Starting phenix.real_space_refine on Wed Aug 27 03:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bgo_7098/08_2025/6bgo_7098_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bgo_7098/08_2025/6bgo_7098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bgo_7098/08_2025/6bgo_7098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bgo_7098/08_2025/6bgo_7098.map" model { file = "/net/cci-nas-00/data/ceres_data/6bgo_7098/08_2025/6bgo_7098_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bgo_7098/08_2025/6bgo_7098_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 112 5.16 5 C 29149 2.51 5 N 8249 2.21 5 O 8990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46500 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "F" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "I" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "J" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Q" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "R" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "S" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "T" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "V" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "W" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "X" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Y" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Z" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "b" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 10.41, per 1000 atoms: 0.22 Number of scatterers: 46500 At special positions: 0 Unit cell: (138.43, 147.15, 178.76, 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 112 16.00 O 8990 8.00 N 8249 7.00 C 29149 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 1.2 microseconds 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11206 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 72 sheets defined 47.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 114 Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR C 84 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 95 through 114 Processing helix chain 'C' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 114 Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.910A pdb=" N LEU D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 95 through 114 Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU F 230 " --> pdb=" O THR F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.612A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU G 230 " --> pdb=" O THR G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 26 Processing helix chain 'H' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 Processing helix chain 'H' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.612A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 Processing helix chain 'I' and resid 226 through 234 removed outlier: 3.910A pdb=" N LEU I 230 " --> pdb=" O THR I 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 26 Processing helix chain 'J' and resid 67 through 89 removed outlier: 3.517A pdb=" N THR J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 Processing helix chain 'J' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU J 230 " --> pdb=" O THR J 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 26 Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.517A pdb=" N THR K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 removed outlier: 3.514A pdb=" N THR L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 26 Processing helix chain 'M' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR M 84 " --> pdb=" O GLN M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU M 230 " --> pdb=" O THR M 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 26 Processing helix chain 'N' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR N 84 " --> pdb=" O GLN N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 95 through 114 Processing helix chain 'N' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE N 163 " --> pdb=" O THR N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 226 through 234 removed outlier: 3.910A pdb=" N LEU N 230 " --> pdb=" O THR N 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 26 Processing helix chain 'O' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU O 230 " --> pdb=" O THR O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 396 Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 390 Processing helix chain 'Q' and resid 390 through 396 Processing helix chain 'Q' and resid 413 through 416 Processing helix chain 'Q' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 396 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 396 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 390 Processing helix chain 'T' and resid 390 through 396 Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 396 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 396 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 390 Processing helix chain 'X' and resid 390 through 396 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 457 No H-bonds generated for 'chain 'X' and resid 455 through 457' Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 4.022A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 390 Processing helix chain 'Z' and resid 390 through 396 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.835A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.835A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 4.022A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 138 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.496A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 138 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 138 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB4, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU H 138 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 153 through 156 Processing sheet with id=AC6, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 153 through 156 Processing sheet with id=AC8, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 153 through 156 Processing sheet with id=AD1, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AD3, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.493A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 436 through 439 Processing sheet with id=AD5, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 436 through 439 Processing sheet with id=AD8, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.386A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 436 through 439 Processing sheet with id=AE2, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 436 through 439 Processing sheet with id=AE5, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 436 through 439 Processing sheet with id=AE8, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.386A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 436 through 439 Processing sheet with id=AF2, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.497A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 436 through 439 Processing sheet with id=AF5, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.494A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 436 through 439 Processing sheet with id=AF8, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 436 through 439 Processing sheet with id=AG2, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER X 320 " --> pdb=" O SER X 327 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR X 341 " --> pdb=" O THR X 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 436 through 439 Processing sheet with id=AG5, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.386A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 436 through 439 Processing sheet with id=AG8, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER Z 320 " --> pdb=" O SER Z 327 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR Z 341 " --> pdb=" O THR Z 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'a' and resid 436 through 439 Processing sheet with id=AH2, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 436 through 439 Processing sheet with id=AH5, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'c' and resid 436 through 439 Processing sheet with id=AH8, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.383A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.494A pdb=" N THR c 341 " --> pdb=" O THR c 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) 3080 hydrogen bonds defined for protein. 8778 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: 12.57 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8052 1.31 - 1.44: 11973 1.44 - 1.56: 26937 1.56 - 1.69: 14 1.69 - 1.81: 210 Bond restraints: 47186 Sorted by residual: bond pdb=" C ILE O 110 " pdb=" O ILE O 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.73e+01 bond pdb=" C ILE A 110 " pdb=" O ILE A 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.72e+01 bond pdb=" C ILE H 110 " pdb=" O ILE H 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.69e+01 bond pdb=" C ILE L 110 " pdb=" O ILE L 110 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.13e-02 7.83e+03 1.69e+01 bond pdb=" C ILE E 110 " pdb=" O ILE E 110 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.13e-02 7.83e+03 1.69e+01 ... (remaining 47181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 63121 3.31 - 6.62: 700 6.62 - 9.93: 36 9.93 - 13.24: 14 13.24 - 16.55: 1 Bond angle restraints: 63872 Sorted by residual: angle pdb=" N PRO K 4 " pdb=" CA PRO K 4 " pdb=" CB PRO K 4 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" N PRO J 4 " pdb=" CA PRO J 4 " pdb=" CB PRO J 4 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N GLY O 227 " pdb=" CA GLY O 227 " pdb=" C GLY O 227 " ideal model delta sigma weight residual 111.50 123.19 -11.69 1.74e+00 3.30e-01 4.51e+01 angle pdb=" N GLY M 227 " pdb=" CA GLY M 227 " pdb=" C GLY M 227 " ideal model delta sigma weight residual 111.50 123.18 -11.68 1.74e+00 3.30e-01 4.50e+01 angle pdb=" N GLY J 227 " pdb=" CA GLY J 227 " pdb=" C GLY J 227 " ideal model delta sigma weight residual 111.50 123.18 -11.68 1.74e+00 3.30e-01 4.50e+01 ... (remaining 63867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 26434 17.23 - 34.47: 1450 34.47 - 51.70: 340 51.70 - 68.93: 127 68.93 - 86.16: 56 Dihedral angle restraints: 28407 sinusoidal: 10807 harmonic: 17600 Sorted by residual: dihedral pdb=" CA THR R 321 " pdb=" C THR R 321 " pdb=" N GLN R 322 " pdb=" CA GLN R 322 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR W 321 " pdb=" C THR W 321 " pdb=" N GLN W 322 " pdb=" CA GLN W 322 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR b 321 " pdb=" C THR b 321 " pdb=" N GLN b 322 " pdb=" CA GLN b 322 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 28404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6023 0.067 - 0.135: 1069 0.135 - 0.202: 144 0.202 - 0.269: 25 0.269 - 0.336: 14 Chirality restraints: 7275 Sorted by residual: chirality pdb=" CA GLN I 114 " pdb=" N GLN I 114 " pdb=" C GLN I 114 " pdb=" CB GLN I 114 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN F 114 " pdb=" N GLN F 114 " pdb=" C GLN F 114 " pdb=" CB GLN F 114 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA GLN G 114 " pdb=" N GLN G 114 " pdb=" C GLN G 114 " pdb=" CB GLN G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 7272 not shown) Planarity restraints: 8424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.096 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO L 9 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 8 " -0.065 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO A 9 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 111 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PHE J 111 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE J 111 " 0.021 2.00e-02 2.50e+03 pdb=" N THR J 112 " 0.019 2.00e-02 2.50e+03 ... (remaining 8421 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.98: 25 1.98 - 2.71: 1842 2.71 - 3.44: 65870 3.44 - 4.17: 104288 4.17 - 4.90: 190256 Nonbonded interactions: 362281 Sorted by model distance: nonbonded pdb=" NH2 ARG D 135 " pdb=" NH1 ARG E 48 " model vdw 1.245 3.200 nonbonded pdb=" NH2 ARG E 135 " pdb=" NH1 ARG F 48 " model vdw 1.289 3.200 nonbonded pdb=" O GLY I 66 " pdb=" O LEU h 174 " model vdw 1.410 3.040 nonbonded pdb=" O GLY F 66 " pdb=" O LEU e 174 " model vdw 1.429 3.040 nonbonded pdb=" NH2 ARG C 135 " pdb=" NH1 ARG D 48 " model vdw 1.485 3.200 ... (remaining 362276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 234) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = (chain 'J' and resid 8 through 234) selection = (chain 'K' and resid 8 through 234) selection = (chain 'L' and resid 8 through 234) selection = (chain 'M' and resid 8 through 234) selection = (chain 'N' and resid 8 through 234) selection = (chain 'O' and resid 8 through 234) } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.530 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 44.350 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.311 47187 Z= 0.396 Angle : 0.987 16.548 63872 Z= 0.614 Chirality : 0.054 0.336 7275 Planarity : 0.007 0.150 8424 Dihedral : 12.926 86.163 17201 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 1.01 % Allowed : 5.00 % Favored : 93.99 % 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 aren not related in a simple way. whole: -0.26 (0.11), residues: 6072 helix: 0.80 (0.11), residues: 2541 sheet: -0.71 (0.12), residues: 1526 loop : -0.80 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 217 TYR 0.015 0.002 TYR F 139 PHE 0.030 0.004 PHE F 68 TRP 0.005 0.002 TRP c 429 HIS 0.006 0.001 HIS P 365 Details of bonding type rmsd covalent geometry : bond 0.00685 (47186) covalent geometry : angle 0.98707 (63872) hydrogen bonds : bond 0.13489 ( 3074) hydrogen bonds : angle 6.89341 ( 8778) Misc. bond : bond 0.31071 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 973 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 PHE cc_start: 0.7780 (m-80) cc_final: 0.7562 (m-80) REVERT: D 118 TYR cc_start: 0.7936 (m-10) cc_final: 0.7215 (m-80) REVERT: E 143 TYR cc_start: 0.6627 (p90) cc_final: 0.6418 (p90) REVERT: E 147 ILE cc_start: 0.6938 (pt) cc_final: 0.6564 (pt) REVERT: G 163 ILE cc_start: 0.7196 (mt) cc_final: 0.6920 (mt) REVERT: H 45 ASN cc_start: 0.6236 (t0) cc_final: 0.5911 (t0) REVERT: H 122 LEU cc_start: 0.8860 (mt) cc_final: 0.8408 (mp) REVERT: H 147 ILE cc_start: 0.7946 (pt) cc_final: 0.7429 (pt) REVERT: H 209 GLU cc_start: 0.5404 (tt0) cc_final: 0.5008 (tt0) REVERT: J 41 PHE cc_start: 0.8232 (m-80) cc_final: 0.8012 (m-80) REVERT: L 58 ASP cc_start: 0.8973 (m-30) cc_final: 0.8683 (t70) REVERT: M 118 TYR cc_start: 0.7993 (m-10) cc_final: 0.7789 (m-80) REVERT: M 163 ILE cc_start: 0.8134 (mt) cc_final: 0.7702 (mt) REVERT: N 52 LYS cc_start: 0.8747 (mttt) cc_final: 0.8529 (mtpt) REVERT: N 121 GLU cc_start: 0.8827 (tt0) cc_final: 0.8508 (tp30) REVERT: O 156 MET cc_start: 0.7996 (mtm) cc_final: 0.7103 (mtm) REVERT: Q 376 PHE cc_start: 0.7961 (t80) cc_final: 0.7516 (t80) REVERT: Q 432 GLU cc_start: 0.8325 (tp30) cc_final: 0.8050 (tm-30) REVERT: S 447 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8203 (ttmm) REVERT: S 450 MET cc_start: 0.7312 (mtm) cc_final: 0.7054 (mtm) REVERT: V 376 PHE cc_start: 0.7898 (t80) cc_final: 0.7564 (t80) REVERT: V 380 ILE cc_start: 0.9258 (mt) cc_final: 0.8968 (mt) REVERT: Z 308 TYR cc_start: 0.8262 (p90) cc_final: 0.7868 (p90) REVERT: Z 390 ASN cc_start: 0.8168 (t0) cc_final: 0.7935 (t0) REVERT: a 390 ASN cc_start: 0.7982 (t0) cc_final: 0.7546 (t0) REVERT: b 376 PHE cc_start: 0.8113 (t80) cc_final: 0.7853 (t80) REVERT: b 383 LEU cc_start: 0.9189 (tp) cc_final: 0.8892 (tp) outliers start: 47 outliers final: 11 residues processed: 1008 average time/residue: 0.2786 time to fit residues: 452.5522 Evaluate side-chains 433 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 422 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 597 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN J 231 GLN K 11 GLN K 231 GLN L 105 GLN L 231 GLN O 11 GLN R 456 GLN S 456 GLN U 456 GLN V 456 GLN Y 456 GLN Z 396 GLN a 456 GLN b 456 GLN c 456 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.040749 restraints weight = 270326.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.042140 restraints weight = 179920.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043120 restraints weight = 134074.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043922 restraints weight = 107485.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.044480 restraints weight = 90340.415| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 47187 Z= 0.171 Angle : 0.614 7.717 63872 Z= 0.338 Chirality : 0.044 0.208 7275 Planarity : 0.005 0.067 8424 Dihedral : 4.631 85.229 6877 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % 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 aren not related in a simple way. whole: 1.06 (0.11), residues: 6072 helix: 2.08 (0.10), residues: 2583 sheet: 0.05 (0.13), residues: 1534 loop : -0.55 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 14 TYR 0.022 0.002 TYR J 57 PHE 0.037 0.002 PHE N 71 TRP 0.006 0.001 TRP b 429 HIS 0.005 0.001 HIS N 129 Details of bonding type rmsd covalent geometry : bond 0.00353 (47186) covalent geometry : angle 0.61355 (63872) hydrogen bonds : bond 0.04692 ( 3074) hydrogen bonds : angle 4.68488 ( 8778) Misc. bond : bond 0.00284 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 539 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.9000 (m-80) cc_final: 0.8714 (m-80) REVERT: C 41 PHE cc_start: 0.9448 (m-80) cc_final: 0.9243 (m-80) REVERT: C 56 LEU cc_start: 0.8975 (tp) cc_final: 0.8743 (tp) REVERT: C 58 ASP cc_start: 0.8354 (m-30) cc_final: 0.8067 (m-30) REVERT: C 130 TYR cc_start: 0.8264 (t80) cc_final: 0.7963 (t80) REVERT: D 58 ASP cc_start: 0.8948 (p0) cc_final: 0.8637 (p0) REVERT: D 71 PHE cc_start: 0.9564 (p90) cc_final: 0.9278 (p90) REVERT: D 149 ASP cc_start: 0.8789 (p0) cc_final: 0.8316 (p0) REVERT: E 90 ASP cc_start: 0.8706 (t70) cc_final: 0.8437 (t70) REVERT: E 93 ASP cc_start: 0.9194 (m-30) cc_final: 0.8788 (m-30) REVERT: E 98 GLN cc_start: 0.9096 (mt0) cc_final: 0.8778 (mt0) REVERT: E 105 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8822 (tm-30) REVERT: E 118 TYR cc_start: 0.8445 (m-80) cc_final: 0.8103 (m-80) REVERT: E 130 TYR cc_start: 0.8653 (t80) cc_final: 0.8141 (t80) REVERT: E 143 TYR cc_start: 0.7748 (p90) cc_final: 0.7196 (p90) REVERT: F 72 ASP cc_start: 0.9073 (t70) cc_final: 0.8708 (m-30) REVERT: F 93 ASP cc_start: 0.9066 (m-30) cc_final: 0.8561 (m-30) REVERT: G 24 ILE cc_start: 0.9278 (pt) cc_final: 0.9002 (pt) REVERT: G 28 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7463 (mmmm) REVERT: G 57 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7485 (t80) REVERT: G 156 MET cc_start: 0.7308 (ttm) cc_final: 0.6991 (ttm) REVERT: H 58 ASP cc_start: 0.9054 (m-30) cc_final: 0.8757 (m-30) REVERT: H 156 MET cc_start: 0.8742 (mtp) cc_final: 0.8139 (mtm) REVERT: H 163 ILE cc_start: 0.7717 (mt) cc_final: 0.7324 (mt) REVERT: H 209 GLU cc_start: 0.7379 (tt0) cc_final: 0.7113 (tt0) REVERT: I 98 GLN cc_start: 0.9268 (mt0) cc_final: 0.9019 (mt0) REVERT: I 114 GLN cc_start: 0.8321 (tp40) cc_final: 0.8066 (tm-30) REVERT: I 156 MET cc_start: 0.8517 (mtp) cc_final: 0.8190 (mtm) REVERT: I 163 ILE cc_start: 0.7884 (mp) cc_final: 0.7517 (mp) REVERT: I 167 LEU cc_start: 0.9596 (mt) cc_final: 0.9360 (mt) REVERT: J 167 LEU cc_start: 0.9401 (mt) cc_final: 0.9136 (tp) REVERT: J 216 ASN cc_start: 0.9018 (t0) cc_final: 0.8778 (t0) REVERT: K 24 ILE cc_start: 0.8935 (pt) cc_final: 0.8660 (mm) REVERT: K 147 ILE cc_start: 0.8337 (pt) cc_final: 0.7871 (pt) REVERT: K 163 ILE cc_start: 0.8902 (mt) cc_final: 0.8203 (mm) REVERT: L 110 ILE cc_start: 0.9517 (tt) cc_final: 0.9282 (tt) REVERT: M 130 TYR cc_start: 0.7717 (t80) cc_final: 0.7515 (t80) REVERT: N 52 LYS cc_start: 0.9430 (mttt) cc_final: 0.9063 (mtpt) REVERT: N 58 ASP cc_start: 0.8972 (p0) cc_final: 0.8757 (p0) REVERT: O 58 ASP cc_start: 0.8740 (p0) cc_final: 0.8493 (p0) REVERT: O 105 GLN cc_start: 0.9279 (tm-30) cc_final: 0.9065 (tm-30) REVERT: O 163 ILE cc_start: 0.9167 (mp) cc_final: 0.8898 (mp) REVERT: P 325 MET cc_start: 0.8221 (mpp) cc_final: 0.7750 (mpp) REVERT: Q 322 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8238 (tm-30) REVERT: Q 447 LYS cc_start: 0.9263 (ttpt) cc_final: 0.8876 (tppt) REVERT: Q 450 MET cc_start: 0.9215 (mtm) cc_final: 0.8972 (mtm) REVERT: T 314 MET cc_start: 0.8742 (ttm) cc_final: 0.8460 (ttm) REVERT: T 478 ASP cc_start: 0.7753 (t0) cc_final: 0.7369 (t0) REVERT: W 386 MET cc_start: 0.8802 (mmp) cc_final: 0.8558 (mtt) REVERT: X 314 MET cc_start: 0.8794 (ttt) cc_final: 0.8563 (ttt) REVERT: X 335 TYR cc_start: 0.8681 (m-80) cc_final: 0.8477 (m-80) REVERT: X 390 ASN cc_start: 0.8297 (t0) cc_final: 0.7780 (t0) REVERT: Y 450 MET cc_start: 0.8922 (mtp) cc_final: 0.8698 (mmp) REVERT: Z 314 MET cc_start: 0.8581 (ttt) cc_final: 0.8379 (ttt) REVERT: Z 330 ASP cc_start: 0.8982 (p0) cc_final: 0.8712 (p0) REVERT: a 325 MET cc_start: 0.7122 (tmm) cc_final: 0.6757 (tmm) REVERT: a 390 ASN cc_start: 0.8041 (t0) cc_final: 0.7187 (t0) REVERT: b 386 MET cc_start: 0.8933 (mmp) cc_final: 0.8674 (mmp) REVERT: b 390 ASN cc_start: 0.7465 (t0) cc_final: 0.7073 (t0) REVERT: c 383 LEU cc_start: 0.9561 (tp) cc_final: 0.9246 (tp) REVERT: e 174 LEU cc_start: 0.6721 (tp) cc_final: 0.6264 (tt) REVERT: g 173 TYR cc_start: 0.6221 (m-10) cc_final: 0.5637 (m-80) REVERT: h 172 GLN cc_start: 0.8440 (tp40) cc_final: 0.7959 (tt0) outliers start: 4 outliers final: 1 residues processed: 542 average time/residue: 0.2791 time to fit residues: 252.7043 Evaluate side-chains 343 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 200 optimal weight: 10.0000 chunk 434 optimal weight: 3.9990 chunk 585 optimal weight: 2.9990 chunk 432 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 247 optimal weight: 1.9990 chunk 571 optimal weight: 1.9990 chunk 546 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN J 114 GLN K 114 GLN L 11 GLN L 105 GLN e 172 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.034837 restraints weight = 287924.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.036113 restraints weight = 185210.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.037020 restraints weight = 135477.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.037658 restraints weight = 107700.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.038155 restraints weight = 90982.004| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47187 Z= 0.163 Angle : 0.564 8.619 63872 Z= 0.310 Chirality : 0.043 0.201 7275 Planarity : 0.004 0.052 8424 Dihedral : 4.300 85.464 6877 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 0.09 % Allowed : 2.59 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.11), residues: 6072 helix: 2.60 (0.10), residues: 2589 sheet: 0.38 (0.13), residues: 1546 loop : -0.60 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 465 TYR 0.029 0.001 TYR G 57 PHE 0.036 0.002 PHE N 71 TRP 0.006 0.001 TRP Z 429 HIS 0.003 0.001 HIS G 129 Details of bonding type rmsd covalent geometry : bond 0.00345 (47186) covalent geometry : angle 0.56397 (63872) hydrogen bonds : bond 0.04963 ( 3074) hydrogen bonds : angle 4.40998 ( 8778) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 423 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.9169 (m-80) cc_final: 0.8657 (m-80) REVERT: C 130 TYR cc_start: 0.8511 (t80) cc_final: 0.8241 (t80) REVERT: D 58 ASP cc_start: 0.9186 (p0) cc_final: 0.8978 (p0) REVERT: D 149 ASP cc_start: 0.8850 (p0) cc_final: 0.8451 (p0) REVERT: D 156 MET cc_start: 0.6344 (ttm) cc_final: 0.6081 (mtp) REVERT: E 83 ASP cc_start: 0.8985 (m-30) cc_final: 0.8347 (p0) REVERT: E 93 ASP cc_start: 0.9149 (m-30) cc_final: 0.8794 (m-30) REVERT: E 98 GLN cc_start: 0.9088 (mt0) cc_final: 0.8721 (mt0) REVERT: E 105 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8863 (tm-30) REVERT: E 118 TYR cc_start: 0.8769 (m-80) cc_final: 0.8345 (m-80) REVERT: E 130 TYR cc_start: 0.8772 (t80) cc_final: 0.8505 (t80) REVERT: E 143 TYR cc_start: 0.8186 (p90) cc_final: 0.7728 (p90) REVERT: F 72 ASP cc_start: 0.9331 (t70) cc_final: 0.8952 (m-30) REVERT: G 28 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8296 (mmtp) REVERT: G 58 ASP cc_start: 0.8820 (p0) cc_final: 0.8509 (m-30) REVERT: G 90 ASP cc_start: 0.8746 (t70) cc_final: 0.8517 (t70) REVERT: G 156 MET cc_start: 0.7221 (ttm) cc_final: 0.6974 (ttm) REVERT: H 28 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8665 (tppp) REVERT: H 71 PHE cc_start: 0.9560 (p90) cc_final: 0.8996 (p90) REVERT: H 105 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9286 (tm-30) REVERT: H 110 ILE cc_start: 0.9427 (pt) cc_final: 0.9123 (pt) REVERT: H 122 LEU cc_start: 0.9574 (mt) cc_final: 0.9278 (mt) REVERT: H 156 MET cc_start: 0.8718 (mtp) cc_final: 0.7819 (mtt) REVERT: H 163 ILE cc_start: 0.8383 (mt) cc_final: 0.8051 (mt) REVERT: H 209 GLU cc_start: 0.7552 (tt0) cc_final: 0.7328 (tt0) REVERT: I 28 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8257 (mmtp) REVERT: I 80 GLN cc_start: 0.9336 (tm-30) cc_final: 0.9109 (tm-30) REVERT: I 156 MET cc_start: 0.8922 (mtp) cc_final: 0.8398 (mtp) REVERT: I 163 ILE cc_start: 0.8348 (mp) cc_final: 0.7957 (mp) REVERT: I 167 LEU cc_start: 0.9613 (mt) cc_final: 0.9340 (mt) REVERT: J 216 ASN cc_start: 0.9174 (t0) cc_final: 0.8866 (t0) REVERT: K 40 LEU cc_start: 0.9642 (tp) cc_final: 0.9173 (mt) REVERT: K 163 ILE cc_start: 0.8996 (mt) cc_final: 0.8780 (mm) REVERT: L 72 ASP cc_start: 0.9392 (t70) cc_final: 0.9039 (m-30) REVERT: L 141 ILE cc_start: 0.9326 (mp) cc_final: 0.9007 (tp) REVERT: M 130 TYR cc_start: 0.7954 (t80) cc_final: 0.7741 (t80) REVERT: M 163 ILE cc_start: 0.8312 (mp) cc_final: 0.7802 (mm) REVERT: N 52 LYS cc_start: 0.9508 (mttt) cc_final: 0.9103 (mtpt) REVERT: N 105 GLN cc_start: 0.9358 (tm-30) cc_final: 0.9145 (tm-30) REVERT: N 118 TYR cc_start: 0.9284 (m-80) cc_final: 0.8903 (m-80) REVERT: O 58 ASP cc_start: 0.9018 (p0) cc_final: 0.8778 (p0) REVERT: O 105 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8956 (tm-30) REVERT: P 325 MET cc_start: 0.8606 (mpp) cc_final: 0.8128 (mpp) REVERT: P 450 MET cc_start: 0.9485 (ptm) cc_final: 0.9114 (tmm) REVERT: Q 447 LYS cc_start: 0.9466 (ttmt) cc_final: 0.9184 (tppt) REVERT: Q 450 MET cc_start: 0.9087 (mtm) cc_final: 0.8869 (mtm) REVERT: R 325 MET cc_start: 0.8745 (mpp) cc_final: 0.8488 (mpp) REVERT: T 478 ASP cc_start: 0.8200 (t0) cc_final: 0.7789 (t0) REVERT: U 314 MET cc_start: 0.8776 (ttm) cc_final: 0.8404 (ttp) REVERT: U 322 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8591 (tm-30) REVERT: X 335 TYR cc_start: 0.8774 (m-80) cc_final: 0.8563 (m-80) REVERT: X 390 ASN cc_start: 0.8687 (t0) cc_final: 0.8257 (t0) REVERT: Z 324 ASN cc_start: 0.9107 (p0) cc_final: 0.8854 (p0) REVERT: Z 330 ASP cc_start: 0.9092 (p0) cc_final: 0.8836 (p0) REVERT: a 325 MET cc_start: 0.7361 (tmm) cc_final: 0.6808 (tmm) REVERT: a 390 ASN cc_start: 0.8418 (t0) cc_final: 0.8149 (t0) REVERT: b 390 ASN cc_start: 0.8415 (t0) cc_final: 0.7547 (t0) REVERT: c 335 TYR cc_start: 0.8197 (m-80) cc_final: 0.7948 (m-80) REVERT: c 355 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: c 395 MET cc_start: 0.8461 (ptt) cc_final: 0.8093 (ptp) REVERT: e 174 LEU cc_start: 0.6664 (tp) cc_final: 0.6167 (tt) REVERT: h 172 GLN cc_start: 0.8595 (tp40) cc_final: 0.8256 (tt0) outliers start: 4 outliers final: 0 residues processed: 427 average time/residue: 0.2378 time to fit residues: 170.7116 Evaluate side-chains 288 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 463 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 472 optimal weight: 2.9990 chunk 588 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 447 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 GLN F 98 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN I 51 GLN I 101 ASN I 114 GLN L 101 ASN M 231 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.033221 restraints weight = 298406.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034458 restraints weight = 187619.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.035288 restraints weight = 136369.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.035918 restraints weight = 109559.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.036320 restraints weight = 92280.446| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 47187 Z= 0.159 Angle : 0.540 7.497 63872 Z= 0.298 Chirality : 0.042 0.220 7275 Planarity : 0.003 0.041 8424 Dihedral : 4.308 89.402 6877 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 0.04 % Allowed : 2.24 % Favored : 97.72 % 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 aren not related in a simple way. whole: 1.72 (0.11), residues: 6072 helix: 2.80 (0.10), residues: 2592 sheet: 0.63 (0.13), residues: 1465 loop : -0.71 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 14 TYR 0.011 0.001 TYR F 103 PHE 0.032 0.002 PHE K 71 TRP 0.005 0.001 TRP V 429 HIS 0.002 0.001 HIS Y 365 Details of bonding type rmsd covalent geometry : bond 0.00337 (47186) covalent geometry : angle 0.54030 (63872) hydrogen bonds : bond 0.04632 ( 3074) hydrogen bonds : angle 4.34233 ( 8778) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 383 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.9245 (m-80) cc_final: 0.8895 (m-80) REVERT: A 156 MET cc_start: 0.8890 (mtp) cc_final: 0.8499 (mtt) REVERT: A 163 ILE cc_start: 0.9027 (mp) cc_final: 0.8744 (mm) REVERT: C 105 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8987 (tm-30) REVERT: C 130 TYR cc_start: 0.8593 (t80) cc_final: 0.8285 (t80) REVERT: D 53 ILE cc_start: 0.9145 (mm) cc_final: 0.8818 (mm) REVERT: D 58 ASP cc_start: 0.9170 (p0) cc_final: 0.8931 (p0) REVERT: D 71 PHE cc_start: 0.9589 (p90) cc_final: 0.9276 (p90) REVERT: D 101 ASN cc_start: 0.9393 (m110) cc_final: 0.9150 (m110) REVERT: D 114 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7173 (tm-30) REVERT: D 139 TYR cc_start: 0.9317 (m-10) cc_final: 0.8997 (m-80) REVERT: D 209 GLU cc_start: 0.7633 (tt0) cc_final: 0.6930 (mp0) REVERT: E 83 ASP cc_start: 0.8651 (m-30) cc_final: 0.8422 (p0) REVERT: E 90 ASP cc_start: 0.8846 (t70) cc_final: 0.8447 (t70) REVERT: E 93 ASP cc_start: 0.9039 (m-30) cc_final: 0.8592 (m-30) REVERT: E 98 GLN cc_start: 0.9157 (mt0) cc_final: 0.8807 (mt0) REVERT: E 105 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8865 (tm-30) REVERT: E 118 TYR cc_start: 0.8681 (m-80) cc_final: 0.8261 (m-80) REVERT: E 130 TYR cc_start: 0.8831 (t80) cc_final: 0.8333 (t80) REVERT: E 143 TYR cc_start: 0.8233 (p90) cc_final: 0.7870 (p90) REVERT: F 72 ASP cc_start: 0.9393 (t70) cc_final: 0.9002 (m-30) REVERT: F 98 GLN cc_start: 0.9339 (tp40) cc_final: 0.9020 (tp-100) REVERT: G 90 ASP cc_start: 0.8896 (t70) cc_final: 0.8684 (t70) REVERT: G 105 GLN cc_start: 0.9218 (tm-30) cc_final: 0.9013 (tm-30) REVERT: H 53 ILE cc_start: 0.8976 (mm) cc_final: 0.8764 (mm) REVERT: H 71 PHE cc_start: 0.9489 (p90) cc_final: 0.9286 (p90) REVERT: H 105 GLN cc_start: 0.9537 (tm-30) cc_final: 0.9329 (tm-30) REVERT: H 110 ILE cc_start: 0.9572 (pt) cc_final: 0.9306 (pt) REVERT: H 122 LEU cc_start: 0.9574 (mt) cc_final: 0.9234 (mt) REVERT: H 156 MET cc_start: 0.8679 (mtp) cc_final: 0.7940 (mtt) REVERT: H 163 ILE cc_start: 0.8668 (mt) cc_final: 0.8386 (mt) REVERT: H 209 GLU cc_start: 0.7561 (tt0) cc_final: 0.7256 (tt0) REVERT: I 80 GLN cc_start: 0.9386 (tm-30) cc_final: 0.9166 (tm-30) REVERT: I 93 ASP cc_start: 0.8928 (m-30) cc_final: 0.8562 (m-30) REVERT: I 114 GLN cc_start: 0.7512 (tm130) cc_final: 0.7049 (tm-30) REVERT: I 116 LYS cc_start: 0.9264 (ttpp) cc_final: 0.9041 (tmtt) REVERT: I 156 MET cc_start: 0.8914 (mtp) cc_final: 0.8182 (mtp) REVERT: I 163 ILE cc_start: 0.8554 (mp) cc_final: 0.8145 (mp) REVERT: I 167 LEU cc_start: 0.9623 (mt) cc_final: 0.9373 (mt) REVERT: J 216 ASN cc_start: 0.9125 (t0) cc_final: 0.8835 (t0) REVERT: K 40 LEU cc_start: 0.9657 (tp) cc_final: 0.9210 (mt) REVERT: K 163 ILE cc_start: 0.9049 (mt) cc_final: 0.8799 (mm) REVERT: L 72 ASP cc_start: 0.9305 (t70) cc_final: 0.9081 (m-30) REVERT: L 141 ILE cc_start: 0.9310 (mp) cc_final: 0.8813 (tp) REVERT: M 122 LEU cc_start: 0.9595 (mt) cc_final: 0.9292 (mt) REVERT: M 163 ILE cc_start: 0.8383 (mp) cc_final: 0.7883 (mm) REVERT: N 52 LYS cc_start: 0.9608 (mttt) cc_final: 0.9239 (mtpt) REVERT: N 105 GLN cc_start: 0.9377 (tm-30) cc_final: 0.9166 (tm-30) REVERT: N 118 TYR cc_start: 0.9482 (m-80) cc_final: 0.9041 (m-80) REVERT: O 58 ASP cc_start: 0.8952 (p0) cc_final: 0.8713 (p0) REVERT: O 90 ASP cc_start: 0.8923 (t70) cc_final: 0.8566 (t70) REVERT: O 93 ASP cc_start: 0.9258 (m-30) cc_final: 0.8998 (m-30) REVERT: O 105 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8963 (tm-30) REVERT: O 130 TYR cc_start: 0.8605 (t80) cc_final: 0.8391 (t80) REVERT: O 156 MET cc_start: 0.8034 (mmm) cc_final: 0.7598 (mmt) REVERT: P 325 MET cc_start: 0.8692 (mpp) cc_final: 0.8208 (mpp) REVERT: P 381 ASN cc_start: 0.9454 (t0) cc_final: 0.9063 (t0) REVERT: R 325 MET cc_start: 0.8916 (mpp) cc_final: 0.8408 (mpp) REVERT: T 478 ASP cc_start: 0.8484 (t0) cc_final: 0.7996 (t0) REVERT: X 335 TYR cc_start: 0.8807 (m-80) cc_final: 0.8580 (m-80) REVERT: Y 325 MET cc_start: 0.8970 (mpp) cc_final: 0.8683 (mpp) REVERT: Z 330 ASP cc_start: 0.9207 (p0) cc_final: 0.9004 (p0) REVERT: Z 430 ASN cc_start: 0.8912 (t0) cc_final: 0.8610 (t0) REVERT: a 390 ASN cc_start: 0.8575 (t0) cc_final: 0.8101 (t0) REVERT: b 390 ASN cc_start: 0.8330 (t0) cc_final: 0.7887 (t0) REVERT: c 335 TYR cc_start: 0.8382 (m-80) cc_final: 0.8134 (m-10) REVERT: c 395 MET cc_start: 0.8590 (ptt) cc_final: 0.8162 (ptt) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.2357 time to fit residues: 153.7110 Evaluate side-chains 284 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 562 optimal weight: 9.9990 chunk 556 optimal weight: 0.5980 chunk 336 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 584 optimal weight: 10.0000 chunk 411 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 501 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 114 GLN U 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.032554 restraints weight = 297929.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.033771 restraints weight = 187460.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.034596 restraints weight = 136234.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.035232 restraints weight = 109278.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.035691 restraints weight = 91848.967| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.7120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47187 Z= 0.146 Angle : 0.523 7.213 63872 Z= 0.289 Chirality : 0.042 0.188 7275 Planarity : 0.003 0.042 8424 Dihedral : 4.256 88.485 6877 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.84 % 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 aren not related in a simple way. whole: 1.83 (0.11), residues: 6072 helix: 2.89 (0.10), residues: 2591 sheet: 0.80 (0.13), residues: 1417 loop : -0.71 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 388 TYR 0.021 0.001 TYR D 57 PHE 0.031 0.002 PHE K 71 TRP 0.005 0.001 TRP V 429 HIS 0.002 0.001 HIS W 365 Details of bonding type rmsd covalent geometry : bond 0.00309 (47186) covalent geometry : angle 0.52285 (63872) hydrogen bonds : bond 0.04475 ( 3074) hydrogen bonds : angle 4.28597 ( 8778) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 118 TYR cc_start: 0.9209 (m-80) cc_final: 0.8897 (m-80) REVERT: A 130 TYR cc_start: 0.8429 (t80) cc_final: 0.8156 (t80) REVERT: A 156 MET cc_start: 0.8836 (mtp) cc_final: 0.8366 (mtt) REVERT: A 163 ILE cc_start: 0.9081 (mp) cc_final: 0.8825 (mm) REVERT: A 179 ASP cc_start: 0.9445 (m-30) cc_final: 0.9096 (p0) REVERT: C 72 ASP cc_start: 0.9365 (t70) cc_final: 0.9003 (m-30) REVERT: C 105 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8940 (tm-30) REVERT: C 130 TYR cc_start: 0.8632 (t80) cc_final: 0.8297 (t80) REVERT: D 58 ASP cc_start: 0.9076 (p0) cc_final: 0.8771 (p0) REVERT: D 101 ASN cc_start: 0.9403 (m110) cc_final: 0.9137 (m110) REVERT: D 114 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7253 (tm-30) REVERT: D 149 ASP cc_start: 0.8758 (p0) cc_final: 0.8236 (p0) REVERT: D 209 GLU cc_start: 0.7524 (tt0) cc_final: 0.7184 (mp0) REVERT: E 90 ASP cc_start: 0.8570 (t70) cc_final: 0.8003 (t70) REVERT: E 93 ASP cc_start: 0.8951 (m-30) cc_final: 0.8458 (m-30) REVERT: E 98 GLN cc_start: 0.9180 (mt0) cc_final: 0.8862 (mt0) REVERT: E 105 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8889 (tm-30) REVERT: E 118 TYR cc_start: 0.8617 (m-80) cc_final: 0.8239 (m-80) REVERT: E 130 TYR cc_start: 0.8897 (t80) cc_final: 0.8678 (t80) REVERT: E 143 TYR cc_start: 0.8224 (p90) cc_final: 0.7816 (p90) REVERT: F 98 GLN cc_start: 0.9395 (tp40) cc_final: 0.9030 (tp-100) REVERT: G 90 ASP cc_start: 0.8887 (t70) cc_final: 0.8678 (t70) REVERT: H 105 GLN cc_start: 0.9500 (tm-30) cc_final: 0.9250 (tm-30) REVERT: H 110 ILE cc_start: 0.9603 (pt) cc_final: 0.9323 (pt) REVERT: H 122 LEU cc_start: 0.9481 (mt) cc_final: 0.9205 (mt) REVERT: H 156 MET cc_start: 0.8663 (mtp) cc_final: 0.7887 (mtp) REVERT: I 28 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8380 (ttpt) REVERT: I 80 GLN cc_start: 0.9416 (tm-30) cc_final: 0.9184 (tm-30) REVERT: I 156 MET cc_start: 0.9012 (mtp) cc_final: 0.8358 (mtp) REVERT: I 163 ILE cc_start: 0.8721 (mp) cc_final: 0.8303 (mp) REVERT: I 167 LEU cc_start: 0.9556 (mt) cc_final: 0.9283 (mt) REVERT: J 90 ASP cc_start: 0.8809 (t70) cc_final: 0.8608 (t70) REVERT: K 40 LEU cc_start: 0.9670 (tp) cc_final: 0.9213 (mt) REVERT: K 163 ILE cc_start: 0.9108 (mt) cc_final: 0.8891 (mm) REVERT: L 72 ASP cc_start: 0.9364 (t70) cc_final: 0.9147 (m-30) REVERT: L 114 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8333 (pt0) REVERT: L 141 ILE cc_start: 0.9233 (mp) cc_final: 0.8741 (tp) REVERT: M 13 MET cc_start: 0.9525 (mtp) cc_final: 0.9323 (mtp) REVERT: M 105 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9036 (tm-30) REVERT: M 163 ILE cc_start: 0.8397 (mp) cc_final: 0.7894 (mm) REVERT: N 52 LYS cc_start: 0.9601 (mttt) cc_final: 0.9105 (mtpt) REVERT: N 105 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9146 (tm-30) REVERT: N 116 LYS cc_start: 0.8415 (tmtt) cc_final: 0.8208 (tmtt) REVERT: N 118 TYR cc_start: 0.9503 (m-80) cc_final: 0.9018 (m-80) REVERT: O 58 ASP cc_start: 0.8965 (p0) cc_final: 0.8706 (p0) REVERT: O 105 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8942 (tm-30) REVERT: O 114 GLN cc_start: 0.9358 (tp-100) cc_final: 0.9000 (tp-100) REVERT: O 156 MET cc_start: 0.8158 (mmm) cc_final: 0.7759 (mmt) REVERT: P 325 MET cc_start: 0.8776 (mpp) cc_final: 0.8247 (mpp) REVERT: P 381 ASN cc_start: 0.9435 (t0) cc_final: 0.9026 (t0) REVERT: R 325 MET cc_start: 0.8926 (mpp) cc_final: 0.8408 (mpp) REVERT: S 359 TYR cc_start: 0.8872 (t80) cc_final: 0.8543 (t80) REVERT: T 314 MET cc_start: 0.8872 (ttm) cc_final: 0.8570 (ttp) REVERT: T 478 ASP cc_start: 0.8443 (t0) cc_final: 0.7919 (t0) REVERT: U 314 MET cc_start: 0.8782 (ttm) cc_final: 0.8547 (ttp) REVERT: U 386 MET cc_start: 0.8965 (ttm) cc_final: 0.8752 (ttm) REVERT: V 433 GLU cc_start: 0.8927 (pp20) cc_final: 0.8437 (pm20) REVERT: Y 325 MET cc_start: 0.9030 (mpp) cc_final: 0.8740 (mpp) REVERT: Z 430 ASN cc_start: 0.8915 (t0) cc_final: 0.8626 (t0) REVERT: a 307 LYS cc_start: 0.9172 (tmmt) cc_final: 0.8951 (tmtt) REVERT: a 325 MET cc_start: 0.7180 (tmm) cc_final: 0.6944 (tmm) REVERT: a 390 ASN cc_start: 0.8715 (t0) cc_final: 0.8080 (t0) REVERT: a 456 GLN cc_start: 0.9363 (mt0) cc_final: 0.9155 (mp10) REVERT: c 335 TYR cc_start: 0.8402 (m-80) cc_final: 0.8105 (m-10) REVERT: c 395 MET cc_start: 0.8658 (ptt) cc_final: 0.8232 (ptt) REVERT: h 172 GLN cc_start: 0.8681 (tp40) cc_final: 0.8123 (mt0) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.2323 time to fit residues: 145.1182 Evaluate side-chains 268 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 342 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 590 optimal weight: 5.9990 chunk 452 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 285 optimal weight: 0.4980 chunk 471 optimal weight: 5.9990 chunk 383 optimal weight: 7.9990 chunk 558 optimal weight: 1.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 390 ASN V 396 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.042004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.031353 restraints weight = 306504.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.032530 restraints weight = 190658.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.033343 restraints weight = 138488.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.033955 restraints weight = 111337.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.034380 restraints weight = 93743.930| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 47187 Z= 0.178 Angle : 0.556 6.582 63872 Z= 0.306 Chirality : 0.042 0.160 7275 Planarity : 0.003 0.040 8424 Dihedral : 4.328 88.268 6877 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.11), residues: 6072 helix: 2.83 (0.10), residues: 2574 sheet: 0.75 (0.13), residues: 1407 loop : -0.76 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 97 TYR 0.015 0.001 TYR L 118 PHE 0.034 0.002 PHE D 71 TRP 0.005 0.001 TRP V 429 HIS 0.003 0.001 HIS O 152 Details of bonding type rmsd covalent geometry : bond 0.00378 (47186) covalent geometry : angle 0.55568 (63872) hydrogen bonds : bond 0.04919 ( 3074) hydrogen bonds : angle 4.39972 ( 8778) Misc. bond : bond 0.00126 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8927 (mtp) cc_final: 0.8300 (mtt) REVERT: A 163 ILE cc_start: 0.9049 (mp) cc_final: 0.8780 (mm) REVERT: C 72 ASP cc_start: 0.9407 (t70) cc_final: 0.9026 (m-30) REVERT: C 105 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8942 (tm-30) REVERT: C 130 TYR cc_start: 0.8686 (t80) cc_final: 0.8391 (t80) REVERT: D 52 LYS cc_start: 0.9285 (mtpt) cc_final: 0.8576 (mtpp) REVERT: D 53 ILE cc_start: 0.9119 (mm) cc_final: 0.8886 (mm) REVERT: D 101 ASN cc_start: 0.9395 (m110) cc_final: 0.9071 (m110) REVERT: D 139 TYR cc_start: 0.9106 (m-80) cc_final: 0.8882 (m-80) REVERT: D 149 ASP cc_start: 0.8787 (p0) cc_final: 0.8221 (p0) REVERT: E 90 ASP cc_start: 0.8644 (t70) cc_final: 0.8086 (t70) REVERT: E 93 ASP cc_start: 0.8926 (m-30) cc_final: 0.8433 (m-30) REVERT: E 98 GLN cc_start: 0.9185 (mt0) cc_final: 0.8855 (mt0) REVERT: E 105 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8904 (tm-30) REVERT: E 118 TYR cc_start: 0.8444 (m-80) cc_final: 0.8057 (m-80) REVERT: E 143 TYR cc_start: 0.8286 (p90) cc_final: 0.7970 (p90) REVERT: F 72 ASP cc_start: 0.9495 (t70) cc_final: 0.9164 (m-30) REVERT: F 98 GLN cc_start: 0.9374 (tp40) cc_final: 0.8990 (tp-100) REVERT: H 105 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9278 (tm-30) REVERT: H 110 ILE cc_start: 0.9626 (pt) cc_final: 0.9354 (pt) REVERT: H 122 LEU cc_start: 0.9514 (mt) cc_final: 0.9136 (mt) REVERT: H 156 MET cc_start: 0.8652 (mtp) cc_final: 0.7949 (mtp) REVERT: I 80 GLN cc_start: 0.9422 (tm-30) cc_final: 0.9178 (tm-30) REVERT: I 93 ASP cc_start: 0.8924 (m-30) cc_final: 0.8590 (m-30) REVERT: I 114 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7492 (tm-30) REVERT: I 156 MET cc_start: 0.8996 (mtp) cc_final: 0.8376 (mtp) REVERT: I 163 ILE cc_start: 0.8907 (mp) cc_final: 0.8694 (mp) REVERT: J 90 ASP cc_start: 0.8882 (t70) cc_final: 0.8661 (t70) REVERT: J 130 TYR cc_start: 0.8406 (t80) cc_final: 0.8157 (t80) REVERT: K 40 LEU cc_start: 0.9650 (tp) cc_final: 0.9209 (mt) REVERT: L 72 ASP cc_start: 0.9328 (t70) cc_final: 0.9122 (m-30) REVERT: L 114 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8235 (pt0) REVERT: M 105 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8945 (tm-30) REVERT: N 52 LYS cc_start: 0.9637 (mttt) cc_final: 0.9217 (mtpt) REVERT: N 105 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9201 (tm-30) REVERT: N 116 LYS cc_start: 0.8416 (tmtt) cc_final: 0.8189 (tmtt) REVERT: N 118 TYR cc_start: 0.9565 (m-80) cc_final: 0.9100 (m-80) REVERT: O 58 ASP cc_start: 0.9076 (p0) cc_final: 0.8867 (p0) REVERT: O 105 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8880 (tm-30) REVERT: O 114 GLN cc_start: 0.9319 (tp-100) cc_final: 0.8910 (tp-100) REVERT: O 156 MET cc_start: 0.8220 (mmm) cc_final: 0.7788 (mmm) REVERT: P 325 MET cc_start: 0.8786 (mpp) cc_final: 0.8273 (mpp) REVERT: P 381 ASN cc_start: 0.9426 (t0) cc_final: 0.9005 (t0) REVERT: R 325 MET cc_start: 0.8968 (mpp) cc_final: 0.8474 (mpp) REVERT: T 478 ASP cc_start: 0.8667 (t0) cc_final: 0.8090 (t0) REVERT: U 314 MET cc_start: 0.8860 (ttm) cc_final: 0.8599 (ttm) REVERT: V 433 GLU cc_start: 0.8936 (pp20) cc_final: 0.8530 (pm20) REVERT: W 325 MET cc_start: 0.8574 (mpp) cc_final: 0.8364 (mpp) REVERT: X 335 TYR cc_start: 0.8812 (m-80) cc_final: 0.8552 (m-80) REVERT: Y 325 MET cc_start: 0.8981 (mpp) cc_final: 0.8716 (mpp) REVERT: Z 430 ASN cc_start: 0.8957 (t0) cc_final: 0.8664 (t0) REVERT: a 325 MET cc_start: 0.7668 (tmm) cc_final: 0.7271 (tmm) REVERT: a 386 MET cc_start: 0.9386 (tpp) cc_final: 0.9148 (tpp) REVERT: a 390 ASN cc_start: 0.8810 (t0) cc_final: 0.8116 (t0) REVERT: a 456 GLN cc_start: 0.9411 (mt0) cc_final: 0.9196 (mp10) REVERT: c 335 TYR cc_start: 0.8530 (m-80) cc_final: 0.8246 (m-10) REVERT: c 395 MET cc_start: 0.8673 (ptt) cc_final: 0.8308 (ptt) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2672 time to fit residues: 154.1653 Evaluate side-chains 247 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 149 optimal weight: 5.9990 chunk 511 optimal weight: 2.9990 chunk 330 optimal weight: 0.9980 chunk 389 optimal weight: 2.9990 chunk 560 optimal weight: 8.9990 chunk 290 optimal weight: 0.0030 chunk 228 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 247 optimal weight: 0.8980 chunk 394 optimal weight: 2.9990 chunk 497 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.032953 restraints weight = 297267.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.034223 restraints weight = 182509.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.035114 restraints weight = 130591.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.035733 restraints weight = 102758.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.036213 restraints weight = 86458.736| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 47187 Z= 0.097 Angle : 0.491 8.200 63872 Z= 0.267 Chirality : 0.042 0.164 7275 Planarity : 0.003 0.038 8424 Dihedral : 4.078 83.884 6877 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.11), residues: 6072 helix: 3.07 (0.10), residues: 2583 sheet: 0.96 (0.13), residues: 1402 loop : -0.63 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 388 TYR 0.020 0.001 TYR M 57 PHE 0.033 0.001 PHE D 71 TRP 0.003 0.000 TRP U 429 HIS 0.001 0.000 HIS S 365 Details of bonding type rmsd covalent geometry : bond 0.00194 (47186) covalent geometry : angle 0.49076 (63872) hydrogen bonds : bond 0.03698 ( 3074) hydrogen bonds : angle 4.10530 ( 8778) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8862 (mtp) cc_final: 0.8423 (mtt) REVERT: A 163 ILE cc_start: 0.8985 (mp) cc_final: 0.8731 (mm) REVERT: C 72 ASP cc_start: 0.9362 (t70) cc_final: 0.8997 (m-30) REVERT: C 105 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 130 TYR cc_start: 0.8651 (t80) cc_final: 0.8376 (t80) REVERT: D 52 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8598 (mtpt) REVERT: D 98 GLN cc_start: 0.9401 (pt0) cc_final: 0.9136 (pt0) REVERT: D 101 ASN cc_start: 0.9418 (m110) cc_final: 0.9118 (m110) REVERT: D 114 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7388 (tm-30) REVERT: D 139 TYR cc_start: 0.9113 (m-80) cc_final: 0.8845 (m-80) REVERT: D 149 ASP cc_start: 0.8892 (p0) cc_final: 0.8333 (p0) REVERT: E 90 ASP cc_start: 0.8627 (t70) cc_final: 0.8093 (t70) REVERT: E 93 ASP cc_start: 0.9106 (m-30) cc_final: 0.8570 (m-30) REVERT: E 98 GLN cc_start: 0.9203 (mt0) cc_final: 0.8864 (mt0) REVERT: E 105 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8912 (tm-30) REVERT: E 118 TYR cc_start: 0.8500 (m-80) cc_final: 0.8206 (m-80) REVERT: E 130 TYR cc_start: 0.8882 (t80) cc_final: 0.8676 (t80) REVERT: E 143 TYR cc_start: 0.8239 (p90) cc_final: 0.7883 (p90) REVERT: F 98 GLN cc_start: 0.9352 (tp40) cc_final: 0.9079 (tp-100) REVERT: G 134 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8226 (tptp) REVERT: H 53 ILE cc_start: 0.8920 (mm) cc_final: 0.8621 (mt) REVERT: H 105 GLN cc_start: 0.9497 (tm-30) cc_final: 0.9239 (tm-30) REVERT: H 122 LEU cc_start: 0.9527 (mt) cc_final: 0.9214 (mm) REVERT: H 156 MET cc_start: 0.8533 (mtp) cc_final: 0.8023 (mtt) REVERT: I 80 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9204 (tm-30) REVERT: I 93 ASP cc_start: 0.8913 (m-30) cc_final: 0.8564 (m-30) REVERT: I 114 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7313 (tm-30) REVERT: I 156 MET cc_start: 0.8986 (mtp) cc_final: 0.8310 (mtp) REVERT: J 90 ASP cc_start: 0.8765 (t70) cc_final: 0.8550 (t70) REVERT: J 130 TYR cc_start: 0.8428 (t80) cc_final: 0.8222 (t80) REVERT: K 40 LEU cc_start: 0.9644 (tp) cc_final: 0.9220 (mt) REVERT: L 72 ASP cc_start: 0.9320 (t70) cc_final: 0.9105 (m-30) REVERT: L 141 ILE cc_start: 0.9205 (mp) cc_final: 0.8699 (tp) REVERT: M 90 ASP cc_start: 0.8746 (t70) cc_final: 0.8517 (t70) REVERT: M 105 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8946 (tm-30) REVERT: M 114 GLN cc_start: 0.9140 (tp40) cc_final: 0.8924 (tm-30) REVERT: N 52 LYS cc_start: 0.9634 (mttt) cc_final: 0.9203 (mtpt) REVERT: N 105 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9163 (tm-30) REVERT: N 116 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8217 (tmtt) REVERT: N 118 TYR cc_start: 0.9555 (m-80) cc_final: 0.9103 (m-80) REVERT: O 58 ASP cc_start: 0.8837 (p0) cc_final: 0.8312 (p0) REVERT: O 105 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8834 (tm-30) REVERT: O 114 GLN cc_start: 0.9336 (tp-100) cc_final: 0.8934 (tp-100) REVERT: O 156 MET cc_start: 0.8158 (mmm) cc_final: 0.7763 (mmm) REVERT: P 325 MET cc_start: 0.8763 (mpp) cc_final: 0.8295 (mpp) REVERT: P 381 ASN cc_start: 0.9429 (t0) cc_final: 0.9101 (t0) REVERT: Q 333 LYS cc_start: 0.9422 (mmpt) cc_final: 0.9116 (mmmt) REVERT: R 325 MET cc_start: 0.8930 (mpp) cc_final: 0.8422 (mpp) REVERT: S 359 TYR cc_start: 0.8795 (t80) cc_final: 0.8555 (t80) REVERT: T 478 ASP cc_start: 0.8276 (t0) cc_final: 0.7866 (t0) REVERT: U 386 MET cc_start: 0.9005 (ttm) cc_final: 0.8776 (ttm) REVERT: V 433 GLU cc_start: 0.8848 (pp20) cc_final: 0.8296 (pm20) REVERT: X 335 TYR cc_start: 0.8810 (m-80) cc_final: 0.8534 (m-80) REVERT: Y 325 MET cc_start: 0.8979 (mpp) cc_final: 0.8772 (mpp) REVERT: Z 430 ASN cc_start: 0.8884 (t0) cc_final: 0.8584 (t0) REVERT: a 325 MET cc_start: 0.7668 (tmm) cc_final: 0.7225 (tmm) REVERT: a 386 MET cc_start: 0.9363 (tpp) cc_final: 0.9123 (tpp) REVERT: a 390 ASN cc_start: 0.8875 (t0) cc_final: 0.8084 (t0) REVERT: b 335 TYR cc_start: 0.9209 (m-80) cc_final: 0.8661 (m-80) REVERT: c 335 TYR cc_start: 0.8389 (m-80) cc_final: 0.8055 (m-10) REVERT: c 395 MET cc_start: 0.8665 (ptt) cc_final: 0.8326 (ptt) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2683 time to fit residues: 170.1423 Evaluate side-chains 263 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 83 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 555 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.030376 restraints weight = 312073.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.031514 restraints weight = 194296.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.032287 restraints weight = 140914.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.032868 restraints weight = 113627.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.033263 restraints weight = 96019.195| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.8107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 47187 Z= 0.232 Angle : 0.616 10.547 63872 Z= 0.339 Chirality : 0.043 0.240 7275 Planarity : 0.004 0.040 8424 Dihedral : 4.469 87.888 6877 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 aren not related in a simple way. whole: 1.64 (0.11), residues: 6072 helix: 2.71 (0.10), residues: 2585 sheet: 0.92 (0.13), residues: 1358 loop : -0.91 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 388 TYR 0.022 0.002 TYR F 103 PHE 0.032 0.002 PHE D 71 TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS O 152 Details of bonding type rmsd covalent geometry : bond 0.00495 (47186) covalent geometry : angle 0.61560 (63872) hydrogen bonds : bond 0.05529 ( 3074) hydrogen bonds : angle 4.57258 ( 8778) Misc. bond : bond 0.00151 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8883 (mtp) cc_final: 0.8135 (mtt) REVERT: A 163 ILE cc_start: 0.9006 (mp) cc_final: 0.8716 (mm) REVERT: C 105 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8816 (tm-30) REVERT: C 130 TYR cc_start: 0.8762 (t80) cc_final: 0.8428 (t80) REVERT: D 52 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8632 (mtpt) REVERT: D 98 GLN cc_start: 0.9402 (pt0) cc_final: 0.9127 (pt0) REVERT: D 101 ASN cc_start: 0.9347 (m110) cc_final: 0.9001 (m110) REVERT: D 139 TYR cc_start: 0.9171 (m-80) cc_final: 0.8965 (m-80) REVERT: D 149 ASP cc_start: 0.8899 (p0) cc_final: 0.8558 (p0) REVERT: E 83 ASP cc_start: 0.9057 (t0) cc_final: 0.8830 (p0) REVERT: E 90 ASP cc_start: 0.8689 (t70) cc_final: 0.8128 (t70) REVERT: E 93 ASP cc_start: 0.8987 (m-30) cc_final: 0.8443 (m-30) REVERT: E 98 GLN cc_start: 0.9201 (mt0) cc_final: 0.8839 (mt0) REVERT: E 105 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8892 (tm-30) REVERT: E 118 TYR cc_start: 0.8434 (m-80) cc_final: 0.8092 (m-80) REVERT: E 143 TYR cc_start: 0.8400 (p90) cc_final: 0.8135 (p90) REVERT: F 72 ASP cc_start: 0.9525 (t70) cc_final: 0.9161 (m-30) REVERT: F 98 GLN cc_start: 0.9362 (tp40) cc_final: 0.8956 (tp-100) REVERT: H 28 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9065 (mmmm) REVERT: I 28 LYS cc_start: 0.9163 (mmtm) cc_final: 0.8774 (mmtp) REVERT: I 80 GLN cc_start: 0.9430 (tm-30) cc_final: 0.9183 (tm-30) REVERT: I 93 ASP cc_start: 0.8968 (m-30) cc_final: 0.8628 (m-30) REVERT: I 156 MET cc_start: 0.8982 (mtp) cc_final: 0.8316 (mtp) REVERT: J 90 ASP cc_start: 0.8908 (t70) cc_final: 0.8667 (t70) REVERT: K 40 LEU cc_start: 0.9656 (tp) cc_final: 0.9224 (mt) REVERT: K 62 PHE cc_start: 0.9080 (t80) cc_final: 0.8786 (t80) REVERT: L 156 MET cc_start: 0.8168 (tpp) cc_final: 0.7569 (tpp) REVERT: M 13 MET cc_start: 0.9613 (mtp) cc_final: 0.9398 (mtp) REVERT: M 105 GLN cc_start: 0.9284 (tm-30) cc_final: 0.9009 (tm-30) REVERT: N 52 LYS cc_start: 0.9653 (mttt) cc_final: 0.9214 (mtpt) REVERT: N 118 TYR cc_start: 0.9590 (m-80) cc_final: 0.9064 (m-80) REVERT: O 105 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8849 (tm-30) REVERT: O 114 GLN cc_start: 0.9346 (tp-100) cc_final: 0.8907 (tp-100) REVERT: O 156 MET cc_start: 0.8179 (mmm) cc_final: 0.7728 (mmt) REVERT: P 325 MET cc_start: 0.8838 (mpp) cc_final: 0.8296 (mpp) REVERT: P 381 ASN cc_start: 0.9366 (t0) cc_final: 0.8935 (t0) REVERT: Q 325 MET cc_start: 0.7767 (tmm) cc_final: 0.7157 (tmm) REVERT: Q 333 LYS cc_start: 0.9421 (mmpt) cc_final: 0.9113 (mmmt) REVERT: R 325 MET cc_start: 0.8947 (mpp) cc_final: 0.8459 (mpp) REVERT: T 364 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8603 (tp30) REVERT: T 478 ASP cc_start: 0.8764 (t0) cc_final: 0.8148 (t0) REVERT: U 314 MET cc_start: 0.8865 (ttm) cc_final: 0.8509 (ttm) REVERT: Y 325 MET cc_start: 0.9009 (mpp) cc_final: 0.8696 (mpp) REVERT: Z 430 ASN cc_start: 0.9045 (t0) cc_final: 0.8793 (t0) REVERT: c 335 TYR cc_start: 0.8611 (m-80) cc_final: 0.8343 (m-10) REVERT: c 386 MET cc_start: 0.8932 (tmm) cc_final: 0.8710 (tmm) REVERT: c 395 MET cc_start: 0.8689 (ptt) cc_final: 0.8354 (ptt) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2773 time to fit residues: 146.2015 Evaluate side-chains 235 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 480 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 516 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 501 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.030174 restraints weight = 311210.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.031318 restraints weight = 192805.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.032126 restraints weight = 139531.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.032679 restraints weight = 110931.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.033103 restraints weight = 94319.451| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 47187 Z= 0.221 Angle : 0.605 10.471 63872 Z= 0.333 Chirality : 0.043 0.221 7275 Planarity : 0.004 0.038 8424 Dihedral : 4.510 87.949 6877 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 aren not related in a simple way. whole: 1.46 (0.11), residues: 6072 helix: 2.57 (0.10), residues: 2583 sheet: 0.83 (0.13), residues: 1358 loop : -1.00 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 388 TYR 0.024 0.001 TYR I 103 PHE 0.029 0.002 PHE D 71 TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS O 152 Details of bonding type rmsd covalent geometry : bond 0.00471 (47186) covalent geometry : angle 0.60541 (63872) hydrogen bonds : bond 0.05228 ( 3074) hydrogen bonds : angle 4.60329 ( 8778) Misc. bond : bond 0.00183 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8314 (t80) cc_final: 0.7819 (t80) REVERT: A 156 MET cc_start: 0.8888 (mtp) cc_final: 0.8318 (mtt) REVERT: C 72 ASP cc_start: 0.9410 (t70) cc_final: 0.9050 (m-30) REVERT: C 105 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8799 (tm-30) REVERT: C 130 TYR cc_start: 0.8817 (t80) cc_final: 0.8477 (t80) REVERT: D 52 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8673 (mtpt) REVERT: D 98 GLN cc_start: 0.9391 (pt0) cc_final: 0.9104 (pt0) REVERT: D 101 ASN cc_start: 0.9349 (m110) cc_final: 0.8997 (m110) REVERT: D 139 TYR cc_start: 0.9206 (m-80) cc_final: 0.8938 (m-80) REVERT: D 149 ASP cc_start: 0.8905 (p0) cc_final: 0.8567 (p0) REVERT: E 83 ASP cc_start: 0.9054 (t0) cc_final: 0.8787 (p0) REVERT: E 93 ASP cc_start: 0.8945 (m-30) cc_final: 0.8518 (m-30) REVERT: E 98 GLN cc_start: 0.9166 (mt0) cc_final: 0.8761 (mt0) REVERT: E 105 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8900 (tm-30) REVERT: E 118 TYR cc_start: 0.8372 (m-80) cc_final: 0.8020 (m-80) REVERT: E 143 TYR cc_start: 0.8519 (p90) cc_final: 0.8012 (p90) REVERT: F 72 ASP cc_start: 0.9516 (t70) cc_final: 0.9172 (m-30) REVERT: F 98 GLN cc_start: 0.9337 (tp40) cc_final: 0.9078 (tp-100) REVERT: F 105 GLN cc_start: 0.9468 (tm-30) cc_final: 0.9235 (tm-30) REVERT: H 28 LYS cc_start: 0.9491 (mmtm) cc_final: 0.9087 (mmmm) REVERT: H 58 ASP cc_start: 0.8745 (m-30) cc_final: 0.8515 (m-30) REVERT: I 80 GLN cc_start: 0.9430 (tm-30) cc_final: 0.9182 (tm-30) REVERT: I 93 ASP cc_start: 0.8942 (m-30) cc_final: 0.8601 (m-30) REVERT: I 118 TYR cc_start: 0.9400 (m-80) cc_final: 0.9197 (m-80) REVERT: I 156 MET cc_start: 0.8865 (mtp) cc_final: 0.8442 (mtp) REVERT: J 90 ASP cc_start: 0.8917 (t70) cc_final: 0.8640 (t70) REVERT: K 40 LEU cc_start: 0.9657 (tp) cc_final: 0.9222 (mt) REVERT: K 62 PHE cc_start: 0.9050 (t80) cc_final: 0.8795 (t80) REVERT: L 118 TYR cc_start: 0.9490 (m-10) cc_final: 0.9045 (m-80) REVERT: L 156 MET cc_start: 0.8193 (tpp) cc_final: 0.7600 (tpp) REVERT: M 13 MET cc_start: 0.9620 (mtp) cc_final: 0.9384 (mtp) REVERT: M 105 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8998 (tm-30) REVERT: M 156 MET cc_start: 0.8680 (mmm) cc_final: 0.8440 (tpp) REVERT: N 52 LYS cc_start: 0.9668 (mttt) cc_final: 0.9228 (mtpt) REVERT: N 105 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9248 (tm-30) REVERT: N 118 TYR cc_start: 0.9572 (m-80) cc_final: 0.9051 (m-80) REVERT: O 105 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8858 (tm-30) REVERT: O 114 GLN cc_start: 0.9344 (tp-100) cc_final: 0.8895 (tp-100) REVERT: O 156 MET cc_start: 0.8025 (mmm) cc_final: 0.7616 (mmt) REVERT: P 325 MET cc_start: 0.8858 (mpp) cc_final: 0.8354 (mpp) REVERT: P 381 ASN cc_start: 0.9351 (t0) cc_final: 0.8926 (t0) REVERT: Q 325 MET cc_start: 0.7766 (tmm) cc_final: 0.7146 (tmm) REVERT: Q 333 LYS cc_start: 0.9466 (mmpt) cc_final: 0.9173 (mmmt) REVERT: R 325 MET cc_start: 0.8984 (mpp) cc_final: 0.8513 (mpp) REVERT: S 359 TYR cc_start: 0.8862 (t80) cc_final: 0.8507 (t80) REVERT: T 359 TYR cc_start: 0.9278 (t80) cc_final: 0.8913 (t80) REVERT: T 364 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8552 (mm-30) REVERT: U 314 MET cc_start: 0.8832 (ttm) cc_final: 0.8487 (ttm) REVERT: U 386 MET cc_start: 0.9015 (ttm) cc_final: 0.8596 (ttm) REVERT: Y 325 MET cc_start: 0.9018 (mpp) cc_final: 0.8731 (mpp) REVERT: Z 325 MET cc_start: 0.8622 (mpp) cc_final: 0.8403 (mpp) REVERT: Z 430 ASN cc_start: 0.9085 (t0) cc_final: 0.8842 (t0) REVERT: a 325 MET cc_start: 0.7716 (tmm) cc_final: 0.7410 (tmm) REVERT: a 386 MET cc_start: 0.9332 (tpp) cc_final: 0.9094 (tpp) REVERT: c 335 TYR cc_start: 0.8622 (m-80) cc_final: 0.8350 (m-10) REVERT: c 386 MET cc_start: 0.8994 (tmm) cc_final: 0.8752 (tmm) REVERT: c 395 MET cc_start: 0.8771 (ptt) cc_final: 0.8490 (ptt) REVERT: h 172 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8527 (mm-40) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2090 time to fit residues: 108.5841 Evaluate side-chains 234 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 183 optimal weight: 5.9990 chunk 513 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 501 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 431 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 557 optimal weight: 1.9990 chunk 551 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.042817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.032185 restraints weight = 300107.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.033427 restraints weight = 182708.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.034320 restraints weight = 130276.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.034957 restraints weight = 102191.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.035411 restraints weight = 85545.150| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.8313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 47187 Z= 0.098 Angle : 0.509 7.415 63872 Z= 0.277 Chirality : 0.043 0.235 7275 Planarity : 0.003 0.037 8424 Dihedral : 4.119 86.551 6877 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 aren not related in a simple way. whole: 1.91 (0.11), residues: 6072 helix: 2.94 (0.10), residues: 2587 sheet: 1.04 (0.14), residues: 1371 loop : -0.78 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 14 TYR 0.021 0.001 TYR J 103 PHE 0.031 0.001 PHE D 71 TRP 0.004 0.001 TRP Q 429 HIS 0.003 0.000 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00192 (47186) covalent geometry : angle 0.50902 (63872) hydrogen bonds : bond 0.03649 ( 3074) hydrogen bonds : angle 4.18770 ( 8778) Misc. bond : bond 0.00133 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.9388 (mt0) cc_final: 0.9137 (mt0) REVERT: A 156 MET cc_start: 0.8900 (mtp) cc_final: 0.8538 (mtt) REVERT: A 163 ILE cc_start: 0.9024 (mp) cc_final: 0.8761 (mm) REVERT: C 72 ASP cc_start: 0.9371 (t70) cc_final: 0.9038 (m-30) REVERT: C 105 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8800 (tm-30) REVERT: C 130 TYR cc_start: 0.8868 (t80) cc_final: 0.8536 (t80) REVERT: D 52 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8761 (mtpt) REVERT: D 98 GLN cc_start: 0.9399 (pt0) cc_final: 0.9106 (pt0) REVERT: D 101 ASN cc_start: 0.9397 (m110) cc_final: 0.9097 (m110) REVERT: D 139 TYR cc_start: 0.9105 (m-80) cc_final: 0.8887 (m-80) REVERT: D 149 ASP cc_start: 0.8882 (p0) cc_final: 0.8563 (p0) REVERT: E 83 ASP cc_start: 0.9032 (t0) cc_final: 0.8675 (p0) REVERT: E 93 ASP cc_start: 0.8969 (m-30) cc_final: 0.8586 (m-30) REVERT: E 98 GLN cc_start: 0.9225 (mt0) cc_final: 0.8880 (mt0) REVERT: E 105 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8901 (tm-30) REVERT: E 118 TYR cc_start: 0.8424 (m-80) cc_final: 0.8155 (m-80) REVERT: E 143 TYR cc_start: 0.8429 (p90) cc_final: 0.7909 (p90) REVERT: F 98 GLN cc_start: 0.9365 (tp40) cc_final: 0.8947 (tp-100) REVERT: F 105 GLN cc_start: 0.9463 (tm-30) cc_final: 0.9215 (tm-30) REVERT: H 28 LYS cc_start: 0.9501 (mmtm) cc_final: 0.9076 (mmmm) REVERT: H 58 ASP cc_start: 0.8711 (m-30) cc_final: 0.8463 (m-30) REVERT: H 122 LEU cc_start: 0.9504 (mt) cc_final: 0.9202 (mm) REVERT: H 156 MET cc_start: 0.8636 (mtp) cc_final: 0.8045 (mtt) REVERT: I 28 LYS cc_start: 0.9189 (mmtm) cc_final: 0.8901 (mttp) REVERT: I 80 GLN cc_start: 0.9445 (tm-30) cc_final: 0.9200 (tm-30) REVERT: I 93 ASP cc_start: 0.8911 (m-30) cc_final: 0.8594 (m-30) REVERT: I 114 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7640 (tm-30) REVERT: J 90 ASP cc_start: 0.8769 (t70) cc_final: 0.8484 (t70) REVERT: K 40 LEU cc_start: 0.9646 (tp) cc_final: 0.9212 (mt) REVERT: L 118 TYR cc_start: 0.9498 (m-10) cc_final: 0.9189 (m-80) REVERT: L 156 MET cc_start: 0.8113 (tpp) cc_final: 0.7515 (tpp) REVERT: M 93 ASP cc_start: 0.9039 (m-30) cc_final: 0.8546 (m-30) REVERT: M 105 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8953 (tm-30) REVERT: N 52 LYS cc_start: 0.9643 (mttt) cc_final: 0.9220 (mtpt) REVERT: N 105 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9190 (tm-30) REVERT: N 118 TYR cc_start: 0.9531 (m-80) cc_final: 0.9008 (m-80) REVERT: O 105 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8799 (tm-30) REVERT: O 114 GLN cc_start: 0.9296 (tp-100) cc_final: 0.8858 (tp-100) REVERT: O 156 MET cc_start: 0.8148 (mmm) cc_final: 0.7858 (mmm) REVERT: P 325 MET cc_start: 0.8806 (mpp) cc_final: 0.8310 (mpp) REVERT: P 381 ASN cc_start: 0.9354 (t0) cc_final: 0.9065 (t0) REVERT: Q 325 MET cc_start: 0.7608 (tmm) cc_final: 0.6918 (tmm) REVERT: Q 333 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9104 (mmmt) REVERT: R 325 MET cc_start: 0.8848 (mpp) cc_final: 0.8376 (mpp) REVERT: S 359 TYR cc_start: 0.8684 (t80) cc_final: 0.8400 (t80) REVERT: T 314 MET cc_start: 0.8646 (ttm) cc_final: 0.8421 (ttm) REVERT: T 359 TYR cc_start: 0.9151 (t80) cc_final: 0.8944 (t80) REVERT: T 478 ASP cc_start: 0.8378 (t0) cc_final: 0.7956 (t0) REVERT: U 314 MET cc_start: 0.8861 (ttm) cc_final: 0.8620 (ttp) REVERT: U 395 MET cc_start: 0.9042 (ppp) cc_final: 0.8743 (ppp) REVERT: Z 430 ASN cc_start: 0.8917 (t0) cc_final: 0.8623 (t0) REVERT: a 325 MET cc_start: 0.7554 (tmm) cc_final: 0.7177 (tmm) REVERT: a 386 MET cc_start: 0.9352 (tpp) cc_final: 0.9119 (tpp) REVERT: a 390 ASN cc_start: 0.8977 (t0) cc_final: 0.8212 (t0) REVERT: a 469 GLU cc_start: 0.9244 (pm20) cc_final: 0.9025 (pm20) REVERT: c 335 TYR cc_start: 0.8487 (m-80) cc_final: 0.8151 (m-10) REVERT: c 395 MET cc_start: 0.8704 (ptt) cc_final: 0.8450 (ptt) REVERT: h 172 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8451 (mm-40) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1704 time to fit residues: 95.9973 Evaluate side-chains 252 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 200 optimal weight: 8.9990 chunk 308 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 560 optimal weight: 4.9990 chunk 411 optimal weight: 2.9990 chunk 416 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.031884 restraints weight = 302948.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.033117 restraints weight = 184729.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.033986 restraints weight = 132144.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.034607 restraints weight = 104150.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.035064 restraints weight = 87481.827| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.8363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 47187 Z= 0.111 Angle : 0.509 7.551 63872 Z= 0.277 Chirality : 0.042 0.207 7275 Planarity : 0.003 0.037 8424 Dihedral : 4.030 82.730 6877 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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 aren not related in a simple way. whole: 1.95 (0.11), residues: 6072 helix: 2.98 (0.10), residues: 2589 sheet: 1.00 (0.13), residues: 1441 loop : -0.79 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 14 TYR 0.019 0.001 TYR J 57 PHE 0.033 0.001 PHE D 71 TRP 0.002 0.000 TRP S 429 HIS 0.002 0.000 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00231 (47186) covalent geometry : angle 0.50907 (63872) hydrogen bonds : bond 0.03846 ( 3074) hydrogen bonds : angle 4.16717 ( 8778) Misc. bond : bond 0.00143 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6084.50 seconds wall clock time: 106 minutes 27.68 seconds (6387.68 seconds total)