021 (m-10) REVERT: N 187 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7799 (tm-30) REVERT: N 189 GLU cc_start: 0.8493 (tp30) cc_final: 0.7857 (tp30) REVERT: N 195 TRP cc_start: 0.9019 (m100) cc_final: 0.8394 (m100) REVERT: N 231 ASN cc_start: 0.8262 (t0) cc_final: 0.8012 (t0) REVERT: N 250 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: O 187 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7694 (tm-30) REVERT: O 189 GLU cc_start: 0.8384 (tp30) cc_final: 0.8007 (tp30) REVERT: O 195 TRP cc_start: 0.9065 (m100) cc_final: 0.8571 (m100) REVERT: O 281 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: P 162 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7857 (t0) REVERT: P 187 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7700 (tm-30) REVERT: P 250 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7277 (mm-30) REVERT: P 254 ARG cc_start: 0.8361 (mmt-90) cc_final: 0.8027 (mmt180) REVERT: P 285 ARG cc_start: 0.7634 (mpt90) cc_final: 0.7311 (mtp-110) REVERT: Q 148 ASN cc_start: 0.8954 (m110) cc_final: 0.8681 (p0) REVERT: Q 187 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7720 (tm-30) REVERT: R 187 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7704 (tm-30) REVERT: R 195 TRP cc_start: 0.9043 (m100) cc_final: 0.8697 (m100) REVERT: R 250 GLU cc_start: 0.7842 (tp30) cc_final: 0.7565 (tt0) REVERT: R 281 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: R 285 ARG cc_start: 0.7851 (mpt90) cc_final: 0.7573 (ttm110) REVERT: S 53 ASN cc_start: 0.8276 (t0) cc_final: 0.7959 (t0) REVERT: S 187 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7789 (tm-30) REVERT: S 189 GLU cc_start: 0.8515 (tp30) cc_final: 0.7903 (tp30) REVERT: S 195 TRP cc_start: 0.9009 (m100) cc_final: 0.8370 (m100) REVERT: S 231 ASN cc_start: 0.8309 (t0) cc_final: 0.8031 (t0) REVERT: S 250 GLU cc_start: 0.7865 (tt0) cc_final: 0.7652 (tt0) REVERT: T 187 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7679 (tm-30) REVERT: T 189 GLU cc_start: 0.8370 (tp30) cc_final: 0.8009 (tp30) REVERT: T 281 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7688 (m-80) outliers start: 273 outliers final: 242 residues processed: 664 average time/residue: 0.5601 time to fit residues: 623.7365 Evaluate side-chains 714 residues out of total 5160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 451 time to evaluate : 5.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL 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 219 THR 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 201 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 ILE 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 162 ASN 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 219 THR Chi-restraints excluded: chain D residue 233 GLU 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 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 113 VAL 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 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 SER 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 297 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE 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 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 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN 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 219 THR 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 296 MET Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 108 LEU 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 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 219 THR Chi-restraints excluded: chain H residue 232 VAL 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 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 162 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 193 TYR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 219 THR 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 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 302 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 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 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 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain K residue 140 ILE 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 219 THR 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 L residue 58 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 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 297 TYR 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 113 VAL Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN 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 280 LEU 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 52 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 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 52 LEU 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 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 207 LEU 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 140 ILE Chi-restraints excluded: chain P residue 162 ASN 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 219 THR 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 302 LEU Chi-restraints excluded: chain Q residue 58 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 214 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 232 VAL 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 58 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 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 286 LEU 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 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 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 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 123 PHE Chi-restraints excluded: chain T residue 140 ILE 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 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 365 optimal weight: 9.9990 chunk 490 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 chunk 67 optimal weight: 0.0370 chunk 127 optimal weight: 0.9980 chunk 460 optimal weight: 0.2980 chunk 192 optimal weight: 7.9990 chunk 473 optimal weight: 20.0000 chunk 58 optimal weight: 120.0000 chunk 84 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 L 53 ASN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.198939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.154965 restraints weight = 79493.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.159516 restraints weight = 43643.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161726 restraints weight = 30041.875| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 45860 Z= 0.155 Angle : 0.617 19.151 62520 Z= 0.311 Chirality : 0.042 0.245 7060 Planarity : 0.004 0.042 7940 Dihedral : 5.806 59.867 6394 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.57 % Allowed : 19.77 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 5820 helix: 1.31 (0.08), residues: 4240 sheet: None (None), residues: 0 loop : -3.07 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T 195 HIS 0.004 0.001 HIS P 135 PHE 0.014 0.001 PHE M 200 TYR 0.016 0.001 TYR A 170 ARG 0.010 0.001 ARG B 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11539.41 seconds wall clock time: 213 minutes 18.05 seconds (12798.05 seconds total)