Starting phenix.real_space_refine on Sat Mar 7 05:13:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x87_22089/03_2026/6x87_22089.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x87_22089/03_2026/6x87_22089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x87_22089/03_2026/6x87_22089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x87_22089/03_2026/6x87_22089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x87_22089/03_2026/6x87_22089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x87_22089/03_2026/6x87_22089.map" } resolution = 3.2 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19656 atoms to isotropic. 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 98 5.16 5 C 14593 2.51 5 N 3856 2.21 5 O 4626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23173 Number of models: 1 Model: "" Number of chains: 15 Chain: "K" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 437 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 32, 'TRANS': 28} Chain: "M" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.74, per 1000 atoms: 0.20 Number of scatterers: 23173 At special positions: 0 Unit cell: (170.66, 169.6, 179.14, 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 98 16.00 O 4626 8.00 N 3856 7.00 C 14593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 216 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 216 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 216 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 216 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 70 sheets defined 6.8% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.518A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.613A pdb=" N SER K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.961A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.519A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.649A pdb=" N SER M 87 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.963A pdb=" N LEU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 182 through 187 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.523A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.678A pdb=" N SER I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.953A pdb=" N LEU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.501A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.639A pdb=" N SER G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.973A pdb=" N LEU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 128 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.537A pdb=" N SER E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.646A pdb=" N SER E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.966A pdb=" N LEU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.537A pdb=" N SER C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.662A pdb=" N SER C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.934A pdb=" N LEU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.522A pdb=" N SER A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.627A pdb=" N SER A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.963A pdb=" N LEU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.777A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.777A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 120 through 124 removed outlier: 4.125A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 120 through 124 removed outlier: 4.125A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.598A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.535A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.597A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.854A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.854A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 120 through 124 removed outlier: 4.166A pdb=" N GLY M 139 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL M 184 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY M 139 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL M 182 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 141 " --> pdb=" O SER M 180 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER M 180 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS M 143 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU M 178 " --> pdb=" O LYS M 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 120 through 124 removed outlier: 4.166A pdb=" N GLY M 139 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL M 184 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY M 139 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL M 182 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 141 " --> pdb=" O SER M 180 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER M 180 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS M 143 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU M 178 " --> pdb=" O LYS M 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 151 through 154 Processing sheet with id=AB8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.503A pdb=" N LEU N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.567A pdb=" N VAL N 133 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL N 132 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 154 through 155 removed outlier: 4.593A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL N 205 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.767A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.767A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 120 through 124 removed outlier: 4.188A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA I 137 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL I 184 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLY I 139 " --> pdb=" O VAL I 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL I 182 " --> pdb=" O GLY I 139 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER I 180 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS I 143 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU I 178 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 120 through 124 removed outlier: 4.188A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA I 137 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL I 184 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLY I 139 " --> pdb=" O VAL I 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL I 182 " --> pdb=" O GLY I 139 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER I 180 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS I 143 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU I 178 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.607A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.602A pdb=" N VAL J 133 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL J 132 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 154 through 155 removed outlier: 4.653A pdb=" N TRP J 148 " --> pdb=" O GLN J 155 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL J 205 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.743A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.743A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.264A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.264A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.623A pdb=" N LEU H 36 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.658A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL H 132 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.574A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL H 205 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.782A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.782A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 120 through 124 removed outlier: 4.036A pdb=" N GLY E 139 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA E 137 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 184 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY E 139 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 182 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU E 141 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 180 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 143 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU E 178 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 131 through 132 removed outlier: 5.083A pdb=" N ALA E 137 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 184 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY E 139 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 182 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU E 141 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 180 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 143 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU E 178 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 151 through 154 Processing sheet with id=AF2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.527A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.526A pdb=" N VAL F 132 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 154 through 155 removed outlier: 4.692A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 205 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.754A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.754A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.208A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.208A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AG3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.521A pdb=" N LEU D 36 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.581A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 132 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 154 through 155 removed outlier: 4.688A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.779A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.779A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.183A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.183A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 151 through 154 Processing sheet with id=AH4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.656A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.620A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 154 through 155 removed outlier: 4.607A pdb=" N TRP B 148 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 205 " --> pdb=" O VAL B 196 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 1962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7353 1.35 - 1.46: 5721 1.46 - 1.58: 10523 1.58 - 1.70: 0 1.70 - 1.81: 126 Bond restraints: 23723 Sorted by residual: bond pdb=" C VAL J 58 " pdb=" N PRO J 59 " ideal model delta sigma weight residual 1.330 1.343 -0.013 1.19e-02 7.06e+03 1.19e+00 bond pdb=" C VAL N 58 " pdb=" N PRO N 59 " ideal model delta sigma weight residual 1.330 1.343 -0.012 1.19e-02 7.06e+03 1.08e+00 bond pdb=" C VAL D 58 " pdb=" N PRO D 59 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.19e-02 7.06e+03 9.70e-01 bond pdb=" C VAL F 58 " pdb=" N PRO F 59 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.19e-02 7.06e+03 8.51e-01 bond pdb=" CG PRO L 141 " pdb=" CD PRO L 141 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.42e-01 ... (remaining 23718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 30835 1.06 - 2.13: 1065 2.13 - 3.19: 327 3.19 - 4.25: 60 4.25 - 5.32: 15 Bond angle restraints: 32302 Sorted by residual: angle pdb=" C LEU H 50 " pdb=" N VAL H 51 " pdb=" CA VAL H 51 " ideal model delta sigma weight residual 121.97 125.23 -3.26 1.80e+00 3.09e-01 3.27e+00 angle pdb=" C LEU J 50 " pdb=" N VAL J 51 " pdb=" CA VAL J 51 " ideal model delta sigma weight residual 121.97 125.14 -3.17 1.80e+00 3.09e-01 3.11e+00 angle pdb=" N VAL F 115 " pdb=" CA VAL F 115 " pdb=" C VAL F 115 " ideal model delta sigma weight residual 108.36 110.85 -2.49 1.43e+00 4.89e-01 3.04e+00 angle pdb=" N PRO F 141 " pdb=" CD PRO F 141 " pdb=" CG PRO F 141 " ideal model delta sigma weight residual 103.80 101.71 2.09 1.20e+00 6.94e-01 3.03e+00 angle pdb=" N VAL J 51 " pdb=" CA VAL J 51 " pdb=" C VAL J 51 " ideal model delta sigma weight residual 109.34 112.96 -3.62 2.08e+00 2.31e-01 3.02e+00 ... (remaining 32297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 13041 15.24 - 30.48: 858 30.48 - 45.71: 286 45.71 - 60.95: 42 60.95 - 76.19: 14 Dihedral angle restraints: 14241 sinusoidal: 5358 harmonic: 8883 Sorted by residual: dihedral pdb=" CB CYS K 216 " pdb=" SG CYS K 216 " pdb=" SG CYS L 214 " pdb=" CB CYS L 214 " ideal model delta sinusoidal sigma weight residual 93.00 122.52 -29.52 1 1.00e+01 1.00e-02 1.25e+01 dihedral pdb=" CB CYS G 216 " pdb=" SG CYS G 216 " pdb=" SG CYS H 214 " pdb=" CB CYS H 214 " ideal model delta sinusoidal sigma weight residual 93.00 120.63 -27.63 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CB CYS M 216 " pdb=" SG CYS M 216 " pdb=" SG CYS N 214 " pdb=" CB CYS N 214 " ideal model delta sinusoidal sigma weight residual 93.00 120.06 -27.06 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 14238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2192 0.028 - 0.056: 987 0.056 - 0.083: 230 0.083 - 0.111: 222 0.111 - 0.139: 56 Chirality restraints: 3687 Sorted by residual: chirality pdb=" CA ILE J 21 " pdb=" N ILE J 21 " pdb=" C ILE J 21 " pdb=" CB ILE J 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE H 21 " pdb=" N ILE H 21 " pdb=" C ILE H 21 " pdb=" CB ILE H 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE N 21 " pdb=" N ILE N 21 " pdb=" C ILE N 21 " pdb=" CB ILE N 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 3684 not shown) Planarity restraints: 4111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO X 2 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO X 3 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO X 3 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO X 3 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 148 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 149 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 148 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 149 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.024 5.00e-02 4.00e+02 ... (remaining 4108 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5207 2.79 - 3.32: 19864 3.32 - 3.84: 36976 3.84 - 4.37: 43810 4.37 - 4.90: 76772 Nonbonded interactions: 182629 Sorted by model distance: nonbonded pdb=" OE1 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.262 3.040 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR H 14 " pdb=" OE1 GLN H 17 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR F 14 " pdb=" OE1 GLN F 17 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR B 14 " pdb=" OE1 GLN B 17 " model vdw 2.311 3.040 ... (remaining 182624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.630 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23758 Z= 0.095 Angle : 0.519 5.316 32372 Z= 0.272 Chirality : 0.040 0.139 3687 Planarity : 0.005 0.078 4111 Dihedral : 11.695 76.187 8456 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3055 helix: -2.44 (0.68), residues: 42 sheet: -1.00 (0.13), residues: 1358 loop : -1.15 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 108 TYR 0.019 0.001 TYR G 50 PHE 0.007 0.001 PHE J 98 TRP 0.017 0.002 TRP J 89 HIS 0.003 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00207 (23723) covalent geometry : angle 0.51912 (32302) SS BOND : bond 0.00150 ( 35) SS BOND : angle 0.61748 ( 70) hydrogen bonds : bond 0.23707 ( 771) hydrogen bonds : angle 9.83521 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 532 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 LEU cc_start: 0.8485 (tp) cc_final: 0.8199 (mm) REVERT: E 155 ASN cc_start: 0.4920 (m-40) cc_final: 0.4714 (m-40) REVERT: A 72 ASP cc_start: 0.7779 (t0) cc_final: 0.7441 (t0) outliers start: 3 outliers final: 2 residues processed: 533 average time/residue: 0.1655 time to fit residues: 134.7586 Evaluate side-chains 313 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain I residue 33 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN K 192 GLN L 38 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 81 GLN M 164 HIS N 137 ASN I 6 GLN I 39 GLN J 38 GLN J 166 GLN G 6 GLN H 189 HIS E 6 GLN E 39 GLN E 43 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS F 27 GLN F 38 GLN C 6 GLN C 35 HIS C 39 GLN D 137 ASN D 166 GLN A 164 HIS A 171 GLN B 137 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.212041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160675 restraints weight = 30942.406| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.04 r_work: 0.3463 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 23758 Z= 0.313 Angle : 0.678 8.312 32372 Z= 0.351 Chirality : 0.046 0.182 3687 Planarity : 0.006 0.059 4111 Dihedral : 4.204 16.396 3270 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.03 % Allowed : 12.21 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3055 helix: -3.62 (0.31), residues: 91 sheet: -0.55 (0.14), residues: 1316 loop : -0.63 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 77 TYR 0.023 0.002 TYR E 50 PHE 0.018 0.002 PHE H 98 TRP 0.026 0.003 TRP F 89 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00728 (23723) covalent geometry : angle 0.67631 (32302) SS BOND : bond 0.00540 ( 35) SS BOND : angle 1.25066 ( 70) hydrogen bonds : bond 0.04182 ( 771) hydrogen bonds : angle 7.01596 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 342 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 LEU cc_start: 0.6894 (mt) cc_final: 0.6320 (tt) REVERT: M 206 LYS cc_start: 0.5029 (tptt) cc_final: 0.4559 (tppt) REVERT: N 105 GLU cc_start: 0.6928 (pt0) cc_final: 0.6725 (pt0) REVERT: I 194 TYR cc_start: 0.7487 (m-10) cc_final: 0.6996 (m-10) REVERT: J 31 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8984 (t) REVERT: G 62 LYS cc_start: 0.8484 (tttt) cc_final: 0.8169 (ttmt) REVERT: G 175 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.3681 (tp) REVERT: H 47 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8097 (mm) REVERT: H 88 CYS cc_start: 0.6831 (p) cc_final: 0.6573 (p) REVERT: F 36 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8557 (pp) REVERT: F 61 ARG cc_start: 0.9025 (ptt-90) cc_final: 0.8685 (ptt90) REVERT: F 116 PHE cc_start: 0.8062 (m-10) cc_final: 0.7824 (m-10) REVERT: C 66 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6285 (tttp) REVERT: C 141 LEU cc_start: 0.6168 (tt) cc_final: 0.5713 (pt) REVERT: D 42 GLN cc_start: 0.7530 (tt0) cc_final: 0.7324 (tt0) REVERT: D 104 LEU cc_start: 0.7410 (tt) cc_final: 0.7093 (mm) outliers start: 80 outliers final: 50 residues processed: 400 average time/residue: 0.1568 time to fit residues: 97.1907 Evaluate side-chains 350 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 104 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 209 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 137 ASN J 166 GLN H 38 GLN H 166 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS B 38 GLN B 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.214016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163055 restraints weight = 31003.840| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.21 r_work: 0.3487 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23758 Z= 0.147 Angle : 0.554 7.550 32372 Z= 0.283 Chirality : 0.043 0.194 3687 Planarity : 0.005 0.070 4111 Dihedral : 3.942 17.652 3266 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.49 % Allowed : 13.23 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3055 helix: -3.52 (0.33), residues: 91 sheet: -0.34 (0.14), residues: 1309 loop : -0.23 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 77 TYR 0.016 0.001 TYR A 145 PHE 0.012 0.001 PHE I 166 TRP 0.015 0.002 TRP B 89 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00334 (23723) covalent geometry : angle 0.55347 (32302) SS BOND : bond 0.00218 ( 35) SS BOND : angle 0.76546 ( 70) hydrogen bonds : bond 0.03214 ( 771) hydrogen bonds : angle 6.24231 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 328 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 145 LYS cc_start: 0.8053 (tttt) cc_final: 0.7532 (mppt) REVERT: X 7 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: M 11 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7644 (mp) REVERT: M 124 LEU cc_start: 0.6819 (mt) cc_final: 0.6271 (tt) REVERT: M 206 LYS cc_start: 0.4993 (tptt) cc_final: 0.4508 (tppt) REVERT: I 175 LEU cc_start: 0.7684 (mt) cc_final: 0.7261 (mt) REVERT: I 194 TYR cc_start: 0.7362 (m-10) cc_final: 0.7041 (m-10) REVERT: J 27 TYR cc_start: 0.8948 (t80) cc_final: 0.8570 (t80) REVERT: G 175 LEU cc_start: 0.4365 (OUTLIER) cc_final: 0.3591 (tp) REVERT: H 88 CYS cc_start: 0.6709 (p) cc_final: 0.6384 (p) REVERT: F 61 ARG cc_start: 0.9012 (ptt-90) cc_final: 0.8661 (ptt90) REVERT: F 116 PHE cc_start: 0.8012 (m-10) cc_final: 0.7783 (m-10) REVERT: F 137 ASN cc_start: 0.7638 (t0) cc_final: 0.7336 (t0) REVERT: F 187 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: C 22 CYS cc_start: 0.4893 (t) cc_final: 0.4640 (t) REVERT: C 34 MET cc_start: 0.8554 (tpp) cc_final: 0.7711 (tpt) REVERT: C 66 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6380 (tttp) REVERT: C 141 LEU cc_start: 0.6197 (tt) cc_final: 0.5766 (pt) REVERT: D 104 LEU cc_start: 0.7428 (tt) cc_final: 0.7124 (mm) REVERT: A 10 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: B 117 ILE cc_start: 0.7204 (tt) cc_final: 0.6900 (pt) REVERT: B 166 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7397 (pt0) outliers start: 92 outliers final: 60 residues processed: 399 average time/residue: 0.1550 time to fit residues: 96.8072 Evaluate side-chains 353 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 286 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN M 81 GLN J 166 GLN E 43 GLN E 105 GLN C 39 GLN D 17 GLN A 6 GLN B 38 GLN B 137 ASN B 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.214068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163977 restraints weight = 30847.350| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.25 r_work: 0.3477 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23758 Z= 0.159 Angle : 0.545 7.699 32372 Z= 0.278 Chirality : 0.043 0.216 3687 Planarity : 0.005 0.055 4111 Dihedral : 3.910 17.851 3266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.17 % Allowed : 13.99 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3055 helix: -3.40 (0.36), residues: 91 sheet: -0.03 (0.14), residues: 1239 loop : -0.16 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 13 TYR 0.016 0.001 TYR A 145 PHE 0.017 0.001 PHE G 91 TRP 0.015 0.002 TRP F 89 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00366 (23723) covalent geometry : angle 0.54452 (32302) SS BOND : bond 0.00213 ( 35) SS BOND : angle 0.69412 ( 70) hydrogen bonds : bond 0.02939 ( 771) hydrogen bonds : angle 5.87885 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 300 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8559 (tp) REVERT: L 145 LYS cc_start: 0.7998 (tttt) cc_final: 0.7494 (mppt) REVERT: X 7 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.7924 (m-40) REVERT: X 47 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8549 (m-40) REVERT: M 11 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7296 (mp) REVERT: M 124 LEU cc_start: 0.6865 (mt) cc_final: 0.6242 (tt) REVERT: M 206 LYS cc_start: 0.4914 (tptt) cc_final: 0.4445 (tppt) REVERT: N 36 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8271 (pt) REVERT: I 108 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8408 (tt) REVERT: I 194 TYR cc_start: 0.7400 (m-10) cc_final: 0.7168 (m-10) REVERT: G 175 LEU cc_start: 0.4345 (OUTLIER) cc_final: 0.3614 (tp) REVERT: H 36 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7563 (pp) REVERT: H 88 CYS cc_start: 0.6379 (p) cc_final: 0.6170 (p) REVERT: E 13 ARG cc_start: 0.8105 (mmt-90) cc_final: 0.7811 (mmt-90) REVERT: E 138 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5868 (pp) REVERT: F 61 ARG cc_start: 0.9032 (ptt-90) cc_final: 0.8655 (ptt90) REVERT: F 187 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: C 22 CYS cc_start: 0.4975 (t) cc_final: 0.4706 (t) REVERT: C 34 MET cc_start: 0.8411 (tpp) cc_final: 0.7638 (tpt) REVERT: C 178 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6206 (mt) REVERT: D 6 GLN cc_start: 0.6449 (mp10) cc_final: 0.5635 (mp10) REVERT: D 104 LEU cc_start: 0.7386 (tt) cc_final: 0.7093 (mm) REVERT: A 10 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: A 175 LEU cc_start: 0.8790 (mt) cc_final: 0.8573 (mp) REVERT: B 117 ILE cc_start: 0.7207 (tt) cc_final: 0.6967 (pt) outliers start: 110 outliers final: 73 residues processed: 388 average time/residue: 0.1550 time to fit residues: 94.5954 Evaluate side-chains 363 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 278 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 251 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 192 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 23 ASN X 31 ASN M 39 GLN M 81 GLN N 38 GLN F 155 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN B 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.208014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157921 restraints weight = 30601.949| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.40 r_work: 0.3391 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.123 23758 Z= 0.389 Angle : 0.725 10.976 32372 Z= 0.371 Chirality : 0.048 0.244 3687 Planarity : 0.006 0.054 4111 Dihedral : 4.729 22.769 3266 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.93 % Allowed : 14.75 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3055 helix: -3.41 (0.35), residues: 91 sheet: -0.23 (0.14), residues: 1211 loop : -0.29 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 77 TYR 0.023 0.002 TYR E 50 PHE 0.023 0.002 PHE F 116 TRP 0.028 0.003 TRP F 89 HIS 0.007 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00913 (23723) covalent geometry : angle 0.72371 (32302) SS BOND : bond 0.00462 ( 35) SS BOND : angle 1.16221 ( 70) hydrogen bonds : bond 0.03701 ( 771) hydrogen bonds : angle 6.47668 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 279 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8494 (tp) REVERT: L 145 LYS cc_start: 0.7821 (tttt) cc_final: 0.7613 (mppt) REVERT: X 7 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7747 (m-40) REVERT: X 47 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8527 (m-40) REVERT: M 206 LYS cc_start: 0.5028 (tptt) cc_final: 0.4591 (tppt) REVERT: I 108 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8409 (tt) REVERT: I 194 TYR cc_start: 0.7055 (m-10) cc_final: 0.6844 (m-10) REVERT: J 33 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8900 (tp) REVERT: G 20 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7230 (ttp) REVERT: G 175 LEU cc_start: 0.4189 (OUTLIER) cc_final: 0.3470 (tp) REVERT: H 36 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7302 (pp) REVERT: F 137 ASN cc_start: 0.7764 (t0) cc_final: 0.7557 (t0) REVERT: C 34 MET cc_start: 0.8644 (tpp) cc_final: 0.7822 (tpt) REVERT: C 178 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6014 (mt) REVERT: D 74 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6782 (mtmm) REVERT: A 10 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: B 36 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8720 (pp) REVERT: B 81 GLU cc_start: 0.7867 (pm20) cc_final: 0.7551 (pm20) REVERT: B 117 ILE cc_start: 0.7145 (tt) cc_final: 0.6901 (pt) outliers start: 130 outliers final: 92 residues processed: 383 average time/residue: 0.1525 time to fit residues: 92.3862 Evaluate side-chains 356 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 252 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 134 optimal weight: 1.9990 chunk 238 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 166 GLN I 164 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN A 6 GLN B 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.211022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.167084 restraints weight = 30579.515| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.12 r_work: 0.3353 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23758 Z= 0.179 Angle : 0.572 7.865 32372 Z= 0.291 Chirality : 0.043 0.244 3687 Planarity : 0.005 0.053 4111 Dihedral : 4.327 19.603 3266 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.44 % Allowed : 16.03 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3055 helix: -3.40 (0.34), residues: 91 sheet: -0.00 (0.15), residues: 1176 loop : -0.21 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.015 0.001 TYR A 145 PHE 0.020 0.001 PHE G 91 TRP 0.020 0.002 TRP B 89 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (23723) covalent geometry : angle 0.57021 (32302) SS BOND : bond 0.00295 ( 35) SS BOND : angle 1.06529 ( 70) hydrogen bonds : bond 0.02910 ( 771) hydrogen bonds : angle 5.97954 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 283 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8511 (tp) REVERT: L 145 LYS cc_start: 0.7910 (tttt) cc_final: 0.7501 (mppt) REVERT: X 7 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7875 (m-40) REVERT: M 27 TYR cc_start: 0.8858 (p90) cc_final: 0.8635 (p90) REVERT: M 124 LEU cc_start: 0.7000 (mt) cc_final: 0.6349 (tt) REVERT: M 206 LYS cc_start: 0.5103 (tptt) cc_final: 0.4622 (tppt) REVERT: I 108 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8405 (tt) REVERT: J 27 TYR cc_start: 0.8982 (t80) cc_final: 0.8628 (t80) REVERT: G 20 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7118 (ttp) REVERT: G 175 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.3675 (tp) REVERT: H 36 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7171 (pp) REVERT: F 137 ASN cc_start: 0.7757 (t0) cc_final: 0.7487 (t0) REVERT: C 34 MET cc_start: 0.8602 (tpp) cc_final: 0.7798 (tpt) REVERT: C 102 TYR cc_start: 0.7493 (m-80) cc_final: 0.7144 (m-80) REVERT: C 178 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.5878 (mt) REVERT: D 104 LEU cc_start: 0.7283 (tt) cc_final: 0.6787 (mm) REVERT: A 10 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: A 175 LEU cc_start: 0.8719 (mt) cc_final: 0.8206 (mp) REVERT: B 36 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8843 (pp) REVERT: B 81 GLU cc_start: 0.7949 (pm20) cc_final: 0.7655 (pm20) REVERT: B 195 GLU cc_start: 0.6623 (pp20) cc_final: 0.6366 (pp20) outliers start: 117 outliers final: 85 residues processed: 374 average time/residue: 0.1464 time to fit residues: 87.3170 Evaluate side-chains 356 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 262 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 166 GLN Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 254 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 185 optimal weight: 0.0370 chunk 54 optimal weight: 0.0670 chunk 159 optimal weight: 8.9990 chunk 246 optimal weight: 0.7980 chunk 120 optimal weight: 0.0770 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 166 GLN J 34 ASN J 166 GLN J 189 HIS G 6 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.214125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168577 restraints weight = 30835.362| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.92 r_work: 0.3414 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23758 Z= 0.098 Angle : 0.527 11.444 32372 Z= 0.268 Chirality : 0.042 0.161 3687 Planarity : 0.005 0.055 4111 Dihedral : 3.953 18.008 3266 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.26 % Allowed : 17.21 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3055 helix: -3.32 (0.35), residues: 91 sheet: -0.09 (0.14), residues: 1372 loop : 0.09 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 13 TYR 0.018 0.001 TYR G 50 PHE 0.022 0.001 PHE G 91 TRP 0.018 0.001 TRP B 89 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00214 (23723) covalent geometry : angle 0.52641 (32302) SS BOND : bond 0.00151 ( 35) SS BOND : angle 0.82424 ( 70) hydrogen bonds : bond 0.02559 ( 771) hydrogen bonds : angle 5.47695 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 294 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8553 (mtp85) REVERT: M 11 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6890 (mp) REVERT: M 81 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7593 (tm130) REVERT: M 124 LEU cc_start: 0.6912 (mt) cc_final: 0.6360 (tt) REVERT: N 165 GLU cc_start: 0.8119 (pt0) cc_final: 0.7905 (pt0) REVERT: I 108 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8427 (tt) REVERT: J 27 TYR cc_start: 0.8905 (t80) cc_final: 0.8576 (t80) REVERT: G 20 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7178 (ttp) REVERT: H 36 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7117 (pp) REVERT: E 13 ARG cc_start: 0.8126 (mmt-90) cc_final: 0.7792 (mmt-90) REVERT: F 36 LEU cc_start: 0.8528 (pp) cc_final: 0.8242 (pt) REVERT: F 104 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8142 (tt) REVERT: F 137 ASN cc_start: 0.7517 (t0) cc_final: 0.7236 (t0) REVERT: C 34 MET cc_start: 0.8565 (tpp) cc_final: 0.7702 (tpt) REVERT: C 102 TYR cc_start: 0.7351 (m-80) cc_final: 0.7036 (m-80) REVERT: C 178 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6177 (mt) REVERT: D 104 LEU cc_start: 0.7439 (tt) cc_final: 0.6889 (mm) REVERT: A 10 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: A 176 TYR cc_start: 0.7789 (m-10) cc_final: 0.7542 (m-10) REVERT: B 81 GLU cc_start: 0.7857 (pm20) cc_final: 0.7573 (pm20) REVERT: B 137 ASN cc_start: 0.6627 (t0) cc_final: 0.6373 (m-40) REVERT: B 195 GLU cc_start: 0.6433 (pp20) cc_final: 0.6135 (pp20) outliers start: 86 outliers final: 57 residues processed: 358 average time/residue: 0.1496 time to fit residues: 84.8753 Evaluate side-chains 336 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 228 optimal weight: 0.0030 chunk 296 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 173 optimal weight: 40.0000 chunk 219 optimal weight: 9.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.206126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.158069 restraints weight = 30625.236| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.31 r_work: 0.3393 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.125 23758 Z= 0.425 Angle : 0.749 10.151 32372 Z= 0.383 Chirality : 0.049 0.232 3687 Planarity : 0.006 0.065 4111 Dihedral : 4.740 19.284 3266 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.51 % Allowed : 16.03 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3055 helix: -3.32 (0.34), residues: 91 sheet: -0.06 (0.14), residues: 1246 loop : -0.30 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 77 TYR 0.027 0.003 TYR D 27D PHE 0.024 0.003 PHE G 91 TRP 0.024 0.003 TRP F 89 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.01004 (23723) covalent geometry : angle 0.74670 (32302) SS BOND : bond 0.00506 ( 35) SS BOND : angle 1.43493 ( 70) hydrogen bonds : bond 0.03671 ( 771) hydrogen bonds : angle 6.27513 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 255 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 85 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: L 122 ASP cc_start: 0.7650 (m-30) cc_final: 0.7095 (p0) REVERT: X 7 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: X 47 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8516 (m-40) REVERT: M 206 LYS cc_start: 0.5195 (tptt) cc_final: 0.4743 (tppt) REVERT: N 36 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8308 (pt) REVERT: I 108 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8419 (tt) REVERT: G 20 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7225 (ttp) REVERT: E 105 GLN cc_start: 0.8683 (pm20) cc_final: 0.8406 (pm20) REVERT: C 178 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.5957 (mt) REVERT: D 30 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7288 (ttmt) REVERT: D 74 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6863 (mtmm) REVERT: A 10 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: A 72 ASP cc_start: 0.8782 (t0) cc_final: 0.8516 (t0) REVERT: A 138 LEU cc_start: 0.8155 (pp) cc_final: 0.7863 (pt) REVERT: B 36 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8657 (pp) REVERT: B 81 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: B 137 ASN cc_start: 0.6761 (t0) cc_final: 0.6529 (m-40) REVERT: B 195 GLU cc_start: 0.6930 (pp20) cc_final: 0.6559 (pp20) outliers start: 119 outliers final: 84 residues processed: 352 average time/residue: 0.1442 time to fit residues: 81.7929 Evaluate side-chains 337 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 242 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 126 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 160 GLN J 34 ASN G 6 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN A 6 GLN B 137 ASN B 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.210220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.158637 restraints weight = 30667.494| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.96 r_work: 0.3472 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23758 Z= 0.195 Angle : 0.589 8.480 32372 Z= 0.300 Chirality : 0.043 0.168 3687 Planarity : 0.005 0.058 4111 Dihedral : 4.381 18.815 3266 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.64 % Allowed : 17.25 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3055 helix: -3.22 (0.35), residues: 91 sheet: 0.02 (0.14), residues: 1309 loop : -0.08 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 77 TYR 0.022 0.002 TYR D 27D PHE 0.023 0.001 PHE G 91 TRP 0.024 0.002 TRP D 89 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00455 (23723) covalent geometry : angle 0.58765 (32302) SS BOND : bond 0.00197 ( 35) SS BOND : angle 1.14977 ( 70) hydrogen bonds : bond 0.02844 ( 771) hydrogen bonds : angle 5.85161 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 254 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 85 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: K 105 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: L 73 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8540 (tp) REVERT: M 27 TYR cc_start: 0.8870 (p90) cc_final: 0.8591 (p90) REVERT: M 206 LYS cc_start: 0.5307 (tptt) cc_final: 0.4856 (tppt) REVERT: N 36 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8228 (pt) REVERT: I 108 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8476 (tt) REVERT: I 154 TRP cc_start: 0.6708 (m100) cc_final: 0.6284 (m100) REVERT: J 27 TYR cc_start: 0.8985 (t80) cc_final: 0.8614 (t80) REVERT: G 6 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7151 (mt0) REVERT: G 20 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7112 (ttt) REVERT: G 175 LEU cc_start: 0.4316 (tp) cc_final: 0.4110 (tp) REVERT: H 36 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7214 (pp) REVERT: C 34 MET cc_start: 0.8527 (mmm) cc_final: 0.8312 (tpt) REVERT: C 102 TYR cc_start: 0.7440 (m-80) cc_final: 0.7118 (m-80) REVERT: C 178 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6073 (mt) REVERT: D 4 MET cc_start: 0.6762 (tpp) cc_final: 0.6293 (tpp) REVERT: D 30 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7288 (ttmt) REVERT: A 10 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: A 72 ASP cc_start: 0.8821 (t0) cc_final: 0.8539 (t0) REVERT: B 137 ASN cc_start: 0.6789 (t0) cc_final: 0.6576 (m-40) REVERT: B 195 GLU cc_start: 0.6714 (pp20) cc_final: 0.6277 (pp20) outliers start: 96 outliers final: 69 residues processed: 328 average time/residue: 0.1447 time to fit residues: 76.4256 Evaluate side-chains 326 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 247 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 164 HIS Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 58 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 270 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN J 199 GLN G 6 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.207731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154281 restraints weight = 30539.586| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.98 r_work: 0.3433 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 23758 Z= 0.297 Angle : 0.659 8.559 32372 Z= 0.335 Chirality : 0.046 0.267 3687 Planarity : 0.005 0.069 4111 Dihedral : 4.577 18.604 3266 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.64 % Allowed : 17.29 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3055 helix: -3.18 (0.36), residues: 91 sheet: -0.08 (0.14), residues: 1239 loop : -0.20 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 77 TYR 0.024 0.002 TYR D 27D PHE 0.020 0.002 PHE G 91 TRP 0.024 0.003 TRP D 89 HIS 0.007 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00702 (23723) covalent geometry : angle 0.65701 (32302) SS BOND : bond 0.00333 ( 35) SS BOND : angle 1.33987 ( 70) hydrogen bonds : bond 0.03164 ( 771) hydrogen bonds : angle 6.03246 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 252 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 85 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: L 73 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8556 (tp) REVERT: M 206 LYS cc_start: 0.5377 (tptt) cc_final: 0.4929 (tppt) REVERT: N 36 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8286 (pt) REVERT: I 108 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8459 (tt) REVERT: G 20 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7191 (ttp) REVERT: G 175 LEU cc_start: 0.4714 (tp) cc_final: 0.4404 (tp) REVERT: H 187 GLU cc_start: 0.3682 (OUTLIER) cc_final: 0.2785 (tp30) REVERT: E 105 GLN cc_start: 0.8734 (pm20) cc_final: 0.8489 (pm20) REVERT: F 137 ASN cc_start: 0.7675 (t0) cc_final: 0.7466 (t0) REVERT: C 102 TYR cc_start: 0.7516 (m-80) cc_final: 0.7173 (m-80) REVERT: C 178 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6029 (mt) REVERT: D 4 MET cc_start: 0.6990 (tpp) cc_final: 0.6533 (tpp) REVERT: D 42 GLN cc_start: 0.7029 (tt0) cc_final: 0.6127 (mt0) REVERT: A 10 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: A 72 ASP cc_start: 0.8854 (t0) cc_final: 0.8576 (t0) REVERT: A 138 LEU cc_start: 0.8168 (pp) cc_final: 0.7912 (pt) REVERT: A 143 LYS cc_start: 0.7774 (tptt) cc_final: 0.7509 (tptt) REVERT: B 195 GLU cc_start: 0.6882 (pp20) cc_final: 0.6275 (pp20) outliers start: 96 outliers final: 81 residues processed: 328 average time/residue: 0.1460 time to fit residues: 77.4950 Evaluate side-chains 332 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 243 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 164 HIS Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN G 6 GLN C 6 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN B 138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.212679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158622 restraints weight = 30551.433| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.04 r_work: 0.3496 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23758 Z= 0.111 Angle : 0.551 8.443 32372 Z= 0.279 Chirality : 0.042 0.186 3687 Planarity : 0.005 0.061 4111 Dihedral : 4.187 27.532 3266 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 17.93 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3055 helix: -3.12 (0.37), residues: 91 sheet: 0.07 (0.14), residues: 1337 loop : 0.04 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 77 TYR 0.020 0.001 TYR I 194 PHE 0.018 0.001 PHE G 91 TRP 0.024 0.002 TRP B 89 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00250 (23723) covalent geometry : angle 0.54942 (32302) SS BOND : bond 0.00222 ( 35) SS BOND : angle 0.92546 ( 70) hydrogen bonds : bond 0.02554 ( 771) hydrogen bonds : angle 5.48909 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7566.81 seconds wall clock time: 129 minutes 53.51 seconds (7793.51 seconds total)