Starting phenix.real_space_refine on Fri Mar 6 22:43:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lu5_63388/03_2026/9lu5_63388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lu5_63388/03_2026/9lu5_63388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lu5_63388/03_2026/9lu5_63388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lu5_63388/03_2026/9lu5_63388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lu5_63388/03_2026/9lu5_63388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lu5_63388/03_2026/9lu5_63388.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 156 5.16 5 C 22230 2.51 5 N 5742 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34464 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "I" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "G" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "T" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "S" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "X" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "V" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "U" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "O" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1251 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1251 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1251 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1251 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1251 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1251 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "A" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "B" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "D" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "F" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "H" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "J" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "K" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Chain: "L" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1990 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Time building chain proxies: 7.63, per 1000 atoms: 0.22 Number of scatterers: 34464 At special positions: 0 Unit cell: (180.88, 179.816, 122.36, 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 156 16.00 O 6336 8.00 N 5742 7.00 C 22230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.6 seconds 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 37 sheets defined 34.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.565A pdb=" N TYR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 removed outlier: 4.438A pdb=" N LEU C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 244 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 279 through 301 Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 30 through 48 removed outlier: 3.573A pdb=" N TYR I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 115 removed outlier: 4.396A pdb=" N LEU I 112 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 149 Processing helix chain 'I' and resid 244 through 264 Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 279 through 301 Processing helix chain 'G' and resid 8 through 21 Processing helix chain 'G' and resid 30 through 48 removed outlier: 3.597A pdb=" N TYR G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 116 removed outlier: 4.362A pdb=" N LEU G 112 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 244 through 264 Processing helix chain 'G' and resid 279 through 301 Processing helix chain 'T' and resid 7 through 18 Processing helix chain 'S' and resid 7 through 18 removed outlier: 3.506A pdb=" N GLU S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 18 removed outlier: 3.512A pdb=" N GLU X 18 " --> pdb=" O ALA X 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 18 Processing helix chain 'V' and resid 7 through 18 removed outlier: 3.528A pdb=" N GLU V 18 " --> pdb=" O ALA V 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 18 removed outlier: 3.507A pdb=" N GLU U 18 " --> pdb=" O ALA U 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 Processing helix chain 'O' and resid 38 through 54 Processing helix chain 'O' and resid 74 through 79 removed outlier: 3.784A pdb=" N ASN O 78 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS O 79 " --> pdb=" O ASP O 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 74 through 79' Processing helix chain 'O' and resid 119 through 127 Processing helix chain 'N' and resid 32 through 36 Processing helix chain 'N' and resid 38 through 54 Processing helix chain 'N' and resid 119 through 128 Processing helix chain 'M' and resid 32 through 36 Processing helix chain 'M' and resid 38 through 54 Processing helix chain 'M' and resid 74 through 79 removed outlier: 3.854A pdb=" N ASN M 78 " --> pdb=" O GLU M 74 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS M 79 " --> pdb=" O ASP M 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 74 through 79' Processing helix chain 'M' and resid 119 through 127 Processing helix chain 'R' and resid 32 through 36 Processing helix chain 'R' and resid 38 through 54 Processing helix chain 'R' and resid 74 through 79 removed outlier: 3.831A pdb=" N ASN R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS R 79 " --> pdb=" O ASP R 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 74 through 79' Processing helix chain 'R' and resid 119 through 127 Processing helix chain 'Q' and resid 32 through 36 Processing helix chain 'Q' and resid 38 through 54 Processing helix chain 'Q' and resid 74 through 79 removed outlier: 3.769A pdb=" N ASN Q 78 " --> pdb=" O GLU Q 74 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS Q 79 " --> pdb=" O ASP Q 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 74 through 79' Processing helix chain 'Q' and resid 119 through 127 Processing helix chain 'P' and resid 32 through 36 Processing helix chain 'P' and resid 38 through 54 Processing helix chain 'P' and resid 119 through 127 Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 30 through 48 removed outlier: 3.606A pdb=" N TYR E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 114 removed outlier: 4.393A pdb=" N LEU E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 244 through 264 Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 279 through 301 Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 30 through 48 removed outlier: 3.594A pdb=" N TYR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 removed outlier: 4.252A pdb=" N LEU A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 244 through 264 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 279 through 301 Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 30 through 48 removed outlier: 3.604A pdb=" N TYR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 removed outlier: 4.498A pdb=" N LEU B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 244 through 265 removed outlier: 3.853A pdb=" N ARG B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 301 removed outlier: 3.586A pdb=" N ILE B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 30 through 48 removed outlier: 3.587A pdb=" N TYR D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 removed outlier: 4.190A pdb=" N ALA D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 244 through 265 removed outlier: 3.829A pdb=" N ARG D 265 " --> pdb=" O GLN D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 301 removed outlier: 3.523A pdb=" N ILE D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 21 Processing helix chain 'F' and resid 30 through 48 removed outlier: 3.601A pdb=" N TYR F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 114 removed outlier: 4.490A pdb=" N LEU F 112 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'F' and resid 244 through 265 removed outlier: 3.863A pdb=" N ARG F 265 " --> pdb=" O GLN F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 301 removed outlier: 3.692A pdb=" N ILE F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 21 Processing helix chain 'H' and resid 30 through 48 removed outlier: 3.743A pdb=" N TYR H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 115 removed outlier: 4.289A pdb=" N ALA H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 148 Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 244 through 265 removed outlier: 3.828A pdb=" N ARG H 265 " --> pdb=" O GLN H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 301 removed outlier: 3.624A pdb=" N ILE H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 301 " --> pdb=" O LEU H 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 21 removed outlier: 3.538A pdb=" N ASP J 14 " --> pdb=" O LYS J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 48 removed outlier: 3.582A pdb=" N TYR J 48 " --> pdb=" O LEU J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 114 removed outlier: 4.080A pdb=" N LEU J 112 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 149 removed outlier: 4.038A pdb=" N TYR J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 265 removed outlier: 3.835A pdb=" N ARG J 265 " --> pdb=" O GLN J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 301 Processing helix chain 'K' and resid 8 through 21 Processing helix chain 'K' and resid 30 through 48 removed outlier: 3.622A pdb=" N TYR K 48 " --> pdb=" O LEU K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 115 removed outlier: 4.418A pdb=" N LEU K 112 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 149 Processing helix chain 'K' and resid 244 through 264 Processing helix chain 'K' and resid 265 through 267 No H-bonds generated for 'chain 'K' and resid 265 through 267' Processing helix chain 'K' and resid 279 through 301 Processing helix chain 'L' and resid 8 through 21 Processing helix chain 'L' and resid 30 through 48 removed outlier: 3.585A pdb=" N TYR L 48 " --> pdb=" O LEU L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 114 removed outlier: 4.355A pdb=" N LEU L 112 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 134 removed outlier: 4.460A pdb=" N PHE L 134 " --> pdb=" O PRO L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 131 through 134' Processing helix chain 'L' and resid 137 through 149 removed outlier: 3.623A pdb=" N PHE L 141 " --> pdb=" O ASP L 137 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 265 removed outlier: 3.833A pdb=" N ARG L 265 " --> pdb=" O GLN L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 301 removed outlier: 3.638A pdb=" N ILE L 283 " --> pdb=" O GLY L 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.635A pdb=" N ARG C 86 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU C 185 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.530A pdb=" N GLN C 169 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 81 through 88 removed outlier: 5.694A pdb=" N VAL I 84 " --> pdb=" O TRP I 187 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TRP I 187 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG I 86 " --> pdb=" O GLU I 185 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU I 185 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 73 through 75 removed outlier: 3.519A pdb=" N GLN I 169 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 81 through 88 removed outlier: 5.857A pdb=" N VAL G 84 " --> pdb=" O TRP G 187 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TRP G 187 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG G 86 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU G 185 " --> pdb=" O ARG G 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA7, first strand: chain 'T' and resid 22 through 26 removed outlier: 7.179A pdb=" N LEU T 45 " --> pdb=" O GLU T 37 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE T 39 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL T 43 " --> pdb=" O PHE T 39 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER T 51 " --> pdb=" O PRO U 64 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER U 60 " --> pdb=" O TYR T 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR U 25 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL U 62 " --> pdb=" O SER U 23 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER U 23 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU U 45 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE U 39 " --> pdb=" O VAL U 43 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL U 43 " --> pdb=" O PHE U 39 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER U 51 " --> pdb=" O PRO V 64 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER V 60 " --> pdb=" O TYR U 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR V 25 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL V 62 " --> pdb=" O SER V 23 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER V 23 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU V 45 " --> pdb=" O GLU V 37 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE V 39 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL V 43 " --> pdb=" O PHE V 39 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER V 51 " --> pdb=" O PRO W 64 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER W 60 " --> pdb=" O TYR V 55 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR W 25 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL W 62 " --> pdb=" O SER W 23 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER W 23 " --> pdb=" O VAL W 62 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU W 45 " --> pdb=" O GLU W 37 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE W 39 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL W 43 " --> pdb=" O PHE W 39 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER W 51 " --> pdb=" O PRO X 64 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER X 60 " --> pdb=" O TYR W 55 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR X 25 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL X 62 " --> pdb=" O SER X 23 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER X 23 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU X 45 " --> pdb=" O GLU X 37 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE X 39 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL X 43 " --> pdb=" O PHE X 39 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER X 51 " --> pdb=" O PRO S 64 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER S 60 " --> pdb=" O TYR X 55 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR S 25 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL S 62 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER S 23 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU S 45 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE S 39 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL S 43 " --> pdb=" O PHE S 39 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER S 51 " --> pdb=" O PRO T 64 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER T 60 " --> pdb=" O TYR S 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR T 25 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL T 62 " --> pdb=" O SER T 23 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER T 23 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 84 through 88 removed outlier: 3.654A pdb=" N SER O 145 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR O 170 " --> pdb=" O ASN O 150 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL O 152 " --> pdb=" O LYS O 168 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LYS O 168 " --> pdb=" O VAL O 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 84 through 88 removed outlier: 3.661A pdb=" N SER N 145 " --> pdb=" O PHE N 140 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR N 170 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL N 152 " --> pdb=" O LYS N 168 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS N 168 " --> pdb=" O VAL N 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 84 through 88 removed outlier: 3.639A pdb=" N SER M 145 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR M 170 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL M 152 " --> pdb=" O LYS M 168 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LYS M 168 " --> pdb=" O VAL M 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 84 through 88 removed outlier: 3.656A pdb=" N SER R 145 " --> pdb=" O PHE R 140 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR R 170 " --> pdb=" O ASN R 150 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL R 152 " --> pdb=" O LYS R 168 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS R 168 " --> pdb=" O VAL R 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 84 through 88 removed outlier: 3.637A pdb=" N SER Q 145 " --> pdb=" O PHE Q 140 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR Q 170 " --> pdb=" O ASN Q 150 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL Q 152 " --> pdb=" O LYS Q 168 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS Q 168 " --> pdb=" O VAL Q 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 84 through 88 removed outlier: 3.594A pdb=" N SER P 145 " --> pdb=" O PHE P 140 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR P 170 " --> pdb=" O ASN P 150 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL P 152 " --> pdb=" O LYS P 168 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS P 168 " --> pdb=" O VAL P 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE P 118 " --> pdb=" O ARG P 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 88 removed outlier: 5.766A pdb=" N VAL E 84 " --> pdb=" O TRP E 187 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP E 187 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG E 86 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU E 185 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 73 through 75 removed outlier: 3.548A pdb=" N GLN E 169 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.049A pdb=" N ARG A 86 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 185 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 88 removed outlier: 4.171A pdb=" N GLU B 185 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE B 87 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 183 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.554A pdb=" N GLN B 169 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.503A pdb=" N VAL B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 85 through 88 removed outlier: 5.056A pdb=" N ARG D 86 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU D 185 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 73 through 75 removed outlier: 3.538A pdb=" N GLN D 169 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 270 through 271 removed outlier: 3.587A pdb=" N VAL D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 85 through 88 removed outlier: 4.626A pdb=" N ARG F 86 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU F 185 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 73 through 75 removed outlier: 3.561A pdb=" N GLN F 169 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 270 through 271 Processing sheet with id=AC9, first strand: chain 'H' and resid 123 through 129 removed outlier: 3.721A pdb=" N GLU H 185 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG H 86 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP H 187 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL H 84 " --> pdb=" O TRP H 187 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LYS H 189 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE H 82 " --> pdb=" O LYS H 189 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE H 87 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD2, first strand: chain 'H' and resid 270 through 271 removed outlier: 3.507A pdb=" N VAL H 275 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 81 through 88 removed outlier: 7.292A pdb=" N GLU J 185 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE J 87 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE J 183 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 73 through 75 Processing sheet with id=AD5, first strand: chain 'J' and resid 270 through 271 removed outlier: 3.578A pdb=" N VAL J 275 " --> pdb=" O LEU J 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 81 through 88 removed outlier: 5.987A pdb=" N VAL K 84 " --> pdb=" O TRP K 187 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP K 187 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG K 86 " --> pdb=" O GLU K 185 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU K 185 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 73 through 75 removed outlier: 3.530A pdb=" N GLN K 169 " --> pdb=" O ASN K 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 81 through 88 removed outlier: 5.880A pdb=" N VAL L 84 " --> pdb=" O TRP L 187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TRP L 187 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG L 86 " --> pdb=" O GLU L 185 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU L 185 " --> pdb=" O ARG L 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 73 through 75 removed outlier: 3.523A pdb=" N GLN L 169 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 270 through 271 removed outlier: 3.536A pdb=" N VAL L 275 " --> pdb=" O LEU L 271 " (cutoff:3.500A) 1425 hydrogen bonds defined for protein. 4038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 3.72 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: 11160 1.34 - 1.46: 6159 1.46 - 1.57: 17673 1.57 - 1.69: 0 1.69 - 1.81: 282 Bond restraints: 35274 Sorted by residual: bond pdb=" CA SER N 67 " pdb=" C SER N 67 " ideal model delta sigma weight residual 1.525 1.491 0.034 1.14e-02 7.69e+03 9.14e+00 bond pdb=" CA ALA L 136 " pdb=" C ALA L 136 " ideal model delta sigma weight residual 1.522 1.484 0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" CA SER P 67 " pdb=" C SER P 67 " ideal model delta sigma weight residual 1.528 1.501 0.027 1.18e-02 7.18e+03 5.10e+00 bond pdb=" CA ASP N 69 " pdb=" C ASP N 69 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.20e-02 6.94e+03 4.49e+00 bond pdb=" CA ASP P 69 " pdb=" C ASP P 69 " ideal model delta sigma weight residual 1.521 1.498 0.024 1.19e-02 7.06e+03 3.97e+00 ... (remaining 35269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 47492 2.75 - 5.49: 186 5.49 - 8.24: 14 8.24 - 10.99: 1 10.99 - 13.74: 1 Bond angle restraints: 47694 Sorted by residual: angle pdb=" N ALA L 136 " pdb=" CA ALA L 136 " pdb=" C ALA L 136 " ideal model delta sigma weight residual 114.09 100.35 13.74 1.55e+00 4.16e-01 7.85e+01 angle pdb=" N PHE L 134 " pdb=" CA PHE L 134 " pdb=" C PHE L 134 " ideal model delta sigma weight residual 112.34 118.56 -6.22 1.30e+00 5.92e-01 2.29e+01 angle pdb=" N PHE P 72 " pdb=" CA PHE P 72 " pdb=" C PHE P 72 " ideal model delta sigma weight residual 113.02 118.06 -5.04 1.20e+00 6.94e-01 1.77e+01 angle pdb=" CA ALA L 136 " pdb=" C ALA L 136 " pdb=" N ASP L 137 " ideal model delta sigma weight residual 119.07 114.39 4.68 1.23e+00 6.61e-01 1.45e+01 angle pdb=" N ASP L 137 " pdb=" CA ASP L 137 " pdb=" C ASP L 137 " ideal model delta sigma weight residual 113.02 109.31 3.71 1.20e+00 6.94e-01 9.55e+00 ... (remaining 47689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 19799 16.74 - 33.48: 861 33.48 - 50.22: 123 50.22 - 66.96: 13 66.96 - 83.70: 6 Dihedral angle restraints: 20802 sinusoidal: 8514 harmonic: 12288 Sorted by residual: dihedral pdb=" CA ALA L 133 " pdb=" C ALA L 133 " pdb=" N PHE L 134 " pdb=" CA PHE L 134 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU P 70 " pdb=" C LEU P 70 " pdb=" N ILE P 71 " pdb=" CA ILE P 71 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" C PHE P 72 " pdb=" N PHE P 72 " pdb=" CA PHE P 72 " pdb=" CB PHE P 72 " ideal model delta harmonic sigma weight residual -122.60 -131.02 8.42 0 2.50e+00 1.60e-01 1.13e+01 ... (remaining 20799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4591 0.073 - 0.147: 450 0.147 - 0.220: 4 0.220 - 0.294: 0 0.294 - 0.367: 1 Chirality restraints: 5046 Sorted by residual: chirality pdb=" CA PHE P 72 " pdb=" N PHE P 72 " pdb=" C PHE P 72 " pdb=" CB PHE P 72 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ALA L 136 " pdb=" N ALA L 136 " pdb=" C ALA L 136 " pdb=" CB ALA L 136 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA LEU N 70 " pdb=" N LEU N 70 " pdb=" C LEU N 70 " pdb=" CB LEU N 70 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 5043 not shown) Planarity restraints: 6204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 66 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C VAL N 66 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL N 66 " -0.015 2.00e-02 2.50e+03 pdb=" N SER N 67 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 66 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL P 66 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL P 66 " 0.013 2.00e-02 2.50e+03 pdb=" N SER P 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP I 301 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO I 302 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO I 302 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 302 " -0.026 5.00e-02 4.00e+02 ... (remaining 6201 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2495 2.74 - 3.28: 34329 3.28 - 3.82: 56325 3.82 - 4.36: 66864 4.36 - 4.90: 116004 Nonbonded interactions: 276017 Sorted by model distance: nonbonded pdb=" O ALA G 83 " pdb=" OG SER G 186 " model vdw 2.201 3.040 nonbonded pdb=" O ALA A 83 " pdb=" OG SER A 186 " model vdw 2.213 3.040 nonbonded pdb=" O ALA D 83 " pdb=" OG SER D 186 " model vdw 2.216 3.040 nonbonded pdb=" O ALA K 83 " pdb=" OG SER K 186 " model vdw 2.287 3.040 nonbonded pdb=" O ALA I 83 " pdb=" OG SER I 186 " model vdw 2.290 3.040 ... (remaining 276012 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: 0.01 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' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.860 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.002 0.046 35274 Z= 0.103 Angle : 0.451 13.736 47694 Z= 0.249 Chirality : 0.040 0.367 5046 Planarity : 0.003 0.048 6204 Dihedral : 9.023 83.700 12978 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 2.63 % Allowed : 7.66 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 4164 helix: 1.31 (0.13), residues: 1326 sheet: -1.56 (0.16), residues: 990 loop : -3.12 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 68 TYR 0.008 0.001 TYR O 159 PHE 0.006 0.001 PHE S 11 TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00185 (35274) covalent geometry : angle 0.45060 (47694) hydrogen bonds : bond 0.17943 ( 1425) hydrogen bonds : angle 6.16949 ( 4038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 943 time to evaluate : 1.189 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: C 5 ASN cc_start: 0.6921 (t0) cc_final: 0.6647 (t0) REVERT: C 8 ASN cc_start: 0.7491 (p0) cc_final: 0.7121 (p0) REVERT: C 11 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7093 (mt-10) REVERT: C 43 GLU cc_start: 0.7149 (tp30) cc_final: 0.6794 (tp30) REVERT: C 54 ASN cc_start: 0.7387 (m110) cc_final: 0.6941 (m-40) REVERT: C 62 VAL cc_start: 0.3712 (OUTLIER) cc_final: 0.3450 (t) REVERT: C 150 MET cc_start: 0.5856 (ptp) cc_final: 0.5514 (ptp) REVERT: I 11 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7030 (mt-10) REVERT: I 43 GLU cc_start: 0.7132 (tp30) cc_final: 0.6771 (tp30) REVERT: I 54 ASN cc_start: 0.7456 (m110) cc_final: 0.7082 (m110) REVERT: I 62 VAL cc_start: 0.3020 (OUTLIER) cc_final: 0.2790 (t) REVERT: I 121 MET cc_start: 0.4963 (tpt) cc_final: 0.4523 (tpt) REVERT: I 150 MET cc_start: 0.6695 (ptp) cc_final: 0.6441 (ptp) REVERT: I 164 ASN cc_start: 0.8278 (t0) cc_final: 0.8071 (t0) REVERT: I 167 ASN cc_start: 0.7171 (t0) cc_final: 0.6882 (t0) REVERT: I 187 TRP cc_start: 0.7373 (m100) cc_final: 0.6988 (m100) REVERT: G 8 ASN cc_start: 0.7597 (p0) cc_final: 0.7233 (OUTLIER) REVERT: G 11 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7151 (mt-10) REVERT: G 43 GLU cc_start: 0.7130 (tp30) cc_final: 0.6819 (tp30) REVERT: G 62 VAL cc_start: 0.3861 (OUTLIER) cc_final: 0.3660 (t) REVERT: G 148 MET cc_start: 0.6661 (tmm) cc_final: 0.6459 (tmm) REVERT: G 150 MET cc_start: 0.6231 (ptp) cc_final: 0.5933 (ptp) REVERT: G 185 GLU cc_start: 0.6857 (pp20) cc_final: 0.6413 (pp20) REVERT: G 257 GLU cc_start: 0.7220 (tp30) cc_final: 0.6817 (tp30) REVERT: G 283 ILE cc_start: 0.8059 (mt) cc_final: 0.7773 (mt) REVERT: T 7 LEU cc_start: 0.8497 (mt) cc_final: 0.8184 (mp) REVERT: S 38 SER cc_start: 0.8066 (t) cc_final: 0.7845 (t) REVERT: X 38 SER cc_start: 0.8135 (t) cc_final: 0.7931 (t) REVERT: W 7 LEU cc_start: 0.8482 (mt) cc_final: 0.8146 (mp) REVERT: V 38 SER cc_start: 0.8288 (t) cc_final: 0.8011 (t) REVERT: U 38 SER cc_start: 0.7984 (t) cc_final: 0.7728 (t) REVERT: N 127 VAL cc_start: 0.8646 (m) cc_final: 0.8225 (t) REVERT: M 27 LEU cc_start: 0.8004 (mp) cc_final: 0.7444 (mt) REVERT: R 84 TRP cc_start: 0.8425 (m-90) cc_final: 0.7739 (m-90) REVERT: R 139 TYR cc_start: 0.8179 (t80) cc_final: 0.7964 (t80) REVERT: R 170 THR cc_start: 0.8082 (p) cc_final: 0.7747 (m) REVERT: Q 60 TYR cc_start: 0.8426 (t80) cc_final: 0.8226 (t80) REVERT: Q 136 ASP cc_start: 0.7564 (m-30) cc_final: 0.7284 (m-30) REVERT: P 34 ASN cc_start: 0.8411 (m110) cc_final: 0.8179 (m-40) REVERT: E 43 GLU cc_start: 0.7139 (tp30) cc_final: 0.6816 (tp30) REVERT: E 62 VAL cc_start: 0.4428 (OUTLIER) cc_final: 0.4215 (t) REVERT: E 150 MET cc_start: 0.5873 (ptp) cc_final: 0.5570 (ptp) REVERT: E 187 TRP cc_start: 0.7304 (m100) cc_final: 0.7090 (m100) REVERT: E 188 THR cc_start: 0.7945 (p) cc_final: 0.7699 (p) REVERT: E 257 GLU cc_start: 0.7204 (tp30) cc_final: 0.6744 (tp30) REVERT: A 43 GLU cc_start: 0.7073 (tp30) cc_final: 0.6722 (tp30) REVERT: A 54 ASN cc_start: 0.7513 (m110) cc_final: 0.7267 (m110) REVERT: A 140 TYR cc_start: 0.6814 (m-10) cc_final: 0.6382 (m-80) REVERT: A 148 MET cc_start: 0.6666 (tmm) cc_final: 0.6444 (tmm) REVERT: A 187 TRP cc_start: 0.7245 (m100) cc_final: 0.6979 (m100) REVERT: A 261 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7837 (mm110) REVERT: B 39 GLN cc_start: 0.7971 (mm110) cc_final: 0.7749 (mp10) REVERT: B 43 GLU cc_start: 0.7176 (tp30) cc_final: 0.6772 (tp30) REVERT: B 45 TYR cc_start: 0.8289 (t80) cc_final: 0.7849 (t80) REVERT: B 47 GLU cc_start: 0.7104 (tt0) cc_final: 0.6808 (tt0) REVERT: B 54 ASN cc_start: 0.7192 (m110) cc_final: 0.6726 (m110) REVERT: B 141 PHE cc_start: 0.7246 (t80) cc_final: 0.6974 (t80) REVERT: B 151 MET cc_start: 0.5868 (tmm) cc_final: 0.5382 (tmt) REVERT: B 167 ASN cc_start: 0.7374 (t0) cc_final: 0.6787 (t0) REVERT: B 188 THR cc_start: 0.7663 (p) cc_final: 0.7449 (p) REVERT: D 8 ASN cc_start: 0.7960 (p0) cc_final: 0.7680 (p0) REVERT: D 11 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7145 (mt-10) REVERT: D 36 ASP cc_start: 0.6852 (m-30) cc_final: 0.6368 (m-30) REVERT: D 62 VAL cc_start: 0.4738 (OUTLIER) cc_final: 0.4446 (t) REVERT: D 82 PHE cc_start: 0.8010 (t80) cc_final: 0.7796 (t80) REVERT: D 128 PHE cc_start: 0.8024 (m-80) cc_final: 0.7819 (m-80) REVERT: D 151 MET cc_start: 0.6301 (tmm) cc_final: 0.5662 (tmt) REVERT: D 187 TRP cc_start: 0.7302 (m100) cc_final: 0.7071 (m100) REVERT: D 249 ASP cc_start: 0.7574 (m-30) cc_final: 0.7337 (m-30) REVERT: D 250 TYR cc_start: 0.8515 (t80) cc_final: 0.8307 (t80) REVERT: D 257 GLU cc_start: 0.7128 (tp30) cc_final: 0.6778 (tp30) REVERT: D 283 ILE cc_start: 0.8091 (mt) cc_final: 0.7623 (mt) REVERT: F 43 GLU cc_start: 0.7156 (tp30) cc_final: 0.6739 (tp30) REVERT: F 54 ASN cc_start: 0.6853 (m110) cc_final: 0.6461 (m110) REVERT: F 127 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6976 (ptm-80) REVERT: F 150 MET cc_start: 0.3873 (ptp) cc_final: 0.3598 (ptp) REVERT: F 151 MET cc_start: 0.5546 (tmm) cc_final: 0.4987 (tmm) REVERT: F 167 ASN cc_start: 0.7582 (t0) cc_final: 0.7167 (t0) REVERT: F 244 ASN cc_start: 0.7689 (t0) cc_final: 0.7400 (t0) REVERT: F 259 ASN cc_start: 0.8367 (t0) cc_final: 0.8148 (t160) REVERT: F 295 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6655 (mm-30) REVERT: H 43 GLU cc_start: 0.7090 (tp30) cc_final: 0.6756 (tp30) REVERT: H 154 MET cc_start: 0.7226 (mtt) cc_final: 0.6953 (mtt) REVERT: H 257 GLU cc_start: 0.7123 (tp30) cc_final: 0.6674 (tp30) REVERT: J 8 ASN cc_start: 0.7365 (p0) cc_final: 0.7024 (p0) REVERT: J 11 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7047 (mt-10) REVERT: J 28 GLU cc_start: 0.6115 (mp0) cc_final: 0.5391 (mp0) REVERT: J 62 VAL cc_start: 0.4956 (OUTLIER) cc_final: 0.4718 (t) REVERT: J 73 VAL cc_start: 0.7307 (p) cc_final: 0.7026 (t) REVERT: J 128 PHE cc_start: 0.7156 (m-80) cc_final: 0.6818 (m-80) REVERT: J 151 MET cc_start: 0.5837 (tmm) cc_final: 0.5256 (tmt) REVERT: J 167 ASN cc_start: 0.6826 (t0) cc_final: 0.6329 (t0) REVERT: J 185 GLU cc_start: 0.7391 (pp20) cc_final: 0.7140 (pp20) REVERT: J 244 ASN cc_start: 0.7948 (t0) cc_final: 0.7746 (t0) REVERT: J 257 GLU cc_start: 0.7191 (tp30) cc_final: 0.6848 (tp30) REVERT: J 283 ILE cc_start: 0.8158 (mt) cc_final: 0.7789 (mt) REVERT: K 36 ASP cc_start: 0.7116 (m-30) cc_final: 0.6872 (m-30) REVERT: K 43 GLU cc_start: 0.7087 (tp30) cc_final: 0.6786 (tp30) REVERT: K 54 ASN cc_start: 0.7329 (m110) cc_final: 0.7001 (m110) REVERT: K 150 MET cc_start: 0.6740 (ptp) cc_final: 0.6511 (ptp) REVERT: K 187 TRP cc_start: 0.7107 (m100) cc_final: 0.6860 (m100) REVERT: L 43 GLU cc_start: 0.7099 (tp30) cc_final: 0.6681 (tp30) REVERT: L 53 LEU cc_start: 0.8518 (mp) cc_final: 0.8273 (mt) REVERT: L 54 ASN cc_start: 0.7201 (m110) cc_final: 0.6717 (m-40) REVERT: L 151 MET cc_start: 0.5816 (tmm) cc_final: 0.5192 (tmt) REVERT: L 167 ASN cc_start: 0.7145 (t0) cc_final: 0.6784 (t0) REVERT: L 168 GLU cc_start: 0.6880 (mp0) cc_final: 0.6470 (mp0) REVERT: L 242 TYR cc_start: 0.7931 (m-80) cc_final: 0.6849 (m-80) REVERT: L 259 ASN cc_start: 0.8444 (t0) cc_final: 0.8222 (t160) REVERT: L 295 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6509 (mm-30) outliers start: 96 outliers final: 38 residues processed: 1019 average time/residue: 0.6357 time to fit residues: 783.3808 Evaluate side-chains 914 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 870 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 49 HIS C 143 GLN C 164 ASN C 239 GLN C 243 ASN ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN I 39 GLN I 267 GLN G 39 GLN ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 GLN G 243 ASN G 261 GLN G 267 GLN T 5 GLN T 8 GLN T 33 GLN T 35 GLN S 5 GLN S 8 GLN S 35 GLN X 5 GLN X 35 GLN W 5 GLN W 33 GLN W 35 GLN V 5 GLN V 8 GLN V 35 GLN U 5 GLN U 35 GLN O 28 ASN O 40 GLN O 119 ASN ** O 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN M 126 GLN R 28 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN Q 126 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN E 7 GLN E 26 ASN ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 243 ASN E 244 ASN E 266 HIS E 267 GLN A 167 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN A 267 GLN B 39 GLN B 143 GLN B 164 ASN B 239 GLN B 244 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN D 8 ASN D 164 ASN D 167 ASN D 239 GLN D 243 ASN D 244 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN F 8 ASN F 39 GLN F 49 HIS F 164 ASN F 239 GLN F 243 ASN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN H 39 GLN H 244 ASN H 259 ASN ** H 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN J 8 ASN J 39 GLN J 49 HIS J 80 ASN J 164 ASN J 239 GLN J 243 ASN J 259 ASN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN K 26 ASN K 239 GLN K 244 ASN K 267 GLN L 7 GLN L 39 GLN L 49 HIS L 126 ASN L 239 GLN ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.183070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146593 restraints weight = 45883.229| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.47 r_work: 0.3658 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35274 Z= 0.180 Angle : 0.572 11.905 47694 Z= 0.284 Chirality : 0.044 0.188 5046 Planarity : 0.004 0.046 6204 Dihedral : 4.619 79.585 4742 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.73 % Allowed : 12.40 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4164 helix: 2.17 (0.14), residues: 1374 sheet: -1.25 (0.16), residues: 1002 loop : -2.67 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 287 TYR 0.011 0.001 TYR F 4 PHE 0.023 0.001 PHE H 141 TRP 0.011 0.001 TRP K 187 HIS 0.008 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00441 (35274) covalent geometry : angle 0.57233 (47694) hydrogen bonds : bond 0.04242 ( 1425) hydrogen bonds : angle 4.29384 ( 4038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 923 time to evaluate : 1.306 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: C 5 ASN cc_start: 0.7057 (t0) cc_final: 0.6821 (t0) REVERT: C 19 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8307 (mtp180) REVERT: C 36 ASP cc_start: 0.7620 (m-30) cc_final: 0.7370 (m-30) REVERT: C 43 GLU cc_start: 0.7848 (tp30) cc_final: 0.7489 (tp30) REVERT: C 49 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6509 (m-70) REVERT: C 62 VAL cc_start: 0.4785 (OUTLIER) cc_final: 0.4523 (t) REVERT: C 150 MET cc_start: 0.5684 (ptp) cc_final: 0.5452 (ptp) REVERT: I 43 GLU cc_start: 0.7858 (tp30) cc_final: 0.7458 (tp30) REVERT: I 62 VAL cc_start: 0.4309 (OUTLIER) cc_final: 0.4075 (t) REVERT: I 121 MET cc_start: 0.4869 (tpt) cc_final: 0.4593 (tpt) REVERT: I 265 ARG cc_start: 0.8357 (ttm170) cc_final: 0.8016 (mtt180) REVERT: G 40 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8153 (mtp180) REVERT: G 43 GLU cc_start: 0.7961 (tp30) cc_final: 0.7625 (tp30) REVERT: G 62 VAL cc_start: 0.4250 (OUTLIER) cc_final: 0.4043 (t) REVERT: G 148 MET cc_start: 0.6801 (tmm) cc_final: 0.6569 (tmm) REVERT: G 243 ASN cc_start: 0.7774 (t0) cc_final: 0.7504 (t0) REVERT: G 257 GLU cc_start: 0.7619 (tp30) cc_final: 0.7304 (tp30) REVERT: X 49 THR cc_start: 0.8222 (t) cc_final: 0.7901 (p) REVERT: X 66 ARG cc_start: 0.8619 (ptt90) cc_final: 0.8409 (ptt180) REVERT: V 38 SER cc_start: 0.8594 (t) cc_final: 0.8388 (t) REVERT: U 38 SER cc_start: 0.8535 (t) cc_final: 0.8331 (t) REVERT: U 49 THR cc_start: 0.8249 (t) cc_final: 0.7953 (p) REVERT: O 54 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7297 (mmp80) REVERT: O 136 ASP cc_start: 0.8004 (m-30) cc_final: 0.7785 (m-30) REVERT: N 28 ASN cc_start: 0.8431 (t0) cc_final: 0.8180 (t0) REVERT: N 44 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: N 50 SER cc_start: 0.8681 (t) cc_final: 0.8441 (p) REVERT: N 147 PHE cc_start: 0.8332 (m-80) cc_final: 0.7972 (m-80) REVERT: M 127 VAL cc_start: 0.8623 (m) cc_final: 0.8419 (t) REVERT: R 37 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7595 (pptt) REVERT: R 54 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: Q 54 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8224 (mpt180) REVERT: E 43 GLU cc_start: 0.8038 (tp30) cc_final: 0.7699 (tp30) REVERT: E 62 VAL cc_start: 0.5158 (OUTLIER) cc_final: 0.4949 (t) REVERT: E 257 GLU cc_start: 0.7721 (tp30) cc_final: 0.7373 (tp30) REVERT: A 43 GLU cc_start: 0.7935 (tp30) cc_final: 0.7558 (tp30) REVERT: B 11 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7545 (mt-10) REVERT: B 19 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8229 (mtp85) REVERT: B 43 GLU cc_start: 0.7981 (tp30) cc_final: 0.7601 (tp30) REVERT: B 45 TYR cc_start: 0.8587 (t80) cc_final: 0.8234 (t80) REVERT: B 47 GLU cc_start: 0.7745 (tt0) cc_final: 0.7471 (tt0) REVERT: B 151 MET cc_start: 0.6568 (tmm) cc_final: 0.6301 (tmt) REVERT: B 167 ASN cc_start: 0.7733 (t0) cc_final: 0.7349 (t0) REVERT: D 8 ASN cc_start: 0.8120 (p0) cc_final: 0.7800 (OUTLIER) REVERT: D 11 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7691 (mt-10) REVERT: D 36 ASP cc_start: 0.7254 (m-30) cc_final: 0.7013 (m-30) REVERT: D 58 HIS cc_start: 0.8542 (m-70) cc_final: 0.8291 (m90) REVERT: D 62 VAL cc_start: 0.5815 (OUTLIER) cc_final: 0.5514 (t) REVERT: D 151 MET cc_start: 0.6523 (tmm) cc_final: 0.6110 (tmm) REVERT: D 167 ASN cc_start: 0.7789 (t0) cc_final: 0.7558 (t0) REVERT: D 250 TYR cc_start: 0.8757 (t80) cc_final: 0.8512 (t80) REVERT: D 257 GLU cc_start: 0.7704 (tp30) cc_final: 0.7401 (tp30) REVERT: D 283 ILE cc_start: 0.8392 (mt) cc_final: 0.7958 (mt) REVERT: F 19 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7994 (mtt90) REVERT: F 36 ASP cc_start: 0.7583 (m-30) cc_final: 0.7353 (m-30) REVERT: F 43 GLU cc_start: 0.8007 (tp30) cc_final: 0.7574 (tp30) REVERT: F 151 MET cc_start: 0.5952 (tmm) cc_final: 0.5666 (tmm) REVERT: F 167 ASN cc_start: 0.7836 (t0) cc_final: 0.7334 (t0) REVERT: F 269 MET cc_start: 0.8343 (ttt) cc_final: 0.8117 (ttm) REVERT: F 281 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7634 (tmm160) REVERT: H 26 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7528 (m-40) REVERT: H 36 ASP cc_start: 0.7374 (m-30) cc_final: 0.7028 (m-30) REVERT: H 43 GLU cc_start: 0.7957 (tp30) cc_final: 0.7583 (tp30) REVERT: H 244 ASN cc_start: 0.8245 (t0) cc_final: 0.8020 (t0) REVERT: H 257 GLU cc_start: 0.7684 (tp30) cc_final: 0.7307 (tp30) REVERT: H 278 ASP cc_start: 0.7576 (t70) cc_final: 0.7371 (t70) REVERT: J 11 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7640 (mt-10) REVERT: J 28 GLU cc_start: 0.6635 (mp0) cc_final: 0.6370 (mp0) REVERT: J 40 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8396 (mtm-85) REVERT: J 54 ASN cc_start: 0.8210 (m110) cc_final: 0.7941 (m110) REVERT: J 62 VAL cc_start: 0.5971 (OUTLIER) cc_final: 0.5707 (t) REVERT: J 167 ASN cc_start: 0.7350 (t0) cc_final: 0.6856 (t0) REVERT: J 257 GLU cc_start: 0.7789 (tp30) cc_final: 0.7435 (tp30) REVERT: J 283 ILE cc_start: 0.8418 (mt) cc_final: 0.8096 (mt) REVERT: K 36 ASP cc_start: 0.7796 (m-30) cc_final: 0.7522 (m-30) REVERT: K 43 GLU cc_start: 0.7877 (tp30) cc_final: 0.7601 (tp30) REVERT: K 167 ASN cc_start: 0.8307 (t0) cc_final: 0.8099 (t0) REVERT: L 19 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8025 (mtt180) REVERT: L 43 GLU cc_start: 0.7872 (tp30) cc_final: 0.7575 (tp30) REVERT: L 49 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6752 (m170) REVERT: L 53 LEU cc_start: 0.8693 (mp) cc_final: 0.8466 (mt) REVERT: L 167 ASN cc_start: 0.7522 (t0) cc_final: 0.7131 (t0) REVERT: L 168 GLU cc_start: 0.7358 (mp0) cc_final: 0.6937 (mp0) REVERT: L 281 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7623 (tmm160) REVERT: L 295 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7255 (mm-30) outliers start: 173 outliers final: 65 residues processed: 1021 average time/residue: 0.7592 time to fit residues: 912.2038 Evaluate side-chains 969 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 889 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain O residue 54 ARG Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 49 HIS Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 371 optimal weight: 1.9990 chunk 184 optimal weight: 0.0070 chunk 339 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 408 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 54 ASN C 266 HIS I 164 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN I 243 ASN ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN Q 40 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN E 267 GLN A 7 GLN A 54 ASN A 143 GLN A 239 GLN A 266 HIS A 267 GLN B 54 ASN B 164 ASN B 266 HIS D 39 GLN D 49 HIS D 164 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 49 HIS F 54 ASN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 80 ASN J 164 ASN J 244 ASN K 54 ASN K 243 ASN K 267 GLN ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146482 restraints weight = 46118.412| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.49 r_work: 0.3653 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35274 Z= 0.122 Angle : 0.530 11.502 47694 Z= 0.262 Chirality : 0.043 0.166 5046 Planarity : 0.004 0.053 6204 Dihedral : 4.573 79.705 4724 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.84 % Allowed : 14.67 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4164 helix: 2.61 (0.14), residues: 1362 sheet: -1.00 (0.16), residues: 1002 loop : -2.47 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 287 TYR 0.017 0.001 TYR A 140 PHE 0.018 0.001 PHE J 161 TRP 0.008 0.001 TRP N 84 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00290 (35274) covalent geometry : angle 0.52995 (47694) hydrogen bonds : bond 0.03536 ( 1425) hydrogen bonds : angle 4.04041 ( 4038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 884 time to evaluate : 1.464 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: C 19 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8265 (mtp180) REVERT: C 36 ASP cc_start: 0.7636 (m-30) cc_final: 0.7386 (m-30) REVERT: C 43 GLU cc_start: 0.7825 (tp30) cc_final: 0.7478 (tp30) REVERT: C 62 VAL cc_start: 0.4797 (OUTLIER) cc_final: 0.4545 (t) REVERT: C 150 MET cc_start: 0.5601 (ptp) cc_final: 0.5379 (ptp) REVERT: C 265 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7935 (mtt180) REVERT: C 271 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7259 (mt) REVERT: I 43 GLU cc_start: 0.7868 (tp30) cc_final: 0.7465 (tp30) REVERT: I 62 VAL cc_start: 0.4310 (OUTLIER) cc_final: 0.4075 (t) REVERT: I 121 MET cc_start: 0.4854 (tpt) cc_final: 0.4600 (tpt) REVERT: I 164 ASN cc_start: 0.8703 (t0) cc_final: 0.8446 (t0) REVERT: I 265 ARG cc_start: 0.8328 (ttm170) cc_final: 0.7973 (mtt180) REVERT: G 36 ASP cc_start: 0.7623 (m-30) cc_final: 0.7347 (m-30) REVERT: G 43 GLU cc_start: 0.7947 (tp30) cc_final: 0.7629 (tp30) REVERT: G 62 VAL cc_start: 0.4204 (OUTLIER) cc_final: 0.3982 (t) REVERT: G 150 MET cc_start: 0.5975 (ptp) cc_final: 0.5718 (ptp) REVERT: G 185 GLU cc_start: 0.7199 (pp20) cc_final: 0.6662 (pp20) REVERT: G 243 ASN cc_start: 0.7776 (t0) cc_final: 0.7382 (t0) REVERT: G 257 GLU cc_start: 0.7633 (tp30) cc_final: 0.7297 (tp30) REVERT: G 283 ILE cc_start: 0.8394 (mt) cc_final: 0.8082 (mt) REVERT: X 49 THR cc_start: 0.8202 (t) cc_final: 0.7919 (p) REVERT: X 66 ARG cc_start: 0.8629 (ptt90) cc_final: 0.8401 (ptt180) REVERT: W 49 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7791 (p) REVERT: V 38 SER cc_start: 0.8586 (t) cc_final: 0.8366 (t) REVERT: U 49 THR cc_start: 0.8177 (t) cc_final: 0.7930 (p) REVERT: O 136 ASP cc_start: 0.7984 (m-30) cc_final: 0.7778 (m-30) REVERT: N 28 ASN cc_start: 0.8410 (t0) cc_final: 0.8179 (t0) REVERT: N 44 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: N 50 SER cc_start: 0.8723 (t) cc_final: 0.8453 (p) REVERT: N 147 PHE cc_start: 0.8271 (m-80) cc_final: 0.7908 (m-80) REVERT: R 54 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7574 (mtp85) REVERT: Q 54 ARG cc_start: 0.8603 (mmt-90) cc_final: 0.8261 (mpt180) REVERT: E 43 GLU cc_start: 0.8020 (tp30) cc_final: 0.7715 (tp30) REVERT: E 62 VAL cc_start: 0.5236 (OUTLIER) cc_final: 0.5007 (t) REVERT: E 257 GLU cc_start: 0.7709 (tp30) cc_final: 0.7380 (tp30) REVERT: A 43 GLU cc_start: 0.7919 (tp30) cc_final: 0.7582 (tp30) REVERT: A 140 TYR cc_start: 0.6563 (m-10) cc_final: 0.6195 (m-80) REVERT: A 151 MET cc_start: 0.7098 (tmt) cc_final: 0.6807 (tmt) REVERT: A 295 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7180 (mm-30) REVERT: B 11 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7476 (mt-10) REVERT: B 19 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8014 (mtp180) REVERT: B 26 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7510 (m-40) REVERT: B 43 GLU cc_start: 0.7940 (tp30) cc_final: 0.7597 (tp30) REVERT: B 47 GLU cc_start: 0.7559 (tt0) cc_final: 0.7276 (tt0) REVERT: B 167 ASN cc_start: 0.7702 (t0) cc_final: 0.7278 (t0) REVERT: B 278 ASP cc_start: 0.7585 (t70) cc_final: 0.7323 (t70) REVERT: D 8 ASN cc_start: 0.8010 (p0) cc_final: 0.7678 (OUTLIER) REVERT: D 11 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7623 (mt-10) REVERT: D 36 ASP cc_start: 0.7332 (m-30) cc_final: 0.7087 (m-30) REVERT: D 39 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8106 (mp10) REVERT: D 58 HIS cc_start: 0.8566 (m-70) cc_final: 0.8262 (m90) REVERT: D 62 VAL cc_start: 0.5755 (OUTLIER) cc_final: 0.5453 (t) REVERT: D 167 ASN cc_start: 0.7773 (t0) cc_final: 0.7504 (t0) REVERT: D 257 GLU cc_start: 0.7711 (tp30) cc_final: 0.7382 (tp30) REVERT: D 283 ILE cc_start: 0.8358 (mt) cc_final: 0.7927 (mt) REVERT: F 27 VAL cc_start: 0.7105 (OUTLIER) cc_final: 0.6879 (t) REVERT: F 43 GLU cc_start: 0.7935 (tp30) cc_final: 0.7550 (tp30) REVERT: F 150 MET cc_start: 0.3709 (ptp) cc_final: 0.3495 (ptp) REVERT: F 167 ASN cc_start: 0.7822 (t0) cc_final: 0.7318 (t0) REVERT: F 281 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7557 (ptt-90) REVERT: F 295 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6968 (mm-30) REVERT: H 43 GLU cc_start: 0.7957 (tp30) cc_final: 0.7612 (tp30) REVERT: H 185 GLU cc_start: 0.7336 (pp20) cc_final: 0.6941 (pp20) REVERT: H 244 ASN cc_start: 0.8292 (t0) cc_final: 0.8040 (t0) REVERT: H 257 GLU cc_start: 0.7634 (tp30) cc_final: 0.7254 (tp30) REVERT: J 11 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7588 (mt-10) REVERT: J 27 VAL cc_start: 0.7177 (OUTLIER) cc_final: 0.6956 (t) REVERT: J 28 GLU cc_start: 0.6562 (mp0) cc_final: 0.6293 (mp0) REVERT: J 40 ARG cc_start: 0.8622 (mtp180) cc_final: 0.8358 (mtm-85) REVERT: J 54 ASN cc_start: 0.8255 (m110) cc_final: 0.7975 (m110) REVERT: J 62 VAL cc_start: 0.5975 (OUTLIER) cc_final: 0.5712 (t) REVERT: J 85 THR cc_start: 0.8755 (m) cc_final: 0.8106 (p) REVERT: J 127 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7024 (ppp80) REVERT: J 167 ASN cc_start: 0.7309 (t0) cc_final: 0.6919 (t0) REVERT: J 257 GLU cc_start: 0.7712 (tp30) cc_final: 0.7370 (tp30) REVERT: J 283 ILE cc_start: 0.8405 (mt) cc_final: 0.8089 (mt) REVERT: K 5 ASN cc_start: 0.6905 (t0) cc_final: 0.6655 (t0) REVERT: K 36 ASP cc_start: 0.7793 (m-30) cc_final: 0.7511 (m-30) REVERT: K 43 GLU cc_start: 0.7863 (tp30) cc_final: 0.7619 (tp30) REVERT: K 167 ASN cc_start: 0.8242 (t0) cc_final: 0.8032 (t0) REVERT: K 257 GLU cc_start: 0.7668 (tp30) cc_final: 0.7303 (tp30) REVERT: L 27 VAL cc_start: 0.6976 (OUTLIER) cc_final: 0.6761 (t) REVERT: L 36 ASP cc_start: 0.7598 (m-30) cc_final: 0.7305 (m-30) REVERT: L 43 GLU cc_start: 0.7843 (tp30) cc_final: 0.7554 (tp30) REVERT: L 48 TYR cc_start: 0.7189 (m-80) cc_final: 0.6981 (m-80) REVERT: L 53 LEU cc_start: 0.8655 (mp) cc_final: 0.8446 (mt) REVERT: L 141 PHE cc_start: 0.7760 (t80) cc_final: 0.7477 (t80) REVERT: L 167 ASN cc_start: 0.7524 (t0) cc_final: 0.7157 (t0) REVERT: L 168 GLU cc_start: 0.7359 (mp0) cc_final: 0.6927 (mp0) REVERT: L 281 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7574 (tmm160) REVERT: L 295 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7064 (mm-30) outliers start: 177 outliers final: 82 residues processed: 985 average time/residue: 0.7269 time to fit residues: 848.6712 Evaluate side-chains 968 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 871 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain P residue 142 MET Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 195 optimal weight: 0.0370 chunk 397 optimal weight: 0.3980 chunk 396 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 359 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 410 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 393 optimal weight: 1.9990 chunk 354 optimal weight: 0.9980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 49 HIS I 49 HIS I 54 ASN I 143 GLN ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 267 GLN O 28 ASN ** O 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 GLN M 164 ASN R 28 ASN R 38 ASN R 40 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN E 167 ASN E 244 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 267 GLN A 54 ASN A 267 GLN B 49 HIS B 54 ASN B 164 ASN D 54 ASN D 164 ASN F 49 HIS ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 239 GLN H 243 ASN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 164 ASN K 26 ASN K 267 GLN L 49 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.181188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144526 restraints weight = 45945.708| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.48 r_work: 0.3624 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35274 Z= 0.154 Angle : 0.547 9.546 47694 Z= 0.272 Chirality : 0.044 0.170 5046 Planarity : 0.004 0.046 6204 Dihedral : 4.704 82.235 4724 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.34 % Allowed : 15.54 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 4164 helix: 2.87 (0.14), residues: 1338 sheet: -0.80 (0.16), residues: 1002 loop : -2.21 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 287 TYR 0.013 0.001 TYR N 139 PHE 0.027 0.001 PHE J 141 TRP 0.010 0.001 TRP N 84 HIS 0.006 0.001 HIS L 266 Details of bonding type rmsd covalent geometry : bond 0.00375 (35274) covalent geometry : angle 0.54707 (47694) hydrogen bonds : bond 0.03590 ( 1425) hydrogen bonds : angle 3.89353 ( 4038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 875 time to evaluate : 1.263 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: C 36 ASP cc_start: 0.7646 (m-30) cc_final: 0.7399 (m-30) REVERT: C 43 GLU cc_start: 0.7837 (tp30) cc_final: 0.7484 (tp30) REVERT: C 62 VAL cc_start: 0.4888 (OUTLIER) cc_final: 0.4634 (t) REVERT: C 150 MET cc_start: 0.5608 (ptp) cc_final: 0.5358 (ptp) REVERT: C 243 ASN cc_start: 0.7986 (t0) cc_final: 0.7750 (t0) REVERT: I 43 GLU cc_start: 0.7888 (tp30) cc_final: 0.7483 (tp30) REVERT: I 62 VAL cc_start: 0.4370 (OUTLIER) cc_final: 0.4133 (t) REVERT: I 121 MET cc_start: 0.4881 (tpt) cc_final: 0.4626 (tpt) REVERT: I 148 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6755 (mmm) REVERT: I 164 ASN cc_start: 0.8716 (t0) cc_final: 0.8480 (t0) REVERT: G 36 ASP cc_start: 0.7699 (m-30) cc_final: 0.7451 (m-30) REVERT: G 43 GLU cc_start: 0.7966 (tp30) cc_final: 0.7625 (tp30) REVERT: G 62 VAL cc_start: 0.4192 (OUTLIER) cc_final: 0.3982 (t) REVERT: G 150 MET cc_start: 0.5935 (ptp) cc_final: 0.5699 (ptp) REVERT: G 185 GLU cc_start: 0.7142 (pp20) cc_final: 0.6589 (pp20) REVERT: G 243 ASN cc_start: 0.7872 (t0) cc_final: 0.7473 (t0) REVERT: G 257 GLU cc_start: 0.7632 (tp30) cc_final: 0.7235 (tp30) REVERT: W 49 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7784 (p) REVERT: V 38 SER cc_start: 0.8611 (t) cc_final: 0.8375 (t) REVERT: O 136 ASP cc_start: 0.8064 (m-30) cc_final: 0.7831 (m-30) REVERT: N 44 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: N 50 SER cc_start: 0.8731 (t) cc_final: 0.8447 (p) REVERT: N 147 PHE cc_start: 0.8295 (m-80) cc_final: 0.7904 (m-80) REVERT: M 66 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7280 (p) REVERT: R 28 ASN cc_start: 0.8545 (t0) cc_final: 0.8296 (t0) REVERT: R 54 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7667 (mtp85) REVERT: R 130 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7435 (mmtt) REVERT: E 18 ARG cc_start: 0.8653 (mtp180) cc_final: 0.8415 (mtm110) REVERT: E 43 GLU cc_start: 0.8018 (tp30) cc_final: 0.7703 (tp30) REVERT: E 62 VAL cc_start: 0.5303 (OUTLIER) cc_final: 0.5071 (t) REVERT: E 257 GLU cc_start: 0.7688 (tp30) cc_final: 0.7378 (tp30) REVERT: A 43 GLU cc_start: 0.7935 (tp30) cc_final: 0.7580 (tp30) REVERT: A 127 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7709 (ptm160) REVERT: A 140 TYR cc_start: 0.6753 (m-10) cc_final: 0.6286 (m-80) REVERT: A 150 MET cc_start: 0.6400 (ptp) cc_final: 0.6195 (ptp) REVERT: A 151 MET cc_start: 0.7145 (tmt) cc_final: 0.6795 (tmt) REVERT: A 295 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7239 (mm-30) REVERT: B 11 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 18 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7933 (mtp180) REVERT: B 19 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8247 (mtp85) REVERT: B 26 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7558 (m-40) REVERT: B 43 GLU cc_start: 0.7964 (tp30) cc_final: 0.7607 (tp30) REVERT: B 47 GLU cc_start: 0.7609 (tt0) cc_final: 0.7333 (tt0) REVERT: B 49 HIS cc_start: 0.6884 (OUTLIER) cc_final: 0.6478 (m-70) REVERT: B 84 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7808 (t) REVERT: B 167 ASN cc_start: 0.7767 (t0) cc_final: 0.7291 (t0) REVERT: D 8 ASN cc_start: 0.8031 (p0) cc_final: 0.7695 (OUTLIER) REVERT: D 11 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7593 (mt-10) REVERT: D 36 ASP cc_start: 0.7351 (m-30) cc_final: 0.7147 (m-30) REVERT: D 39 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8122 (mp10) REVERT: D 48 TYR cc_start: 0.7299 (m-80) cc_final: 0.7092 (m-80) REVERT: D 49 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6698 (m170) REVERT: D 62 VAL cc_start: 0.5799 (OUTLIER) cc_final: 0.5519 (t) REVERT: D 167 ASN cc_start: 0.7790 (t0) cc_final: 0.7495 (t0) REVERT: D 242 TYR cc_start: 0.8824 (m-80) cc_final: 0.8469 (m-80) REVERT: D 243 ASN cc_start: 0.7701 (t0) cc_final: 0.7311 (t0) REVERT: D 248 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8555 (mttt) REVERT: D 257 GLU cc_start: 0.7773 (tp30) cc_final: 0.7443 (tp30) REVERT: D 281 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7672 (tmm160) REVERT: D 283 ILE cc_start: 0.8377 (mt) cc_final: 0.7937 (mt) REVERT: F 19 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8086 (mtt180) REVERT: F 36 ASP cc_start: 0.7692 (m-30) cc_final: 0.7465 (m-30) REVERT: F 43 GLU cc_start: 0.7920 (tp30) cc_final: 0.7548 (tp30) REVERT: F 49 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6183 (m-70) REVERT: F 150 MET cc_start: 0.4040 (ptp) cc_final: 0.3702 (ptp) REVERT: F 151 MET cc_start: 0.6107 (tmm) cc_final: 0.5774 (tmm) REVERT: F 167 ASN cc_start: 0.7810 (t0) cc_final: 0.7269 (t0) REVERT: F 270 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8139 (mpp) REVERT: F 281 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7606 (ptt-90) REVERT: F 295 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7007 (mm-30) REVERT: H 43 GLU cc_start: 0.7962 (tp30) cc_final: 0.7607 (tp30) REVERT: H 185 GLU cc_start: 0.7205 (pp20) cc_final: 0.6822 (pp20) REVERT: H 244 ASN cc_start: 0.8368 (t0) cc_final: 0.8081 (t0) REVERT: H 257 GLU cc_start: 0.7626 (tp30) cc_final: 0.7281 (tp30) REVERT: H 283 ILE cc_start: 0.8460 (mt) cc_final: 0.8238 (mt) REVERT: J 8 ASN cc_start: 0.7523 (p0) cc_final: 0.7315 (p0) REVERT: J 27 VAL cc_start: 0.7213 (OUTLIER) cc_final: 0.6942 (t) REVERT: J 28 GLU cc_start: 0.6672 (mp0) cc_final: 0.6307 (mp0) REVERT: J 40 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8350 (mtm-85) REVERT: J 62 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5758 (t) REVERT: J 127 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7444 (ptm160) REVERT: J 167 ASN cc_start: 0.7360 (t0) cc_final: 0.7070 (t0) REVERT: J 242 TYR cc_start: 0.8804 (m-80) cc_final: 0.8200 (m-80) REVERT: J 257 GLU cc_start: 0.7717 (tp30) cc_final: 0.7355 (tp30) REVERT: J 283 ILE cc_start: 0.8396 (mt) cc_final: 0.8067 (mt) REVERT: K 36 ASP cc_start: 0.7818 (m-30) cc_final: 0.7546 (m-30) REVERT: K 43 GLU cc_start: 0.7866 (tp30) cc_final: 0.7622 (tp30) REVERT: K 257 GLU cc_start: 0.7685 (tp30) cc_final: 0.7288 (tp30) REVERT: K 284 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7026 (mm-30) REVERT: L 19 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8018 (mtt180) REVERT: L 36 ASP cc_start: 0.7598 (m-30) cc_final: 0.7397 (m-30) REVERT: L 43 GLU cc_start: 0.7821 (tp30) cc_final: 0.7547 (tp30) REVERT: L 53 LEU cc_start: 0.8591 (mp) cc_final: 0.8384 (mt) REVERT: L 141 PHE cc_start: 0.7777 (t80) cc_final: 0.7563 (t80) REVERT: L 167 ASN cc_start: 0.7531 (t0) cc_final: 0.7102 (t0) REVERT: L 168 GLU cc_start: 0.7388 (mp0) cc_final: 0.6941 (mp0) REVERT: L 281 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7763 (tmm160) REVERT: L 295 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7085 (mm-30) outliers start: 195 outliers final: 93 residues processed: 972 average time/residue: 0.7711 time to fit residues: 880.1321 Evaluate side-chains 979 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 863 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 123 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 324 optimal weight: 0.9990 chunk 399 optimal weight: 2.9990 chunk 231 optimal weight: 0.0980 chunk 388 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 164 ASN I 54 ASN ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN I 280 GLN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN W 33 GLN O 28 ASN ** O 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN R 38 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN E 164 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 54 ASN A 267 GLN A 280 GLN B 54 ASN B 164 ASN B 243 ASN D 143 GLN D 164 ASN F 39 GLN F 126 ASN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 164 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 ASN K 267 GLN L 8 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141435 restraints weight = 45677.224| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.46 r_work: 0.3587 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 35274 Z= 0.271 Angle : 0.613 8.708 47694 Z= 0.306 Chirality : 0.047 0.178 5046 Planarity : 0.005 0.044 6204 Dihedral : 4.953 83.025 4719 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.39 % Allowed : 16.39 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4164 helix: 2.67 (0.13), residues: 1338 sheet: -0.59 (0.16), residues: 990 loop : -2.19 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 287 TYR 0.018 0.001 TYR C 242 PHE 0.018 0.001 PHE I 82 TRP 0.014 0.002 TRP M 84 HIS 0.035 0.003 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00663 (35274) covalent geometry : angle 0.61305 (47694) hydrogen bonds : bond 0.04313 ( 1425) hydrogen bonds : angle 3.95198 ( 4038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 906 time to evaluate : 1.136 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: C 18 ARG cc_start: 0.8597 (mtm110) cc_final: 0.8349 (mtm110) REVERT: C 19 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8338 (mtp180) REVERT: C 36 ASP cc_start: 0.8038 (m-30) cc_final: 0.7761 (m-30) REVERT: C 43 GLU cc_start: 0.8211 (tp30) cc_final: 0.7910 (tp30) REVERT: C 62 VAL cc_start: 0.5113 (OUTLIER) cc_final: 0.4822 (t) REVERT: C 150 MET cc_start: 0.5877 (ptp) cc_final: 0.5632 (ptp) REVERT: I 43 GLU cc_start: 0.8269 (tp30) cc_final: 0.7839 (tp30) REVERT: I 62 VAL cc_start: 0.4536 (OUTLIER) cc_final: 0.4278 (t) REVERT: I 121 MET cc_start: 0.4876 (tpt) cc_final: 0.4668 (tpt) REVERT: I 148 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7013 (mmm) REVERT: I 164 ASN cc_start: 0.8867 (t0) cc_final: 0.8638 (t0) REVERT: I 284 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7295 (mm-30) REVERT: G 36 ASP cc_start: 0.8150 (m-30) cc_final: 0.7931 (m-30) REVERT: G 43 GLU cc_start: 0.8391 (tp30) cc_final: 0.8059 (tp30) REVERT: G 62 VAL cc_start: 0.4288 (OUTLIER) cc_final: 0.4072 (t) REVERT: G 127 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7677 (ptm160) REVERT: G 150 MET cc_start: 0.6207 (ptp) cc_final: 0.5975 (ptp) REVERT: G 243 ASN cc_start: 0.8294 (t0) cc_final: 0.8041 (t0) REVERT: G 257 GLU cc_start: 0.7998 (tp30) cc_final: 0.7644 (tp30) REVERT: W 49 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8115 (p) REVERT: V 38 SER cc_start: 0.8788 (t) cc_final: 0.8563 (t) REVERT: O 136 ASP cc_start: 0.8274 (m-30) cc_final: 0.8056 (m-30) REVERT: N 50 SER cc_start: 0.8802 (t) cc_final: 0.8581 (p) REVERT: N 147 PHE cc_start: 0.8456 (m-80) cc_final: 0.8073 (m-80) REVERT: M 66 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.7480 (p) REVERT: M 134 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: R 54 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7948 (mtp85) REVERT: R 130 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7891 (mmtt) REVERT: Q 50 SER cc_start: 0.8805 (t) cc_final: 0.8580 (p) REVERT: P 45 VAL cc_start: 0.8813 (t) cc_final: 0.8580 (t) REVERT: P 80 PHE cc_start: 0.4456 (OUTLIER) cc_final: 0.4137 (t80) REVERT: P 134 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: E 43 GLU cc_start: 0.8413 (tp30) cc_final: 0.8058 (tp30) REVERT: E 62 VAL cc_start: 0.5483 (OUTLIER) cc_final: 0.5244 (t) REVERT: E 150 MET cc_start: 0.5895 (ptp) cc_final: 0.5671 (ptp) REVERT: E 173 MET cc_start: 0.8041 (mmt) cc_final: 0.7791 (mtt) REVERT: E 257 GLU cc_start: 0.8022 (tp30) cc_final: 0.7771 (tp30) REVERT: A 43 GLU cc_start: 0.8274 (tp30) cc_final: 0.7909 (tp30) REVERT: A 140 TYR cc_start: 0.6921 (m-10) cc_final: 0.6437 (m-80) REVERT: A 150 MET cc_start: 0.6745 (ptp) cc_final: 0.6538 (ptp) REVERT: A 151 MET cc_start: 0.7213 (tmt) cc_final: 0.6931 (tmt) REVERT: B 18 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8106 (mtp180) REVERT: B 43 GLU cc_start: 0.8343 (tp30) cc_final: 0.7991 (tp30) REVERT: B 47 GLU cc_start: 0.8039 (tt0) cc_final: 0.7764 (tt0) REVERT: B 167 ASN cc_start: 0.7785 (t0) cc_final: 0.7326 (t0) REVERT: B 243 ASN cc_start: 0.8041 (t0) cc_final: 0.7735 (t0) REVERT: D 8 ASN cc_start: 0.8364 (p0) cc_final: 0.8029 (OUTLIER) REVERT: D 36 ASP cc_start: 0.7684 (m-30) cc_final: 0.7467 (m-30) REVERT: D 49 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6872 (m170) REVERT: D 62 VAL cc_start: 0.6052 (OUTLIER) cc_final: 0.5772 (t) REVERT: D 151 MET cc_start: 0.6890 (tmm) cc_final: 0.6574 (tmm) REVERT: D 167 ASN cc_start: 0.7929 (t0) cc_final: 0.7669 (t0) REVERT: D 242 TYR cc_start: 0.8915 (m-80) cc_final: 0.8574 (m-80) REVERT: D 243 ASN cc_start: 0.8075 (t0) cc_final: 0.7703 (t0) REVERT: D 245 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8312 (ttp-170) REVERT: D 257 GLU cc_start: 0.8097 (tp30) cc_final: 0.7785 (tp30) REVERT: D 281 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8058 (tmm160) REVERT: D 283 ILE cc_start: 0.8490 (mt) cc_final: 0.8066 (mt) REVERT: F 19 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8382 (mtt180) REVERT: F 43 GLU cc_start: 0.8296 (tp30) cc_final: 0.8043 (tp30) REVERT: F 150 MET cc_start: 0.4306 (ptp) cc_final: 0.4000 (ptp) REVERT: F 167 ASN cc_start: 0.7865 (t0) cc_final: 0.7311 (t0) REVERT: F 270 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8479 (mpp) REVERT: F 295 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7480 (mm-30) REVERT: H 43 GLU cc_start: 0.8375 (tp30) cc_final: 0.8063 (tp30) REVERT: H 242 TYR cc_start: 0.8990 (m-80) cc_final: 0.8676 (m-80) REVERT: H 244 ASN cc_start: 0.8624 (t0) cc_final: 0.8343 (t0) REVERT: H 257 GLU cc_start: 0.7947 (tp30) cc_final: 0.7649 (tp30) REVERT: H 278 ASP cc_start: 0.7801 (t70) cc_final: 0.7572 (t70) REVERT: J 27 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7066 (t) REVERT: J 28 GLU cc_start: 0.7024 (mp0) cc_final: 0.6758 (mp0) REVERT: J 62 VAL cc_start: 0.6097 (OUTLIER) cc_final: 0.5838 (t) REVERT: J 167 ASN cc_start: 0.7359 (t0) cc_final: 0.7127 (t0) REVERT: J 242 TYR cc_start: 0.8930 (m-80) cc_final: 0.8335 (m-80) REVERT: J 245 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8472 (ttp-170) REVERT: J 257 GLU cc_start: 0.8115 (tp30) cc_final: 0.7675 (tp30) REVERT: K 36 ASP cc_start: 0.8183 (m-30) cc_final: 0.7940 (m-30) REVERT: K 43 GLU cc_start: 0.8238 (tp30) cc_final: 0.7996 (tp30) REVERT: K 150 MET cc_start: 0.6762 (ptp) cc_final: 0.6479 (ptp) REVERT: K 257 GLU cc_start: 0.8021 (tp30) cc_final: 0.7628 (tp30) REVERT: K 284 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7517 (mm-30) REVERT: L 19 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8176 (mtt180) REVERT: L 36 ASP cc_start: 0.7986 (m-30) cc_final: 0.7745 (m-30) REVERT: L 43 GLU cc_start: 0.8215 (tp30) cc_final: 0.7944 (tp30) REVERT: L 49 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6927 (m-70) REVERT: L 53 LEU cc_start: 0.8620 (mp) cc_final: 0.8359 (mt) REVERT: L 54 ASN cc_start: 0.8585 (m110) cc_final: 0.8312 (m-40) REVERT: L 141 PHE cc_start: 0.7903 (t80) cc_final: 0.7674 (t80) REVERT: L 151 MET cc_start: 0.6799 (tmm) cc_final: 0.6420 (tmt) REVERT: L 167 ASN cc_start: 0.7612 (t0) cc_final: 0.7188 (t0) REVERT: L 168 GLU cc_start: 0.7590 (mp0) cc_final: 0.7129 (mp0) REVERT: L 281 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7997 (tmm160) REVERT: L 295 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7564 (mm-30) outliers start: 197 outliers final: 109 residues processed: 997 average time/residue: 0.7413 time to fit residues: 867.3911 Evaluate side-chains 1031 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 902 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 127 ARG Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain W residue 41 GLN Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 37 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 80 PHE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain H residue 167 ASN Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 49 HIS Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 371 optimal weight: 0.7980 chunk 369 optimal weight: 0.8980 chunk 413 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 364 optimal weight: 0.9990 chunk 386 optimal weight: 0.1980 chunk 303 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN C 8 ASN C 39 GLN C 49 HIS C 54 ASN C 164 ASN C 243 ASN I 54 ASN ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN X 8 GLN O 28 ASN ** O 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 54 ASN A 80 ASN A 267 GLN A 280 GLN B 54 ASN B 164 ASN B 167 ASN D 126 ASN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 164 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 GLN L 8 ASN L 164 ASN L 259 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.179638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142869 restraints weight = 45468.966| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.47 r_work: 0.3606 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 35274 Z= 0.145 Angle : 0.562 10.862 47694 Z= 0.278 Chirality : 0.043 0.206 5046 Planarity : 0.004 0.069 6204 Dihedral : 4.852 84.278 4719 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.82 % Allowed : 17.87 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 4164 helix: 2.82 (0.14), residues: 1338 sheet: -0.63 (0.16), residues: 1020 loop : -2.04 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG W 17 TYR 0.018 0.001 TYR H 35 PHE 0.015 0.001 PHE J 161 TRP 0.010 0.001 TRP N 84 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00355 (35274) covalent geometry : angle 0.56196 (47694) hydrogen bonds : bond 0.03593 ( 1425) hydrogen bonds : angle 3.84205 ( 4038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 889 time to evaluate : 1.164 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: C 19 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8363 (mtp180) REVERT: C 43 GLU cc_start: 0.7801 (tp30) cc_final: 0.7531 (tp30) REVERT: C 62 VAL cc_start: 0.4960 (OUTLIER) cc_final: 0.4684 (t) REVERT: C 150 MET cc_start: 0.5517 (ptp) cc_final: 0.5295 (ptp) REVERT: C 158 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7517 (tt) REVERT: I 43 GLU cc_start: 0.7826 (tp30) cc_final: 0.7429 (tp30) REVERT: I 62 VAL cc_start: 0.4414 (OUTLIER) cc_final: 0.4165 (t) REVERT: I 148 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6744 (mmm) REVERT: I 164 ASN cc_start: 0.8762 (t0) cc_final: 0.8527 (t0) REVERT: G 36 ASP cc_start: 0.7701 (m-30) cc_final: 0.7486 (m-30) REVERT: G 43 GLU cc_start: 0.7999 (tp30) cc_final: 0.7649 (tp30) REVERT: G 62 VAL cc_start: 0.4194 (OUTLIER) cc_final: 0.3982 (t) REVERT: G 127 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7667 (ptm160) REVERT: G 185 GLU cc_start: 0.7157 (pp20) cc_final: 0.6578 (pp20) REVERT: G 243 ASN cc_start: 0.8077 (t0) cc_final: 0.7808 (t0) REVERT: G 257 GLU cc_start: 0.7613 (tp30) cc_final: 0.7267 (tp30) REVERT: G 267 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8066 (mm-40) REVERT: V 38 SER cc_start: 0.8608 (t) cc_final: 0.8365 (t) REVERT: O 54 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7175 (mmp80) REVERT: N 28 ASN cc_start: 0.8518 (t0) cc_final: 0.8283 (t0) REVERT: N 50 SER cc_start: 0.8702 (t) cc_final: 0.8448 (p) REVERT: N 147 PHE cc_start: 0.8304 (m-80) cc_final: 0.7881 (m-80) REVERT: N 150 ASN cc_start: 0.8188 (p0) cc_final: 0.7970 (p0) REVERT: M 66 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7308 (p) REVERT: M 134 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: R 50 SER cc_start: 0.8785 (t) cc_final: 0.8445 (p) REVERT: R 54 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7729 (mtp85) REVERT: R 130 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7716 (mmtt) REVERT: R 133 LYS cc_start: 0.8064 (tppt) cc_final: 0.7863 (tppt) REVERT: Q 54 ARG cc_start: 0.8668 (mmt180) cc_final: 0.8325 (mpt180) REVERT: Q 147 PHE cc_start: 0.8342 (m-80) cc_final: 0.7853 (m-80) REVERT: P 45 VAL cc_start: 0.8690 (t) cc_final: 0.8451 (t) REVERT: P 80 PHE cc_start: 0.4179 (OUTLIER) cc_final: 0.3916 (t80) REVERT: E 43 GLU cc_start: 0.7997 (tp30) cc_final: 0.7682 (tp30) REVERT: E 62 VAL cc_start: 0.5407 (OUTLIER) cc_final: 0.5184 (t) REVERT: E 173 MET cc_start: 0.7475 (mmt) cc_final: 0.7063 (mtt) REVERT: E 257 GLU cc_start: 0.7657 (tp30) cc_final: 0.7417 (tp30) REVERT: A 43 GLU cc_start: 0.7860 (tp30) cc_final: 0.7487 (tp30) REVERT: A 140 TYR cc_start: 0.6781 (m-10) cc_final: 0.6278 (m-80) REVERT: A 150 MET cc_start: 0.6417 (ptp) cc_final: 0.6214 (ptp) REVERT: A 151 MET cc_start: 0.7101 (tmt) cc_final: 0.6858 (tmt) REVERT: A 269 MET cc_start: 0.7092 (tpt) cc_final: 0.6855 (ttt) REVERT: B 43 GLU cc_start: 0.7944 (tp30) cc_final: 0.7581 (tp30) REVERT: B 47 GLU cc_start: 0.7581 (tt0) cc_final: 0.7276 (tt0) REVERT: B 127 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7441 (ptm160) REVERT: B 167 ASN cc_start: 0.7721 (t0) cc_final: 0.7265 (t0) REVERT: B 243 ASN cc_start: 0.7710 (t0) cc_final: 0.7331 (t0) REVERT: D 39 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8160 (mp10) REVERT: D 49 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6598 (m170) REVERT: D 62 VAL cc_start: 0.5779 (OUTLIER) cc_final: 0.5504 (t) REVERT: D 151 MET cc_start: 0.6807 (tmm) cc_final: 0.6532 (tmm) REVERT: D 167 ASN cc_start: 0.7838 (t0) cc_final: 0.7531 (t0) REVERT: D 242 TYR cc_start: 0.8839 (m-80) cc_final: 0.8521 (m-80) REVERT: D 243 ASN cc_start: 0.7798 (t0) cc_final: 0.7379 (t0) REVERT: D 245 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8074 (ttp-170) REVERT: D 257 GLU cc_start: 0.7756 (tp30) cc_final: 0.7429 (tp30) REVERT: D 281 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7892 (tmm160) REVERT: D 283 ILE cc_start: 0.8372 (mt) cc_final: 0.7894 (mt) REVERT: F 43 GLU cc_start: 0.7902 (tp30) cc_final: 0.7655 (tp30) REVERT: F 150 MET cc_start: 0.4023 (ptp) cc_final: 0.3759 (ptp) REVERT: F 167 ASN cc_start: 0.7801 (t0) cc_final: 0.7216 (t0) REVERT: F 270 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: F 295 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7068 (mm-30) REVERT: H 43 GLU cc_start: 0.7956 (tp30) cc_final: 0.7616 (tp30) REVERT: H 242 TYR cc_start: 0.8926 (m-80) cc_final: 0.8554 (m-80) REVERT: H 243 ASN cc_start: 0.7741 (t0) cc_final: 0.7434 (t0) REVERT: H 244 ASN cc_start: 0.8423 (t0) cc_final: 0.8120 (t0) REVERT: H 257 GLU cc_start: 0.7641 (tp30) cc_final: 0.7350 (tp30) REVERT: H 278 ASP cc_start: 0.7606 (t70) cc_final: 0.7367 (t70) REVERT: J 27 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6947 (t) REVERT: J 28 GLU cc_start: 0.6639 (mp0) cc_final: 0.6354 (mp0) REVERT: J 62 VAL cc_start: 0.5908 (OUTLIER) cc_final: 0.5652 (t) REVERT: J 127 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7331 (ptm160) REVERT: J 167 ASN cc_start: 0.7192 (t0) cc_final: 0.6942 (t0) REVERT: J 245 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: J 257 GLU cc_start: 0.7726 (tp30) cc_final: 0.7298 (tp30) REVERT: K 36 ASP cc_start: 0.7794 (m-30) cc_final: 0.7530 (m-30) REVERT: K 43 GLU cc_start: 0.7848 (tp30) cc_final: 0.7622 (tp30) REVERT: K 257 GLU cc_start: 0.7650 (tp30) cc_final: 0.7246 (tp30) REVERT: K 284 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7125 (mm-30) REVERT: L 19 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8065 (mtt180) REVERT: L 36 ASP cc_start: 0.7600 (m-30) cc_final: 0.7379 (m-30) REVERT: L 43 GLU cc_start: 0.7836 (tp30) cc_final: 0.7582 (tp30) REVERT: L 53 LEU cc_start: 0.8587 (mp) cc_final: 0.8298 (mt) REVERT: L 54 ASN cc_start: 0.8450 (m110) cc_final: 0.8165 (m-40) REVERT: L 141 PHE cc_start: 0.7816 (t80) cc_final: 0.7597 (t80) REVERT: L 151 MET cc_start: 0.6806 (tmm) cc_final: 0.6530 (tmt) REVERT: L 167 ASN cc_start: 0.7526 (t0) cc_final: 0.7072 (t0) REVERT: L 168 GLU cc_start: 0.7316 (mp0) cc_final: 0.6847 (mp0) REVERT: L 281 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7840 (tmm160) REVERT: L 295 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7099 (mm-30) outliers start: 176 outliers final: 103 residues processed: 975 average time/residue: 0.7500 time to fit residues: 859.5748 Evaluate side-chains 1008 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 884 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 127 ARG Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain W residue 41 GLN Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 54 ARG Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 37 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 80 PHE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 142 MET Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 166 optimal weight: 0.0770 chunk 59 optimal weight: 10.0000 chunk 370 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 39 GLN C 49 HIS C 54 ASN C 164 ASN I 54 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 49 HIS G 54 ASN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 267 GLN O 28 ASN N 119 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 54 ASN A 80 ASN A 267 GLN B 54 ASN B 164 ASN D 80 ASN F 39 GLN F 49 HIS F 143 GLN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 80 ASN J 164 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 267 GLN L 8 ASN L 49 HIS L 54 ASN L 126 ASN L 164 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.179094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142314 restraints weight = 45806.077| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.48 r_work: 0.3600 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 35274 Z= 0.166 Angle : 0.570 11.302 47694 Z= 0.283 Chirality : 0.044 0.169 5046 Planarity : 0.004 0.054 6204 Dihedral : 4.667 58.634 4713 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.57 % Allowed : 18.53 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 4164 helix: 2.83 (0.13), residues: 1338 sheet: -0.58 (0.16), residues: 1020 loop : -1.99 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG W 17 TYR 0.014 0.001 TYR H 35 PHE 0.029 0.001 PHE J 141 TRP 0.010 0.001 TRP N 84 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00409 (35274) covalent geometry : angle 0.57035 (47694) hydrogen bonds : bond 0.03658 ( 1425) hydrogen bonds : angle 3.82577 ( 4038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 884 time to evaluate : 1.214 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: C 19 ARG cc_start: 0.8542 (ttm170) cc_final: 0.8325 (mtp180) REVERT: C 43 GLU cc_start: 0.7821 (tp30) cc_final: 0.7548 (tp30) REVERT: C 62 VAL cc_start: 0.4990 (OUTLIER) cc_final: 0.4708 (t) REVERT: C 76 LEU cc_start: 0.8769 (mp) cc_final: 0.8517 (mt) REVERT: C 150 MET cc_start: 0.5474 (ptp) cc_final: 0.5265 (ptp) REVERT: I 43 GLU cc_start: 0.7846 (tp30) cc_final: 0.7439 (tp30) REVERT: I 62 VAL cc_start: 0.4433 (OUTLIER) cc_final: 0.4184 (t) REVERT: I 148 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6739 (mmm) REVERT: I 164 ASN cc_start: 0.8759 (t0) cc_final: 0.8532 (t0) REVERT: G 43 GLU cc_start: 0.7997 (tp30) cc_final: 0.7656 (tp30) REVERT: G 50 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.4653 (p90) REVERT: G 62 VAL cc_start: 0.4228 (OUTLIER) cc_final: 0.4017 (t) REVERT: G 148 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6673 (tmm) REVERT: G 150 MET cc_start: 0.5864 (ptp) cc_final: 0.5576 (ptp) REVERT: G 185 GLU cc_start: 0.7137 (pp20) cc_final: 0.6536 (pp20) REVERT: G 243 ASN cc_start: 0.8139 (t0) cc_final: 0.7894 (t0) REVERT: G 257 GLU cc_start: 0.7625 (tp30) cc_final: 0.7296 (tp30) REVERT: V 38 SER cc_start: 0.8605 (t) cc_final: 0.8359 (t) REVERT: O 54 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7188 (mmp80) REVERT: N 28 ASN cc_start: 0.8519 (t0) cc_final: 0.8285 (t0) REVERT: N 50 SER cc_start: 0.8705 (t) cc_final: 0.8447 (p) REVERT: N 147 PHE cc_start: 0.8311 (m-80) cc_final: 0.7886 (m-80) REVERT: N 150 ASN cc_start: 0.8238 (p0) cc_final: 0.7986 (p0) REVERT: M 66 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7307 (p) REVERT: M 134 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: R 50 SER cc_start: 0.8772 (t) cc_final: 0.8434 (p) REVERT: R 54 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7789 (mtp85) REVERT: R 130 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7881 (mmtt) REVERT: Q 147 PHE cc_start: 0.8353 (m-80) cc_final: 0.7969 (m-80) REVERT: P 80 PHE cc_start: 0.4214 (OUTLIER) cc_final: 0.3948 (t80) REVERT: E 43 GLU cc_start: 0.7997 (tp30) cc_final: 0.7681 (tp30) REVERT: E 62 VAL cc_start: 0.5427 (OUTLIER) cc_final: 0.5199 (t) REVERT: E 173 MET cc_start: 0.7517 (mmt) cc_final: 0.7072 (mtt) REVERT: E 257 GLU cc_start: 0.7677 (tp30) cc_final: 0.7435 (tp30) REVERT: A 43 GLU cc_start: 0.7875 (tp30) cc_final: 0.7502 (tp30) REVERT: A 140 TYR cc_start: 0.6814 (m-10) cc_final: 0.6379 (m-80) REVERT: A 150 MET cc_start: 0.6412 (ptp) cc_final: 0.6211 (ptp) REVERT: B 43 GLU cc_start: 0.7966 (tp30) cc_final: 0.7599 (tp30) REVERT: B 47 GLU cc_start: 0.7611 (tt0) cc_final: 0.7307 (tt0) REVERT: B 85 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7369 (p) REVERT: B 127 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7525 (ptm160) REVERT: B 167 ASN cc_start: 0.7731 (t0) cc_final: 0.7353 (t0) REVERT: B 243 ASN cc_start: 0.7760 (t0) cc_final: 0.7425 (t0) REVERT: D 36 ASP cc_start: 0.7345 (m-30) cc_final: 0.7126 (m-30) REVERT: D 39 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8175 (mp10) REVERT: D 49 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6653 (m170) REVERT: D 62 VAL cc_start: 0.5798 (OUTLIER) cc_final: 0.5525 (t) REVERT: D 167 ASN cc_start: 0.7846 (t0) cc_final: 0.7546 (t0) REVERT: D 242 TYR cc_start: 0.8841 (m-80) cc_final: 0.8522 (m-80) REVERT: D 243 ASN cc_start: 0.7836 (t0) cc_final: 0.7425 (t0) REVERT: D 245 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8064 (ttp-170) REVERT: D 257 GLU cc_start: 0.7752 (tp30) cc_final: 0.7427 (tp30) REVERT: D 281 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7915 (tmm160) REVERT: D 283 ILE cc_start: 0.8392 (mt) cc_final: 0.7911 (mt) REVERT: F 19 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8110 (mtt180) REVERT: F 43 GLU cc_start: 0.7921 (tp30) cc_final: 0.7665 (tp30) REVERT: F 150 MET cc_start: 0.4070 (ptp) cc_final: 0.3792 (ptp) REVERT: F 167 ASN cc_start: 0.7800 (t0) cc_final: 0.7180 (t0) REVERT: F 270 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: F 295 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7099 (mm-30) REVERT: H 43 GLU cc_start: 0.7960 (tp30) cc_final: 0.7606 (tp30) REVERT: H 242 TYR cc_start: 0.8935 (m-80) cc_final: 0.8605 (m-80) REVERT: H 243 ASN cc_start: 0.7832 (t0) cc_final: 0.7504 (t0) REVERT: H 244 ASN cc_start: 0.8439 (t0) cc_final: 0.8138 (t0) REVERT: H 257 GLU cc_start: 0.7650 (tp30) cc_final: 0.7349 (tp30) REVERT: J 27 VAL cc_start: 0.7281 (OUTLIER) cc_final: 0.6968 (t) REVERT: J 28 GLU cc_start: 0.6657 (mp0) cc_final: 0.6369 (mp0) REVERT: J 62 VAL cc_start: 0.5927 (OUTLIER) cc_final: 0.5667 (t) REVERT: J 127 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7352 (ptm160) REVERT: J 167 ASN cc_start: 0.7189 (t0) cc_final: 0.6941 (t0) REVERT: J 245 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8227 (ttp-170) REVERT: J 257 GLU cc_start: 0.7721 (tp30) cc_final: 0.7303 (tp30) REVERT: K 36 ASP cc_start: 0.7794 (m-30) cc_final: 0.7535 (m-30) REVERT: K 43 GLU cc_start: 0.7844 (tp30) cc_final: 0.7618 (tp30) REVERT: K 86 ARG cc_start: 0.7432 (mmt180) cc_final: 0.7067 (mmt180) REVERT: K 257 GLU cc_start: 0.7646 (tp30) cc_final: 0.7247 (tp30) REVERT: K 287 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8037 (ttp80) REVERT: L 19 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8063 (mtt180) REVERT: L 43 GLU cc_start: 0.7830 (tp30) cc_final: 0.7578 (tp30) REVERT: L 49 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6753 (m-70) REVERT: L 53 LEU cc_start: 0.8576 (mp) cc_final: 0.8307 (mt) REVERT: L 54 ASN cc_start: 0.8452 (m-40) cc_final: 0.8221 (m-40) REVERT: L 167 ASN cc_start: 0.7528 (t0) cc_final: 0.7062 (t0) REVERT: L 168 GLU cc_start: 0.7320 (mp0) cc_final: 0.6834 (mp0) REVERT: L 281 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7857 (tmm160) REVERT: L 295 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7136 (mm-30) outliers start: 167 outliers final: 105 residues processed: 970 average time/residue: 0.7704 time to fit residues: 878.0355 Evaluate side-chains 1012 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 884 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 50 PHE Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain W residue 41 GLN Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 54 ARG Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 37 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 80 PHE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 49 HIS Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 280 optimal weight: 0.0270 chunk 138 optimal weight: 1.9990 chunk 410 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 337 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 412 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 39 GLN C 54 ASN I 54 ASN ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 49 HIS G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN S 41 GLN O 28 ASN N 119 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 49 HIS A 54 ASN A 80 ASN A 267 GLN B 54 ASN B 164 ASN D 80 ASN F 266 HIS H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 80 ASN J 164 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN K 267 GLN L 8 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143208 restraints weight = 45516.379| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.47 r_work: 0.3613 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 35274 Z= 0.123 Angle : 0.561 12.556 47694 Z= 0.277 Chirality : 0.043 0.150 5046 Planarity : 0.004 0.047 6204 Dihedral : 4.593 58.898 4712 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.13 % Allowed : 19.40 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 4164 helix: 2.90 (0.13), residues: 1338 sheet: -0.55 (0.16), residues: 1020 loop : -1.92 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 17 TYR 0.013 0.001 TYR H 35 PHE 0.018 0.001 PHE B 141 TRP 0.008 0.001 TRP I 246 HIS 0.020 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00301 (35274) covalent geometry : angle 0.56148 (47694) hydrogen bonds : bond 0.03319 ( 1425) hydrogen bonds : angle 3.76678 ( 4038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 883 time to evaluate : 1.239 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: C 19 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8271 (mtp180) REVERT: C 43 GLU cc_start: 0.7832 (tp30) cc_final: 0.7544 (tp30) REVERT: C 62 VAL cc_start: 0.4958 (OUTLIER) cc_final: 0.4680 (t) REVERT: C 76 LEU cc_start: 0.8763 (mp) cc_final: 0.8490 (mt) REVERT: C 150 MET cc_start: 0.5439 (ptp) cc_final: 0.5227 (ptp) REVERT: I 43 GLU cc_start: 0.7854 (tp30) cc_final: 0.7448 (tp30) REVERT: I 62 VAL cc_start: 0.4430 (OUTLIER) cc_final: 0.4179 (t) REVERT: I 148 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6716 (mmm) REVERT: I 164 ASN cc_start: 0.8762 (t0) cc_final: 0.8531 (t0) REVERT: I 271 LEU cc_start: 0.7714 (mm) cc_final: 0.7492 (mp) REVERT: G 43 GLU cc_start: 0.7987 (tp30) cc_final: 0.7650 (tp30) REVERT: G 62 VAL cc_start: 0.4184 (OUTLIER) cc_final: 0.3975 (t) REVERT: G 148 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6605 (tmm) REVERT: G 150 MET cc_start: 0.5843 (ptp) cc_final: 0.5534 (ptp) REVERT: G 185 GLU cc_start: 0.7165 (pp20) cc_final: 0.6611 (pp20) REVERT: G 243 ASN cc_start: 0.8070 (t0) cc_final: 0.7753 (t0) REVERT: G 257 GLU cc_start: 0.7628 (tp30) cc_final: 0.7293 (tp30) REVERT: V 38 SER cc_start: 0.8599 (t) cc_final: 0.8356 (t) REVERT: O 12 LEU cc_start: 0.8356 (mt) cc_final: 0.8087 (mt) REVERT: O 80 PHE cc_start: 0.4392 (OUTLIER) cc_final: 0.4189 (t80) REVERT: N 28 ASN cc_start: 0.8422 (t0) cc_final: 0.8208 (t0) REVERT: N 50 SER cc_start: 0.8701 (t) cc_final: 0.8440 (p) REVERT: N 147 PHE cc_start: 0.8297 (m-80) cc_final: 0.7877 (m-80) REVERT: N 150 ASN cc_start: 0.8228 (p0) cc_final: 0.7980 (p0) REVERT: M 66 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7312 (p) REVERT: M 134 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: R 50 SER cc_start: 0.8763 (t) cc_final: 0.8408 (p) REVERT: R 54 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: R 130 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7816 (mmtt) REVERT: Q 147 PHE cc_start: 0.8345 (m-80) cc_final: 0.7950 (m-80) REVERT: Q 150 ASN cc_start: 0.8310 (p0) cc_final: 0.7812 (p0) REVERT: P 80 PHE cc_start: 0.4163 (OUTLIER) cc_final: 0.3898 (t80) REVERT: E 43 GLU cc_start: 0.7975 (tp30) cc_final: 0.7665 (tp30) REVERT: E 62 VAL cc_start: 0.5432 (OUTLIER) cc_final: 0.5194 (t) REVERT: E 173 MET cc_start: 0.7487 (mmt) cc_final: 0.7023 (mtt) REVERT: E 245 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8140 (ttp-110) REVERT: E 257 GLU cc_start: 0.7684 (tp30) cc_final: 0.7422 (tp30) REVERT: A 43 GLU cc_start: 0.7860 (tp30) cc_final: 0.7490 (tp30) REVERT: A 140 TYR cc_start: 0.6797 (m-10) cc_final: 0.6355 (m-80) REVERT: A 269 MET cc_start: 0.6983 (tpt) cc_final: 0.6710 (ttt) REVERT: B 43 GLU cc_start: 0.7933 (tp30) cc_final: 0.7584 (tp30) REVERT: B 47 GLU cc_start: 0.7598 (tt0) cc_final: 0.7302 (tt0) REVERT: B 85 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7368 (p) REVERT: B 127 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7509 (ptm160) REVERT: B 151 MET cc_start: 0.6776 (tmm) cc_final: 0.5819 (ttm) REVERT: B 167 ASN cc_start: 0.7681 (t0) cc_final: 0.7217 (t0) REVERT: B 168 GLU cc_start: 0.7765 (mp0) cc_final: 0.7286 (mp0) REVERT: B 243 ASN cc_start: 0.7747 (t0) cc_final: 0.7380 (t0) REVERT: D 39 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8162 (mp10) REVERT: D 49 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6613 (m170) REVERT: D 62 VAL cc_start: 0.5753 (OUTLIER) cc_final: 0.5478 (t) REVERT: D 167 ASN cc_start: 0.7833 (t0) cc_final: 0.7524 (t0) REVERT: D 242 TYR cc_start: 0.8829 (m-80) cc_final: 0.8522 (m-80) REVERT: D 243 ASN cc_start: 0.7789 (t0) cc_final: 0.7304 (t0) REVERT: D 248 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8545 (mtmt) REVERT: D 257 GLU cc_start: 0.7751 (tp30) cc_final: 0.7422 (tp30) REVERT: D 281 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7838 (tmm160) REVERT: D 283 ILE cc_start: 0.8368 (mt) cc_final: 0.7890 (mt) REVERT: F 19 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8068 (mtt180) REVERT: F 43 GLU cc_start: 0.7918 (tp30) cc_final: 0.7664 (tp30) REVERT: F 148 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5788 (mmm) REVERT: F 150 MET cc_start: 0.4057 (ptp) cc_final: 0.3775 (ptp) REVERT: F 167 ASN cc_start: 0.7792 (t0) cc_final: 0.7177 (t0) REVERT: F 270 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: F 295 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6993 (mm-30) REVERT: H 43 GLU cc_start: 0.7947 (tp30) cc_final: 0.7606 (tp30) REVERT: H 242 TYR cc_start: 0.8929 (m-80) cc_final: 0.8620 (m-80) REVERT: H 243 ASN cc_start: 0.7839 (t0) cc_final: 0.7495 (t0) REVERT: H 244 ASN cc_start: 0.8414 (t0) cc_final: 0.8117 (t0) REVERT: H 257 GLU cc_start: 0.7649 (tp30) cc_final: 0.7338 (tp30) REVERT: J 27 VAL cc_start: 0.7264 (OUTLIER) cc_final: 0.6907 (t) REVERT: J 28 GLU cc_start: 0.6648 (mp0) cc_final: 0.6388 (mp0) REVERT: J 62 VAL cc_start: 0.5898 (OUTLIER) cc_final: 0.5626 (t) REVERT: J 127 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7366 (ptm160) REVERT: J 167 ASN cc_start: 0.7138 (t0) cc_final: 0.6890 (t0) REVERT: J 242 TYR cc_start: 0.8874 (m-80) cc_final: 0.8262 (m-80) REVERT: J 257 GLU cc_start: 0.7720 (tp30) cc_final: 0.7251 (tp30) REVERT: K 36 ASP cc_start: 0.7787 (m-30) cc_final: 0.7519 (m-30) REVERT: K 43 GLU cc_start: 0.7858 (tp30) cc_final: 0.7612 (tp30) REVERT: K 257 GLU cc_start: 0.7651 (tp30) cc_final: 0.7251 (tp30) REVERT: L 19 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8031 (mtt180) REVERT: L 43 GLU cc_start: 0.7825 (tp30) cc_final: 0.7580 (tp30) REVERT: L 53 LEU cc_start: 0.8555 (mp) cc_final: 0.8275 (mt) REVERT: L 54 ASN cc_start: 0.8440 (m-40) cc_final: 0.8227 (m-40) REVERT: L 167 ASN cc_start: 0.7517 (t0) cc_final: 0.7042 (t0) REVERT: L 168 GLU cc_start: 0.7320 (mp0) cc_final: 0.6836 (mp0) REVERT: L 281 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7801 (tmm160) REVERT: L 295 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7059 (mm-30) outliers start: 151 outliers final: 98 residues processed: 964 average time/residue: 0.7527 time to fit residues: 855.8721 Evaluate side-chains 989 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 868 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 37 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 80 PHE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 142 MET Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 10 optimal weight: 40.0000 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 341 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 168 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 39 GLN C 280 GLN I 54 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 49 HIS G 54 ASN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN S 41 GLN O 28 ASN N 119 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN Q 28 ASN Q 38 ASN Q 119 ASN ** Q 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 49 HIS A 54 ASN A 80 ASN A 267 GLN B 54 ASN B 164 ASN D 80 ASN F 39 GLN H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 80 ASN J 164 ASN J 244 ASN J 259 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN K 267 GLN L 8 ASN L 49 HIS L 164 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.178975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142132 restraints weight = 45494.839| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.48 r_work: 0.3604 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 35274 Z= 0.175 Angle : 0.595 15.369 47694 Z= 0.292 Chirality : 0.044 0.166 5046 Planarity : 0.004 0.044 6204 Dihedral : 4.643 59.236 4711 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.32 % Allowed : 19.46 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 4164 helix: 2.86 (0.13), residues: 1338 sheet: -0.50 (0.16), residues: 1020 loop : -1.89 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 17 TYR 0.011 0.001 TYR F 48 PHE 0.019 0.001 PHE L 141 TRP 0.009 0.001 TRP I 246 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00434 (35274) covalent geometry : angle 0.59531 (47694) hydrogen bonds : bond 0.03622 ( 1425) hydrogen bonds : angle 3.77916 ( 4038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 882 time to evaluate : 0.810 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: C 19 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8287 (mtp180) REVERT: C 43 GLU cc_start: 0.7858 (tp30) cc_final: 0.7558 (tp30) REVERT: C 62 VAL cc_start: 0.4968 (OUTLIER) cc_final: 0.4687 (t) REVERT: C 76 LEU cc_start: 0.8775 (mp) cc_final: 0.8524 (mt) REVERT: I 43 GLU cc_start: 0.7878 (tp30) cc_final: 0.7452 (tp30) REVERT: I 62 VAL cc_start: 0.4528 (OUTLIER) cc_final: 0.4264 (t) REVERT: I 76 LEU cc_start: 0.8721 (mp) cc_final: 0.8459 (mt) REVERT: I 148 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6751 (mmm) REVERT: I 154 MET cc_start: 0.5929 (pp-130) cc_final: 0.5530 (pp-130) REVERT: I 164 ASN cc_start: 0.8773 (t0) cc_final: 0.8528 (t0) REVERT: G 43 GLU cc_start: 0.8015 (tp30) cc_final: 0.7652 (tp30) REVERT: G 50 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.4717 (p90) REVERT: G 62 VAL cc_start: 0.4224 (OUTLIER) cc_final: 0.4016 (t) REVERT: G 148 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6575 (tmm) REVERT: G 150 MET cc_start: 0.5822 (ptp) cc_final: 0.5541 (ptp) REVERT: G 185 GLU cc_start: 0.7158 (pp20) cc_final: 0.6564 (pp20) REVERT: G 243 ASN cc_start: 0.8077 (t0) cc_final: 0.7775 (t0) REVERT: G 257 GLU cc_start: 0.7670 (tp30) cc_final: 0.7327 (tp30) REVERT: V 38 SER cc_start: 0.8617 (t) cc_final: 0.8367 (t) REVERT: O 80 PHE cc_start: 0.4490 (OUTLIER) cc_final: 0.4264 (t80) REVERT: N 28 ASN cc_start: 0.8422 (t0) cc_final: 0.8202 (t0) REVERT: N 50 SER cc_start: 0.8743 (t) cc_final: 0.8452 (p) REVERT: N 147 PHE cc_start: 0.8316 (m-80) cc_final: 0.7891 (m-80) REVERT: N 150 ASN cc_start: 0.8260 (p0) cc_final: 0.8000 (p0) REVERT: M 66 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7307 (p) REVERT: M 134 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: R 50 SER cc_start: 0.8749 (t) cc_final: 0.8425 (p) REVERT: R 54 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7796 (mtp85) REVERT: R 130 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7883 (mmtt) REVERT: R 131 GLU cc_start: 0.7372 (pm20) cc_final: 0.7129 (pm20) REVERT: R 150 ASN cc_start: 0.8506 (p0) cc_final: 0.8296 (p0) REVERT: Q 147 PHE cc_start: 0.8352 (m-80) cc_final: 0.7942 (m-80) REVERT: P 54 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8402 (mtt-85) REVERT: P 80 PHE cc_start: 0.4254 (OUTLIER) cc_final: 0.3978 (t80) REVERT: E 43 GLU cc_start: 0.7984 (tp30) cc_final: 0.7663 (tp30) REVERT: E 62 VAL cc_start: 0.5521 (OUTLIER) cc_final: 0.5273 (t) REVERT: E 173 MET cc_start: 0.7550 (mmt) cc_final: 0.7067 (mtt) REVERT: E 245 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8170 (ttp-110) REVERT: E 257 GLU cc_start: 0.7660 (tp30) cc_final: 0.7428 (tp30) REVERT: A 43 GLU cc_start: 0.7878 (tp30) cc_final: 0.7486 (tp30) REVERT: A 140 TYR cc_start: 0.6821 (m-10) cc_final: 0.6372 (m-80) REVERT: A 269 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6650 (ttt) REVERT: B 43 GLU cc_start: 0.7966 (tp30) cc_final: 0.7590 (tp30) REVERT: B 47 GLU cc_start: 0.7641 (tt0) cc_final: 0.7339 (tt0) REVERT: B 85 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7363 (p) REVERT: B 127 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7553 (ptm160) REVERT: B 151 MET cc_start: 0.6820 (tmm) cc_final: 0.5913 (ttm) REVERT: B 167 ASN cc_start: 0.7687 (t0) cc_final: 0.7218 (t0) REVERT: B 168 GLU cc_start: 0.7779 (mp0) cc_final: 0.7305 (mp0) REVERT: B 185 GLU cc_start: 0.7333 (pp20) cc_final: 0.6994 (pp20) REVERT: B 243 ASN cc_start: 0.7758 (t0) cc_final: 0.7415 (t0) REVERT: D 8 ASN cc_start: 0.8259 (p0) cc_final: 0.7991 (p0) REVERT: D 39 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8146 (mp10) REVERT: D 49 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6681 (m170) REVERT: D 62 VAL cc_start: 0.5779 (OUTLIER) cc_final: 0.5503 (t) REVERT: D 167 ASN cc_start: 0.7840 (t0) cc_final: 0.7581 (t0) REVERT: D 242 TYR cc_start: 0.8825 (m-80) cc_final: 0.8528 (m-80) REVERT: D 243 ASN cc_start: 0.7788 (t0) cc_final: 0.7332 (t0) REVERT: D 257 GLU cc_start: 0.7763 (tp30) cc_final: 0.7435 (tp30) REVERT: D 281 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7908 (tmm160) REVERT: D 283 ILE cc_start: 0.8371 (mt) cc_final: 0.7881 (mt) REVERT: F 19 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8115 (mtt180) REVERT: F 43 GLU cc_start: 0.7931 (tp30) cc_final: 0.7670 (tp30) REVERT: F 148 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5803 (mmm) REVERT: F 150 MET cc_start: 0.4129 (ptp) cc_final: 0.3858 (ptp) REVERT: F 167 ASN cc_start: 0.7772 (t0) cc_final: 0.7158 (t0) REVERT: F 270 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: F 295 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7043 (mm-30) REVERT: H 43 GLU cc_start: 0.7952 (tp30) cc_final: 0.7602 (tp30) REVERT: H 138 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5863 (pp) REVERT: H 242 TYR cc_start: 0.8945 (m-80) cc_final: 0.8680 (m-80) REVERT: H 243 ASN cc_start: 0.7849 (t0) cc_final: 0.7496 (t0) REVERT: H 244 ASN cc_start: 0.8426 (t0) cc_final: 0.8122 (t0) REVERT: H 257 GLU cc_start: 0.7671 (tp30) cc_final: 0.7362 (tp30) REVERT: J 27 VAL cc_start: 0.7368 (OUTLIER) cc_final: 0.7047 (t) REVERT: J 28 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: J 62 VAL cc_start: 0.5961 (OUTLIER) cc_final: 0.5690 (t) REVERT: J 127 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7428 (ptm160) REVERT: J 167 ASN cc_start: 0.7111 (t0) cc_final: 0.6856 (t0) REVERT: K 36 ASP cc_start: 0.7794 (m-30) cc_final: 0.7528 (m-30) REVERT: K 43 GLU cc_start: 0.7861 (tp30) cc_final: 0.7598 (tp30) REVERT: K 257 GLU cc_start: 0.7678 (tp30) cc_final: 0.7272 (tp30) REVERT: L 19 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8051 (mtt180) REVERT: L 43 GLU cc_start: 0.7851 (tp30) cc_final: 0.7593 (tp30) REVERT: L 53 LEU cc_start: 0.8556 (mp) cc_final: 0.8305 (mt) REVERT: L 167 ASN cc_start: 0.7518 (t0) cc_final: 0.7037 (t0) REVERT: L 168 GLU cc_start: 0.7330 (mp0) cc_final: 0.6849 (mp0) REVERT: L 281 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7854 (tmm160) REVERT: L 295 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7074 (mm-30) outliers start: 158 outliers final: 106 residues processed: 969 average time/residue: 0.7297 time to fit residues: 833.2456 Evaluate side-chains 1007 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 874 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 50 PHE Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 37 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 80 PHE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 59 optimal weight: 0.9990 chunk 160 optimal weight: 0.0060 chunk 234 optimal weight: 0.8980 chunk 397 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 390 optimal weight: 0.2980 chunk 351 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 ASN C 7 GLN C 8 ASN C 39 GLN C 54 ASN C 164 ASN I 54 ASN ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 49 HIS G 54 ASN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN S 41 GLN O 28 ASN O 38 ASN N 38 ASN N 119 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** Q 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 49 HIS A 54 ASN A 80 ASN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 49 HIS B 54 ASN B 164 ASN D 80 ASN H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 80 ASN J 164 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 GLN L 8 ASN L 39 GLN L 54 ASN L 164 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.179926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143208 restraints weight = 45481.530| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.48 r_work: 0.3615 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35274 Z= 0.129 Angle : 0.577 14.388 47694 Z= 0.283 Chirality : 0.043 0.166 5046 Planarity : 0.004 0.042 6204 Dihedral : 4.599 59.310 4711 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.08 % Allowed : 19.95 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 4164 helix: 2.92 (0.13), residues: 1338 sheet: -0.49 (0.16), residues: 1020 loop : -1.83 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 287 TYR 0.021 0.001 TYR L 69 PHE 0.018 0.001 PHE L 141 TRP 0.008 0.001 TRP C 246 HIS 0.005 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00320 (35274) covalent geometry : angle 0.57696 (47694) hydrogen bonds : bond 0.03317 ( 1425) hydrogen bonds : angle 3.75026 ( 4038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 890 time to evaluate : 1.278 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: C 43 GLU cc_start: 0.7859 (tp30) cc_final: 0.7559 (tp30) REVERT: C 62 VAL cc_start: 0.4962 (OUTLIER) cc_final: 0.4680 (t) REVERT: C 76 LEU cc_start: 0.8787 (mp) cc_final: 0.8514 (mt) REVERT: I 43 GLU cc_start: 0.7882 (tp30) cc_final: 0.7463 (tp30) REVERT: I 62 VAL cc_start: 0.4519 (OUTLIER) cc_final: 0.4262 (t) REVERT: I 148 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6752 (mmm) REVERT: I 154 MET cc_start: 0.5977 (pp-130) cc_final: 0.5577 (pp-130) REVERT: I 164 ASN cc_start: 0.8795 (t0) cc_final: 0.8559 (t0) REVERT: I 271 LEU cc_start: 0.7670 (mm) cc_final: 0.7466 (mp) REVERT: G 43 GLU cc_start: 0.7990 (tp30) cc_final: 0.7644 (tp30) REVERT: G 62 VAL cc_start: 0.4229 (OUTLIER) cc_final: 0.4026 (t) REVERT: G 148 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6570 (tmm) REVERT: G 150 MET cc_start: 0.5794 (ptp) cc_final: 0.5493 (ptp) REVERT: G 185 GLU cc_start: 0.7170 (pp20) cc_final: 0.6601 (pp20) REVERT: G 242 TYR cc_start: 0.8851 (m-80) cc_final: 0.8417 (m-80) REVERT: G 243 ASN cc_start: 0.8055 (t0) cc_final: 0.7742 (t0) REVERT: G 257 GLU cc_start: 0.7683 (tp30) cc_final: 0.7339 (tp30) REVERT: V 38 SER cc_start: 0.8616 (t) cc_final: 0.8371 (t) REVERT: U 66 ARG cc_start: 0.8749 (ptt-90) cc_final: 0.8431 (ptt180) REVERT: O 80 PHE cc_start: 0.4417 (OUTLIER) cc_final: 0.4214 (t80) REVERT: O 85 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8206 (ttpp) REVERT: N 28 ASN cc_start: 0.8426 (t0) cc_final: 0.8208 (t0) REVERT: N 50 SER cc_start: 0.8735 (t) cc_final: 0.8445 (p) REVERT: N 147 PHE cc_start: 0.8305 (m-80) cc_final: 0.7885 (m-80) REVERT: N 150 ASN cc_start: 0.8305 (p0) cc_final: 0.8038 (p0) REVERT: M 66 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7293 (p) REVERT: M 134 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: R 50 SER cc_start: 0.8779 (t) cc_final: 0.8428 (p) REVERT: R 54 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7790 (mtp85) REVERT: R 131 GLU cc_start: 0.7384 (pm20) cc_final: 0.7126 (pm20) REVERT: Q 147 PHE cc_start: 0.8336 (m-80) cc_final: 0.7920 (m-80) REVERT: P 80 PHE cc_start: 0.4214 (OUTLIER) cc_final: 0.3953 (t80) REVERT: E 18 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8483 (mtm110) REVERT: E 43 GLU cc_start: 0.7986 (tp30) cc_final: 0.7665 (tp30) REVERT: E 62 VAL cc_start: 0.5538 (OUTLIER) cc_final: 0.5294 (t) REVERT: E 173 MET cc_start: 0.7541 (mmt) cc_final: 0.7049 (mtt) REVERT: E 257 GLU cc_start: 0.7661 (tp30) cc_final: 0.7431 (tp30) REVERT: A 43 GLU cc_start: 0.7862 (tp30) cc_final: 0.7483 (tp30) REVERT: A 140 TYR cc_start: 0.6810 (m-10) cc_final: 0.6360 (m-80) REVERT: A 265 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8172 (mmt180) REVERT: A 269 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6615 (ttt) REVERT: B 43 GLU cc_start: 0.7935 (tp30) cc_final: 0.7576 (tp30) REVERT: B 47 GLU cc_start: 0.7616 (tt0) cc_final: 0.7332 (tt0) REVERT: B 85 THR cc_start: 0.7686 (OUTLIER) cc_final: 0.7374 (p) REVERT: B 127 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7523 (ptm160) REVERT: B 151 MET cc_start: 0.6879 (tmm) cc_final: 0.6036 (ttm) REVERT: B 167 ASN cc_start: 0.7644 (t0) cc_final: 0.7206 (t0) REVERT: B 168 GLU cc_start: 0.7765 (mp0) cc_final: 0.7290 (mp0) REVERT: B 185 GLU cc_start: 0.7335 (pp20) cc_final: 0.6990 (pp20) REVERT: B 243 ASN cc_start: 0.7749 (t0) cc_final: 0.7398 (t0) REVERT: D 39 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8153 (mp10) REVERT: D 49 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6648 (m170) REVERT: D 62 VAL cc_start: 0.5765 (OUTLIER) cc_final: 0.5488 (t) REVERT: D 167 ASN cc_start: 0.7832 (t0) cc_final: 0.7551 (t0) REVERT: D 242 TYR cc_start: 0.8832 (m-80) cc_final: 0.8486 (m-80) REVERT: D 243 ASN cc_start: 0.7831 (t0) cc_final: 0.7371 (t0) REVERT: D 257 GLU cc_start: 0.7767 (tp30) cc_final: 0.7433 (tp30) REVERT: D 281 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7841 (tmm160) REVERT: D 283 ILE cc_start: 0.8350 (mt) cc_final: 0.7863 (mt) REVERT: F 19 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8102 (mtt180) REVERT: F 43 GLU cc_start: 0.7932 (tp30) cc_final: 0.7681 (tp30) REVERT: F 148 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5778 (mmm) REVERT: F 150 MET cc_start: 0.4112 (ptp) cc_final: 0.3845 (ptp) REVERT: F 167 ASN cc_start: 0.7756 (t0) cc_final: 0.7137 (t0) REVERT: F 270 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: F 295 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7032 (mm-30) REVERT: H 43 GLU cc_start: 0.7969 (tp30) cc_final: 0.7623 (tp30) REVERT: H 138 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5837 (pp) REVERT: H 242 TYR cc_start: 0.8938 (m-80) cc_final: 0.8719 (m-80) REVERT: H 243 ASN cc_start: 0.7844 (t0) cc_final: 0.7490 (t0) REVERT: H 244 ASN cc_start: 0.8411 (t0) cc_final: 0.8134 (t0) REVERT: H 257 GLU cc_start: 0.7679 (tp30) cc_final: 0.7361 (tp30) REVERT: J 27 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7107 (t) REVERT: J 28 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: J 62 VAL cc_start: 0.5928 (OUTLIER) cc_final: 0.5654 (t) REVERT: J 127 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7442 (ptm160) REVERT: J 141 PHE cc_start: 0.7361 (t80) cc_final: 0.7160 (t80) REVERT: J 167 ASN cc_start: 0.7040 (t0) cc_final: 0.6779 (t0) REVERT: J 242 TYR cc_start: 0.8868 (m-80) cc_final: 0.8254 (m-80) REVERT: K 36 ASP cc_start: 0.7781 (m-30) cc_final: 0.7510 (m-30) REVERT: K 43 GLU cc_start: 0.7861 (tp30) cc_final: 0.7601 (tp30) REVERT: K 257 GLU cc_start: 0.7663 (tp30) cc_final: 0.7261 (tp30) REVERT: L 19 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8019 (mtt180) REVERT: L 43 GLU cc_start: 0.7850 (tp30) cc_final: 0.7596 (tp30) REVERT: L 53 LEU cc_start: 0.8553 (mp) cc_final: 0.8326 (mt) REVERT: L 167 ASN cc_start: 0.7515 (t0) cc_final: 0.7028 (t0) REVERT: L 168 GLU cc_start: 0.7330 (mp0) cc_final: 0.6845 (mp0) REVERT: L 281 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7800 (tmm160) outliers start: 149 outliers final: 101 residues processed: 973 average time/residue: 0.7600 time to fit residues: 871.9278 Evaluate side-chains 1004 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 878 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 37 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 80 PHE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 178 LYS Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 180 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 352 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 26 ASN C 39 GLN C 54 ASN I 26 ASN I 54 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN G 49 HIS G 54 ASN G 80 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 41 GLN O 28 ASN O 38 ASN N 119 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN A 49 HIS A 54 ASN A 80 ASN A 267 GLN B 54 ASN B 164 ASN F 39 GLN H 39 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 80 ASN J 164 ASN J 244 ASN J 259 ASN ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN K 267 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142179 restraints weight = 45357.207| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.47 r_work: 0.3606 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 35274 Z= 0.164 Angle : 0.596 12.827 47694 Z= 0.293 Chirality : 0.044 0.182 5046 Planarity : 0.004 0.046 6204 Dihedral : 4.632 59.412 4711 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.11 % Allowed : 20.20 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 4164 helix: 2.87 (0.13), residues: 1338 sheet: -0.45 (0.16), residues: 1020 loop : -1.81 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 287 TYR 0.019 0.001 TYR C 4 PHE 0.019 0.001 PHE B 141 TRP 0.009 0.001 TRP C 246 HIS 0.005 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00408 (35274) covalent geometry : angle 0.59561 (47694) hydrogen bonds : bond 0.03489 ( 1425) hydrogen bonds : angle 3.76463 ( 4038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15456.56 seconds wall clock time: 262 minutes 51.11 seconds (15771.11 seconds total)