Starting phenix.real_space_refine on Thu Mar 5 10:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rwk_10040/03_2026/6rwk_10040.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwk_10040/03_2026/6rwk_10040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rwk_10040/03_2026/6rwk_10040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwk_10040/03_2026/6rwk_10040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwk_10040/03_2026/6rwk_10040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwk_10040/03_2026/6rwk_10040.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 14224 2.51 5 N 3408 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 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: 21760 Number of models: 1 Model: "" Number of chains: 32 Chain: "X" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "Y" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "Z" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "0" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "2" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "4" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "6" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "8" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "x" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "y" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "z" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "1" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "3" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "5" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "7" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "9" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "P" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "S" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "U" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "H" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "K" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "N" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "Q" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "T" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "V" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Time building chain proxies: 4.67, per 1000 atoms: 0.21 Number of scatterers: 21760 At special positions: 0 Unit cell: (170.194, 170.194, 88.5562, 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 32 16.00 O 4096 8.00 N 3408 7.00 C 14224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 33 sheets defined 34.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'X' and resid 45 through 57 Processing helix chain 'X' and resid 65 through 68 Processing helix chain 'X' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET X 83 " --> pdb=" O ASN X 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 110 No H-bonds generated for 'chain 'X' and resid 108 through 110' Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 155 through 168 Processing helix chain 'Y' and resid 45 through 57 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET Y 83 " --> pdb=" O ASN Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 110 No H-bonds generated for 'chain 'Y' and resid 108 through 110' Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 155 through 168 Processing helix chain 'Z' and resid 45 through 57 Processing helix chain 'Z' and resid 65 through 68 Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET Z 83 " --> pdb=" O ASN Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 110 No H-bonds generated for 'chain 'Z' and resid 108 through 110' Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 155 through 168 Processing helix chain '0' and resid 45 through 57 Processing helix chain '0' and resid 65 through 68 Processing helix chain '0' and resid 79 through 91 removed outlier: 3.842A pdb=" N MET 0 83 " --> pdb=" O ASN 0 79 " (cutoff:3.500A) Processing helix chain '0' and resid 108 through 110 No H-bonds generated for 'chain '0' and resid 108 through 110' Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 155 through 168 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 65 through 68 Processing helix chain '2' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET 2 83 " --> pdb=" O ASN 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 110 No H-bonds generated for 'chain '2' and resid 108 through 110' Processing helix chain '2' and resid 121 through 132 Processing helix chain '2' and resid 155 through 168 Processing helix chain '4' and resid 45 through 57 Processing helix chain '4' and resid 65 through 68 Processing helix chain '4' and resid 79 through 91 removed outlier: 3.842A pdb=" N MET 4 83 " --> pdb=" O ASN 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 108 through 110 No H-bonds generated for 'chain '4' and resid 108 through 110' Processing helix chain '4' and resid 121 through 132 Processing helix chain '4' and resid 155 through 168 Processing helix chain '6' and resid 45 through 57 Processing helix chain '6' and resid 65 through 68 Processing helix chain '6' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET 6 83 " --> pdb=" O ASN 6 79 " (cutoff:3.500A) Processing helix chain '6' and resid 108 through 110 No H-bonds generated for 'chain '6' and resid 108 through 110' Processing helix chain '6' and resid 121 through 132 Processing helix chain '6' and resid 155 through 168 Processing helix chain '8' and resid 45 through 57 Processing helix chain '8' and resid 65 through 68 Processing helix chain '8' and resid 79 through 91 removed outlier: 3.844A pdb=" N MET 8 83 " --> pdb=" O ASN 8 79 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 110 No H-bonds generated for 'chain '8' and resid 108 through 110' Processing helix chain '8' and resid 121 through 132 Processing helix chain '8' and resid 155 through 168 Processing helix chain 'x' and resid 45 through 57 Processing helix chain 'x' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET x 83 " --> pdb=" O ASN x 79 " (cutoff:3.500A) Processing helix chain 'x' and resid 108 through 110 No H-bonds generated for 'chain 'x' and resid 108 through 110' Processing helix chain 'x' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU x 125 " --> pdb=" O SER x 121 " (cutoff:3.500A) Processing helix chain 'x' and resid 155 through 168 Processing helix chain 'y' and resid 45 through 57 Processing helix chain 'y' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET y 83 " --> pdb=" O ASN y 79 " (cutoff:3.500A) Processing helix chain 'y' and resid 108 through 110 No H-bonds generated for 'chain 'y' and resid 108 through 110' Processing helix chain 'y' and resid 121 through 132 removed outlier: 3.541A pdb=" N LEU y 125 " --> pdb=" O SER y 121 " (cutoff:3.500A) Processing helix chain 'y' and resid 155 through 168 Processing helix chain 'z' and resid 45 through 57 Processing helix chain 'z' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET z 83 " --> pdb=" O ASN z 79 " (cutoff:3.500A) Processing helix chain 'z' and resid 108 through 110 No H-bonds generated for 'chain 'z' and resid 108 through 110' Processing helix chain 'z' and resid 121 through 132 removed outlier: 3.541A pdb=" N LEU z 125 " --> pdb=" O SER z 121 " (cutoff:3.500A) Processing helix chain 'z' and resid 155 through 168 Processing helix chain '1' and resid 45 through 57 Processing helix chain '1' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET 1 83 " --> pdb=" O ASN 1 79 " (cutoff:3.500A) Processing helix chain '1' and resid 108 through 110 No H-bonds generated for 'chain '1' and resid 108 through 110' Processing helix chain '1' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 1 125 " --> pdb=" O SER 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 155 through 168 Processing helix chain '3' and resid 45 through 57 Processing helix chain '3' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET 3 83 " --> pdb=" O ASN 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 110 No H-bonds generated for 'chain '3' and resid 108 through 110' Processing helix chain '3' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 3 125 " --> pdb=" O SER 3 121 " (cutoff:3.500A) Processing helix chain '3' and resid 155 through 168 Processing helix chain '5' and resid 45 through 57 Processing helix chain '5' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET 5 83 " --> pdb=" O ASN 5 79 " (cutoff:3.500A) Processing helix chain '5' and resid 108 through 110 No H-bonds generated for 'chain '5' and resid 108 through 110' Processing helix chain '5' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 5 125 " --> pdb=" O SER 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 155 through 168 Processing helix chain '7' and resid 45 through 57 Processing helix chain '7' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET 7 83 " --> pdb=" O ASN 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 108 through 110 No H-bonds generated for 'chain '7' and resid 108 through 110' Processing helix chain '7' and resid 121 through 132 removed outlier: 3.541A pdb=" N LEU 7 125 " --> pdb=" O SER 7 121 " (cutoff:3.500A) Processing helix chain '7' and resid 155 through 168 Processing helix chain '9' and resid 45 through 57 Processing helix chain '9' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET 9 83 " --> pdb=" O ASN 9 79 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 110 No H-bonds generated for 'chain '9' and resid 108 through 110' Processing helix chain '9' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 9 125 " --> pdb=" O SER 9 121 " (cutoff:3.500A) Processing helix chain '9' and resid 155 through 168 Processing sheet with id=AA1, first strand: chain 'X' and resid 37 through 44 removed outlier: 4.537A pdb=" N SER X 42 " --> pdb=" O ILE X 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE X 71 " --> pdb=" O SER X 42 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG X 70 " --> pdb=" O TRP E 364 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE E 366 " --> pdb=" O ARG X 70 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER X 72 " --> pdb=" O PHE E 366 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER x 42 " --> pdb=" O ILE x 71 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE x 71 " --> pdb=" O SER x 42 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG x 70 " --> pdb=" O TRP G 364 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE G 366 " --> pdb=" O ARG x 70 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER x 72 " --> pdb=" O PHE G 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER Y 42 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Y 71 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG Y 70 " --> pdb=" O TRP H 364 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE H 366 " --> pdb=" O ARG Y 70 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER Y 72 " --> pdb=" O PHE H 366 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 349 " --> pdb=" O VAL y 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER y 42 " --> pdb=" O ILE y 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE y 71 " --> pdb=" O SER y 42 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG y 70 " --> pdb=" O TRP J 364 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE J 366 " --> pdb=" O ARG y 70 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER y 72 " --> pdb=" O PHE J 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER Z 42 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Z 71 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG Z 70 " --> pdb=" O TRP K 364 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE K 366 " --> pdb=" O ARG Z 70 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER Z 72 " --> pdb=" O PHE K 366 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER z 42 " --> pdb=" O ILE z 71 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE z 71 " --> pdb=" O SER z 42 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG z 70 " --> pdb=" O TRP M 364 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE M 366 " --> pdb=" O ARG z 70 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER z 72 " --> pdb=" O PHE M 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 0 42 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 0 71 " --> pdb=" O SER 0 42 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG 0 70 " --> pdb=" O TRP N 364 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE N 366 " --> pdb=" O ARG 0 70 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER 0 72 " --> pdb=" O PHE N 366 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR N 349 " --> pdb=" O VAL 1 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 1 42 " --> pdb=" O ILE 1 71 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE 1 71 " --> pdb=" O SER 1 42 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG 1 70 " --> pdb=" O TRP P 364 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE P 366 " --> pdb=" O ARG 1 70 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER 1 72 " --> pdb=" O PHE P 366 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER 2 42 " --> pdb=" O ILE 2 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 2 71 " --> pdb=" O SER 2 42 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG 2 70 " --> pdb=" O TRP Q 364 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE Q 366 " --> pdb=" O ARG 2 70 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER 2 72 " --> pdb=" O PHE Q 366 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR Q 349 " --> pdb=" O VAL 3 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 3 42 " --> pdb=" O ILE 3 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 3 71 " --> pdb=" O SER 3 42 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG 3 70 " --> pdb=" O TRP S 364 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE S 366 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER 3 72 " --> pdb=" O PHE S 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 4 42 " --> pdb=" O ILE 4 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 4 71 " --> pdb=" O SER 4 42 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG 4 70 " --> pdb=" O TRP T 364 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE T 366 " --> pdb=" O ARG 4 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER 4 72 " --> pdb=" O PHE T 366 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR T 349 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER 5 42 " --> pdb=" O ILE 5 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 5 71 " --> pdb=" O SER 5 42 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG 5 70 " --> pdb=" O TRP U 364 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE U 366 " --> pdb=" O ARG 5 70 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER 5 72 " --> pdb=" O PHE U 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 6 42 " --> pdb=" O ILE 6 71 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE 6 71 " --> pdb=" O SER 6 42 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG 6 70 " --> pdb=" O TRP V 364 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE V 366 " --> pdb=" O ARG 6 70 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER 6 72 " --> pdb=" O PHE V 366 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR V 349 " --> pdb=" O VAL 7 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 7 42 " --> pdb=" O ILE 7 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 7 71 " --> pdb=" O SER 7 42 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG 7 70 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE A 366 " --> pdb=" O ARG 7 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER 7 72 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 8 42 " --> pdb=" O ILE 8 71 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE 8 71 " --> pdb=" O SER 8 42 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG 8 70 " --> pdb=" O TRP B 364 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE B 366 " --> pdb=" O ARG 8 70 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER 8 72 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 9 42 " --> pdb=" O ILE 9 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 9 71 " --> pdb=" O SER 9 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG 9 70 " --> pdb=" O TRP D 364 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE D 366 " --> pdb=" O ARG 9 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER 9 72 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 60 through 62 Processing sheet with id=AA3, first strand: chain 'X' and resid 111 through 116 Processing sheet with id=AA4, first strand: chain 'Y' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'Y' and resid 111 through 116 Processing sheet with id=AA6, first strand: chain 'Z' and resid 60 through 62 Processing sheet with id=AA7, first strand: chain 'Z' and resid 111 through 116 Processing sheet with id=AA8, first strand: chain '0' and resid 60 through 62 Processing sheet with id=AA9, first strand: chain '0' and resid 111 through 116 Processing sheet with id=AB1, first strand: chain '2' and resid 60 through 62 Processing sheet with id=AB2, first strand: chain '2' and resid 111 through 116 Processing sheet with id=AB3, first strand: chain '4' and resid 60 through 62 Processing sheet with id=AB4, first strand: chain '4' and resid 111 through 116 Processing sheet with id=AB5, first strand: chain '6' and resid 60 through 62 Processing sheet with id=AB6, first strand: chain '6' and resid 111 through 116 Processing sheet with id=AB7, first strand: chain '8' and resid 60 through 62 Processing sheet with id=AB8, first strand: chain '8' and resid 111 through 116 Processing sheet with id=AB9, first strand: chain 'x' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL x 61 " --> pdb=" O ILE x 104 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP x 106 " --> pdb=" O VAL x 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'x' and resid 111 through 116 Processing sheet with id=AC2, first strand: chain 'y' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL y 61 " --> pdb=" O ILE y 104 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP y 106 " --> pdb=" O VAL y 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'y' and resid 111 through 116 Processing sheet with id=AC4, first strand: chain 'z' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL z 61 " --> pdb=" O ILE z 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP z 106 " --> pdb=" O VAL z 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'z' and resid 111 through 116 Processing sheet with id=AC6, first strand: chain '1' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 1 61 " --> pdb=" O ILE 1 104 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP 1 106 " --> pdb=" O VAL 1 61 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '1' and resid 111 through 116 Processing sheet with id=AC8, first strand: chain '3' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 3 61 " --> pdb=" O ILE 3 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 3 106 " --> pdb=" O VAL 3 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 111 through 116 Processing sheet with id=AD1, first strand: chain '5' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 5 61 " --> pdb=" O ILE 5 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 5 106 " --> pdb=" O VAL 5 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 111 through 116 Processing sheet with id=AD3, first strand: chain '7' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 7 61 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 7 106 " --> pdb=" O VAL 7 61 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 111 through 116 Processing sheet with id=AD5, first strand: chain '9' and resid 61 through 62 removed outlier: 6.787A pdb=" N VAL 9 61 " --> pdb=" O ILE 9 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 9 106 " --> pdb=" O VAL 9 61 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '9' and resid 111 through 116 1021 hydrogen bonds defined for protein. 2784 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: 4.20 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6720 1.34 - 1.45: 3854 1.45 - 1.57: 11586 1.57 - 1.68: 0 1.68 - 1.80: 64 Bond restraints: 22224 Sorted by residual: bond pdb=" C PRO x 140 " pdb=" O PRO x 140 " ideal model delta sigma weight residual 1.235 1.255 -0.020 1.30e-02 5.92e+03 2.38e+00 bond pdb=" C PRO z 140 " pdb=" O PRO z 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C PRO y 140 " pdb=" O PRO y 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C PRO 9 140 " pdb=" O PRO 9 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C PRO 7 140 " pdb=" O PRO 7 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 ... (remaining 22219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 28186 1.37 - 2.74: 1481 2.74 - 4.11: 305 4.11 - 5.48: 76 5.48 - 6.85: 32 Bond angle restraints: 30080 Sorted by residual: angle pdb=" CA PRO 6 140 " pdb=" C PRO 6 140 " pdb=" N ILE 6 141 " ideal model delta sigma weight residual 116.70 109.85 6.85 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO 2 140 " pdb=" C PRO 2 140 " pdb=" N ILE 2 141 " ideal model delta sigma weight residual 116.70 109.85 6.85 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO 0 140 " pdb=" C PRO 0 140 " pdb=" N ILE 0 141 " ideal model delta sigma weight residual 116.70 109.86 6.84 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO Y 140 " pdb=" C PRO Y 140 " pdb=" N ILE Y 141 " ideal model delta sigma weight residual 116.70 109.87 6.83 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO 4 140 " pdb=" C PRO 4 140 " pdb=" N ILE 4 141 " ideal model delta sigma weight residual 116.70 109.88 6.82 2.07e+00 2.33e-01 1.09e+01 ... (remaining 30075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 10852 11.41 - 22.83: 1604 22.83 - 34.24: 489 34.24 - 45.65: 175 45.65 - 57.06: 128 Dihedral angle restraints: 13248 sinusoidal: 5280 harmonic: 7968 Sorted by residual: dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP S 341 " pdb=" C ASP S 341 " pdb=" N ASP S 342 " pdb=" CA ASP S 342 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP U 341 " pdb=" C ASP U 341 " pdb=" N ASP U 342 " pdb=" CA ASP U 342 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 13245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2045 0.034 - 0.068: 873 0.068 - 0.102: 311 0.102 - 0.135: 131 0.135 - 0.169: 32 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA PRO Y 140 " pdb=" N PRO Y 140 " pdb=" C PRO Y 140 " pdb=" CB PRO Y 140 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA PRO X 140 " pdb=" N PRO X 140 " pdb=" C PRO X 140 " pdb=" CB PRO X 140 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA PRO 6 140 " pdb=" N PRO 6 140 " pdb=" C PRO 6 140 " pdb=" CB PRO 6 140 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 3389 not shown) Planarity restraints: 3744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 3 139 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO 3 140 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO 3 140 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO 3 140 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR z 139 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO z 140 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO z 140 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO z 140 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR Z 139 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO Z 140 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO Z 140 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO Z 140 " -0.028 5.00e-02 4.00e+02 ... (remaining 3741 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1576 2.73 - 3.27: 22031 3.27 - 3.81: 34195 3.81 - 4.36: 39761 4.36 - 4.90: 70636 Nonbonded interactions: 168199 Sorted by model distance: nonbonded pdb=" OG SER 4 47 " pdb=" NH1 ARG 4 51 " model vdw 2.183 3.120 nonbonded pdb=" OG SER Z 47 " pdb=" NH1 ARG Z 51 " model vdw 2.184 3.120 nonbonded pdb=" OG SER 0 47 " pdb=" NH1 ARG 0 51 " model vdw 2.184 3.120 nonbonded pdb=" OG SER 2 47 " pdb=" NH1 ARG 2 51 " model vdw 2.184 3.120 nonbonded pdb=" OG SER X 47 " pdb=" NH1 ARG X 51 " model vdw 2.184 3.120 ... (remaining 168194 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.940 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 22224 Z= 0.325 Angle : 0.757 6.848 30080 Z= 0.403 Chirality : 0.046 0.169 3392 Planarity : 0.005 0.050 3744 Dihedral : 13.644 57.064 8128 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 5.83 % Allowed : 10.50 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.14), residues: 2624 helix: -1.48 (0.16), residues: 928 sheet: -2.44 (0.17), residues: 752 loop : -3.75 (0.14), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 6 138 TYR 0.014 0.002 TYR 2 151 PHE 0.010 0.002 PHE U 366 TRP 0.006 0.001 TRP T 364 HIS 0.003 0.001 HIS S 363 Details of bonding type rmsd covalent geometry : bond 0.00707 (22224) covalent geometry : angle 0.75725 (30080) hydrogen bonds : bond 0.11667 ( 1021) hydrogen bonds : angle 7.12063 ( 2784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1030 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 68 LYS cc_start: 0.9387 (mttt) cc_final: 0.9184 (mttp) REVERT: X 85 GLU cc_start: 0.8561 (tp30) cc_final: 0.8225 (tm-30) REVERT: X 88 THR cc_start: 0.9574 (m) cc_final: 0.9248 (p) REVERT: X 106 ASP cc_start: 0.8447 (t0) cc_final: 0.8051 (t0) REVERT: X 117 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8395 (pp) REVERT: X 133 ASN cc_start: 0.9082 (m-40) cc_final: 0.8251 (t0) REVERT: X 144 ASN cc_start: 0.8769 (t0) cc_final: 0.8424 (t0) REVERT: Y 37 LYS cc_start: 0.9197 (tttt) cc_final: 0.8039 (tptm) REVERT: Y 88 THR cc_start: 0.9626 (m) cc_final: 0.9324 (p) REVERT: Y 97 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8717 (tttm) REVERT: Y 106 ASP cc_start: 0.8465 (t0) cc_final: 0.8166 (t0) REVERT: Y 117 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8155 (pp) REVERT: Y 133 ASN cc_start: 0.9143 (m-40) cc_final: 0.8691 (t0) REVERT: Y 144 ASN cc_start: 0.8694 (t0) cc_final: 0.8310 (t0) REVERT: Z 68 LYS cc_start: 0.9394 (mttt) cc_final: 0.9159 (mttp) REVERT: Z 85 GLU cc_start: 0.8555 (tp30) cc_final: 0.8255 (tm-30) REVERT: Z 88 THR cc_start: 0.9579 (m) cc_final: 0.9262 (p) REVERT: Z 106 ASP cc_start: 0.8451 (t0) cc_final: 0.8063 (t0) REVERT: Z 117 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8397 (pp) REVERT: Z 133 ASN cc_start: 0.9085 (m-40) cc_final: 0.8245 (t0) REVERT: Z 144 ASN cc_start: 0.8778 (t0) cc_final: 0.8438 (t0) REVERT: 0 88 THR cc_start: 0.9649 (m) cc_final: 0.9362 (p) REVERT: 0 97 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8759 (tttm) REVERT: 0 106 ASP cc_start: 0.8498 (t0) cc_final: 0.8215 (t0) REVERT: 0 117 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.7905 (pp) REVERT: 0 133 ASN cc_start: 0.9130 (m-40) cc_final: 0.8588 (t0) REVERT: 0 144 ASN cc_start: 0.8648 (t0) cc_final: 0.8281 (t0) REVERT: 2 68 LYS cc_start: 0.9395 (mttt) cc_final: 0.9167 (mttp) REVERT: 2 85 GLU cc_start: 0.8570 (tp30) cc_final: 0.8316 (tm-30) REVERT: 2 88 THR cc_start: 0.9596 (m) cc_final: 0.9293 (p) REVERT: 2 106 ASP cc_start: 0.8492 (t0) cc_final: 0.8172 (t0) REVERT: 2 117 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8385 (pp) REVERT: 2 133 ASN cc_start: 0.9099 (m-40) cc_final: 0.8274 (t0) REVERT: 2 144 ASN cc_start: 0.8789 (t0) cc_final: 0.8423 (t0) REVERT: 4 88 THR cc_start: 0.9669 (m) cc_final: 0.9427 (p) REVERT: 4 97 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8781 (tttm) REVERT: 4 106 ASP cc_start: 0.8506 (t0) cc_final: 0.8232 (t0) REVERT: 4 117 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7938 (pp) REVERT: 4 133 ASN cc_start: 0.9069 (m-40) cc_final: 0.8494 (t0) REVERT: 4 144 ASN cc_start: 0.8648 (t0) cc_final: 0.8283 (t0) REVERT: 6 68 LYS cc_start: 0.9403 (mttt) cc_final: 0.9157 (mttp) REVERT: 6 85 GLU cc_start: 0.8564 (tp30) cc_final: 0.8311 (tm-30) REVERT: 6 88 THR cc_start: 0.9594 (m) cc_final: 0.9290 (p) REVERT: 6 106 ASP cc_start: 0.8475 (t0) cc_final: 0.8157 (t0) REVERT: 6 117 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8396 (pp) REVERT: 6 133 ASN cc_start: 0.9094 (m-40) cc_final: 0.8267 (t0) REVERT: 6 144 ASN cc_start: 0.8781 (t0) cc_final: 0.8430 (t0) REVERT: 8 37 LYS cc_start: 0.9165 (tttt) cc_final: 0.7828 (tptm) REVERT: 8 88 THR cc_start: 0.9599 (m) cc_final: 0.9286 (p) REVERT: 8 97 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8630 (tttm) REVERT: 8 106 ASP cc_start: 0.8441 (t0) cc_final: 0.8157 (t0) REVERT: 8 117 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7919 (pp) REVERT: 8 133 ASN cc_start: 0.9089 (m-40) cc_final: 0.8649 (t0) REVERT: 8 144 ASN cc_start: 0.8696 (t0) cc_final: 0.8367 (t0) REVERT: x 37 LYS cc_start: 0.8946 (mttt) cc_final: 0.8643 (tttt) REVERT: x 70 ARG cc_start: 0.8707 (mtt-85) cc_final: 0.8267 (mtt-85) REVERT: x 85 GLU cc_start: 0.8449 (tp30) cc_final: 0.8078 (tm-30) REVERT: x 86 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8367 (ttpp) REVERT: x 97 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8388 (tttp) REVERT: x 109 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7735 (mt-10) REVERT: x 117 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8158 (pp) REVERT: x 120 ILE cc_start: 0.9132 (mt) cc_final: 0.8796 (mm) REVERT: x 138 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8295 (mtm-85) REVERT: y 48 PHE cc_start: 0.9212 (t80) cc_final: 0.8869 (t80) REVERT: y 51 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: y 58 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: y 82 GLU cc_start: 0.8487 (mp0) cc_final: 0.8264 (mp0) REVERT: y 84 LEU cc_start: 0.9321 (tp) cc_final: 0.8942 (tp) REVERT: y 85 GLU cc_start: 0.8609 (tp30) cc_final: 0.8256 (tm-30) REVERT: y 86 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8636 (ttpp) REVERT: y 97 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8489 (tttm) REVERT: y 109 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7909 (mt-10) REVERT: y 117 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8225 (pp) REVERT: y 120 ILE cc_start: 0.9057 (mt) cc_final: 0.8515 (mp) REVERT: y 128 TYR cc_start: 0.9154 (t80) cc_final: 0.8915 (t80) REVERT: z 37 LYS cc_start: 0.8864 (mttt) cc_final: 0.8600 (ttmt) REVERT: z 74 GLU cc_start: 0.7914 (tt0) cc_final: 0.7382 (tt0) REVERT: z 82 GLU cc_start: 0.8704 (mp0) cc_final: 0.8372 (mp0) REVERT: z 85 GLU cc_start: 0.8515 (tp30) cc_final: 0.8055 (tm-30) REVERT: z 86 LYS cc_start: 0.9272 (ttpt) cc_final: 0.8378 (ttpp) REVERT: z 109 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7691 (mt-10) REVERT: z 117 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8304 (pp) REVERT: z 120 ILE cc_start: 0.9167 (mt) cc_final: 0.8930 (mp) REVERT: z 127 GLN cc_start: 0.9076 (tp40) cc_final: 0.8825 (tp-100) REVERT: z 128 TYR cc_start: 0.9086 (t80) cc_final: 0.8886 (t80) REVERT: z 138 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8312 (mtm-85) REVERT: 1 50 GLU cc_start: 0.8946 (tt0) cc_final: 0.8255 (tm-30) REVERT: 1 51 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: 1 58 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: 1 82 GLU cc_start: 0.8511 (mp0) cc_final: 0.8281 (mp0) REVERT: 1 84 LEU cc_start: 0.9303 (tp) cc_final: 0.8900 (tp) REVERT: 1 85 GLU cc_start: 0.8660 (tp30) cc_final: 0.8299 (tm-30) REVERT: 1 86 LYS cc_start: 0.9157 (ttpt) cc_final: 0.8771 (ttpp) REVERT: 1 97 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8498 (tttm) REVERT: 1 109 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7774 (mt-10) REVERT: 1 117 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8212 (pp) REVERT: 1 120 ILE cc_start: 0.9065 (mt) cc_final: 0.8527 (mp) REVERT: 3 37 LYS cc_start: 0.8949 (mttt) cc_final: 0.8629 (tttt) REVERT: 3 48 PHE cc_start: 0.9292 (t80) cc_final: 0.9081 (t80) REVERT: 3 65 GLN cc_start: 0.8849 (tt0) cc_final: 0.8594 (tm-30) REVERT: 3 70 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8328 (mtt-85) REVERT: 3 74 GLU cc_start: 0.7727 (tt0) cc_final: 0.7290 (tt0) REVERT: 3 85 GLU cc_start: 0.8405 (tp30) cc_final: 0.8104 (tm-30) REVERT: 3 86 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8746 (mtpt) REVERT: 3 97 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8413 (tttp) REVERT: 3 106 ASP cc_start: 0.8298 (t0) cc_final: 0.7944 (t0) REVERT: 3 117 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8200 (pp) REVERT: 3 120 ILE cc_start: 0.9147 (mt) cc_final: 0.8820 (mm) REVERT: 3 138 ARG cc_start: 0.8575 (mtp-110) cc_final: 0.8299 (mtm-85) REVERT: 5 50 GLU cc_start: 0.8937 (tt0) cc_final: 0.8241 (tm-30) REVERT: 5 51 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.7060 (mtm-85) REVERT: 5 58 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: 5 82 GLU cc_start: 0.8502 (mp0) cc_final: 0.8273 (mp0) REVERT: 5 84 LEU cc_start: 0.9303 (tp) cc_final: 0.8918 (tp) REVERT: 5 85 GLU cc_start: 0.8668 (tp30) cc_final: 0.8297 (tm-30) REVERT: 5 86 LYS cc_start: 0.9152 (ttpt) cc_final: 0.8666 (ttpp) REVERT: 5 97 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8494 (tttm) REVERT: 5 109 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7899 (mt-10) REVERT: 5 117 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8211 (pp) REVERT: 5 120 ILE cc_start: 0.9066 (mt) cc_final: 0.8524 (mp) REVERT: 5 128 TYR cc_start: 0.9184 (t80) cc_final: 0.8978 (t80) REVERT: 7 37 LYS cc_start: 0.8880 (mttt) cc_final: 0.8563 (tttt) REVERT: 7 65 GLN cc_start: 0.8857 (tt0) cc_final: 0.8570 (tm-30) REVERT: 7 70 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8280 (mtt-85) REVERT: 7 85 GLU cc_start: 0.8410 (tp30) cc_final: 0.8103 (tm-30) REVERT: 7 86 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8713 (mtpt) REVERT: 7 106 ASP cc_start: 0.8319 (t0) cc_final: 0.8056 (t0) REVERT: 7 117 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8221 (pp) REVERT: 7 120 ILE cc_start: 0.9144 (mt) cc_final: 0.8802 (mm) REVERT: 7 138 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8310 (mtm-85) REVERT: 9 48 PHE cc_start: 0.9221 (t80) cc_final: 0.8908 (t80) REVERT: 9 50 GLU cc_start: 0.8941 (tt0) cc_final: 0.8257 (tm-30) REVERT: 9 51 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.7165 (mtm-85) REVERT: 9 58 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: 9 82 GLU cc_start: 0.8494 (mp0) cc_final: 0.8267 (mp0) REVERT: 9 84 LEU cc_start: 0.9315 (tp) cc_final: 0.8938 (tp) REVERT: 9 85 GLU cc_start: 0.8679 (tp30) cc_final: 0.8312 (tm-30) REVERT: 9 86 LYS cc_start: 0.9177 (ttpt) cc_final: 0.8607 (ttpp) REVERT: 9 97 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8476 (tttm) REVERT: 9 109 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7879 (mt-10) REVERT: 9 117 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8217 (pp) REVERT: 9 120 ILE cc_start: 0.9057 (mt) cc_final: 0.8513 (mp) REVERT: 9 128 TYR cc_start: 0.9183 (t80) cc_final: 0.8943 (t80) REVERT: A 359 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7266 (pp) REVERT: D 345 LYS cc_start: 0.8671 (mttt) cc_final: 0.8344 (tppp) REVERT: D 358 MET cc_start: 0.8448 (tpp) cc_final: 0.7653 (tpp) REVERT: D 359 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7469 (pp) REVERT: G 359 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7228 (pp) REVERT: J 358 MET cc_start: 0.8158 (tpp) cc_final: 0.7743 (tpp) REVERT: M 359 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7444 (pp) REVERT: P 358 MET cc_start: 0.8324 (tpp) cc_final: 0.7707 (tpp) REVERT: S 359 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7347 (pp) REVERT: U 345 LYS cc_start: 0.8656 (mttt) cc_final: 0.8265 (tppp) REVERT: U 356 TYR cc_start: 0.9492 (p90) cc_final: 0.9206 (p90) REVERT: U 358 MET cc_start: 0.8486 (tpp) cc_final: 0.7788 (tpp) REVERT: U 359 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7483 (pp) REVERT: B 358 MET cc_start: 0.8658 (tpp) cc_final: 0.8129 (tpp) REVERT: B 359 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8560 (pt) REVERT: E 345 LYS cc_start: 0.8156 (mttt) cc_final: 0.7949 (tmtt) REVERT: E 365 PHE cc_start: 0.8995 (t80) cc_final: 0.8753 (t80) REVERT: H 358 MET cc_start: 0.8668 (tpp) cc_final: 0.8156 (tpp) REVERT: H 359 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8575 (pt) REVERT: K 339 LEU cc_start: 0.9036 (mt) cc_final: 0.8680 (tt) REVERT: K 345 LYS cc_start: 0.8214 (mttt) cc_final: 0.8004 (tmtt) REVERT: K 365 PHE cc_start: 0.9012 (t80) cc_final: 0.8738 (t80) REVERT: N 358 MET cc_start: 0.8442 (tpp) cc_final: 0.8194 (ttm) REVERT: Q 353 LYS cc_start: 0.9025 (pttt) cc_final: 0.8807 (mmmt) REVERT: Q 358 MET cc_start: 0.8779 (tpp) cc_final: 0.8276 (tpp) REVERT: T 358 MET cc_start: 0.8620 (tpp) cc_final: 0.8193 (ttm) REVERT: T 359 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8524 (pt) REVERT: V 345 LYS cc_start: 0.8271 (mttt) cc_final: 0.8047 (tmtt) REVERT: V 353 LYS cc_start: 0.9067 (pttt) cc_final: 0.8851 (mmmt) REVERT: V 358 MET cc_start: 0.8783 (tpp) cc_final: 0.8299 (tpp) outliers start: 140 outliers final: 54 residues processed: 1115 average time/residue: 0.1515 time to fit residues: 253.0504 Evaluate side-chains 952 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 869 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 126 ILE Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 144 ASN Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 79 ASN Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 126 ILE Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 144 ASN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 126 ILE Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 144 ASN Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 79 ASN Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 126 ILE Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 144 ASN Chi-restraints excluded: chain 1 residue 165 THR Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 126 ILE Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 144 ASN Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 79 ASN Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 126 ILE Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 144 ASN Chi-restraints excluded: chain 5 residue 165 THR Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 126 ILE Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 144 ASN Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 79 ASN Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 126 ILE Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 144 ASN Chi-restraints excluded: chain 9 residue 165 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain T residue 359 LEU Chi-restraints excluded: chain V residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 41 GLN Y 79 ASN Z 41 GLN Z 79 ASN 0 41 GLN 0 79 ASN 2 41 GLN 2 79 ASN 6 79 ASN 8 79 ASN x 144 ASN y 144 ASN z 144 ASN 1 144 ASN 3 65 GLN 3 144 ASN 5 144 ASN 7 65 GLN 7 144 ASN 9 144 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.083743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.073440 restraints weight = 54200.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.075757 restraints weight = 27468.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.077352 restraints weight = 17006.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.078445 restraints weight = 11818.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.079252 restraints weight = 8886.657| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22224 Z= 0.153 Angle : 0.627 7.707 30080 Z= 0.334 Chirality : 0.045 0.167 3392 Planarity : 0.005 0.057 3744 Dihedral : 8.913 59.929 3070 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.83 % Allowed : 17.33 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.16), residues: 2624 helix: -0.29 (0.18), residues: 944 sheet: -1.64 (0.19), residues: 752 loop : -3.44 (0.15), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Z 138 TYR 0.015 0.001 TYR 3 128 PHE 0.018 0.001 PHE y 150 TRP 0.006 0.001 TRP M 364 HIS 0.002 0.001 HIS 5 137 Details of bonding type rmsd covalent geometry : bond 0.00348 (22224) covalent geometry : angle 0.62732 (30080) hydrogen bonds : bond 0.03658 ( 1021) hydrogen bonds : angle 5.50153 ( 2784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1022 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 65 GLN cc_start: 0.8208 (tt0) cc_final: 0.7922 (tt0) REVERT: X 88 THR cc_start: 0.9456 (m) cc_final: 0.9180 (p) REVERT: X 97 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8563 (tttm) REVERT: X 117 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8302 (pp) REVERT: X 133 ASN cc_start: 0.8846 (m-40) cc_final: 0.8115 (t0) REVERT: X 144 ASN cc_start: 0.8538 (t0) cc_final: 0.8247 (t0) REVERT: Y 37 LYS cc_start: 0.9118 (tttt) cc_final: 0.8805 (ttmm) REVERT: Y 65 GLN cc_start: 0.8323 (tt0) cc_final: 0.8116 (tt0) REVERT: Y 74 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6967 (tm-30) REVERT: Y 85 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8080 (tm-30) REVERT: Y 88 THR cc_start: 0.9578 (m) cc_final: 0.9318 (p) REVERT: Y 97 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8796 (tttp) REVERT: Y 133 ASN cc_start: 0.8977 (m-40) cc_final: 0.8670 (t0) REVERT: Y 144 ASN cc_start: 0.8467 (t0) cc_final: 0.8252 (t0) REVERT: Z 65 GLN cc_start: 0.8195 (tt0) cc_final: 0.7805 (tt0) REVERT: Z 68 LYS cc_start: 0.9232 (mttt) cc_final: 0.8896 (mttp) REVERT: Z 88 THR cc_start: 0.9477 (m) cc_final: 0.9208 (p) REVERT: Z 97 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8571 (tttm) REVERT: Z 117 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8270 (pp) REVERT: Z 133 ASN cc_start: 0.8849 (m-40) cc_final: 0.8110 (t0) REVERT: Z 144 ASN cc_start: 0.8550 (t0) cc_final: 0.8259 (t0) REVERT: 0 37 LYS cc_start: 0.9241 (tttt) cc_final: 0.7759 (tptm) REVERT: 0 85 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7985 (tm-30) REVERT: 0 88 THR cc_start: 0.9608 (m) cc_final: 0.9344 (p) REVERT: 0 97 LYS cc_start: 0.9133 (mtpp) cc_final: 0.8890 (tttp) REVERT: 0 133 ASN cc_start: 0.8988 (m-40) cc_final: 0.8581 (t0) REVERT: 0 138 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7743 (mtp85) REVERT: 2 65 GLN cc_start: 0.8272 (tt0) cc_final: 0.7837 (tt0) REVERT: 2 88 THR cc_start: 0.9488 (m) cc_final: 0.9204 (p) REVERT: 2 97 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8596 (tttm) REVERT: 2 117 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8362 (pp) REVERT: 2 133 ASN cc_start: 0.8868 (m-40) cc_final: 0.8145 (t0) REVERT: 2 144 ASN cc_start: 0.8581 (t0) cc_final: 0.8276 (t0) REVERT: 4 65 GLN cc_start: 0.8334 (tt0) cc_final: 0.8125 (tt0) REVERT: 4 85 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8002 (tm-30) REVERT: 4 88 THR cc_start: 0.9596 (m) cc_final: 0.9304 (p) REVERT: 4 133 ASN cc_start: 0.8989 (m-40) cc_final: 0.8586 (t0) REVERT: 4 138 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7717 (mtp85) REVERT: 6 65 GLN cc_start: 0.8306 (tt0) cc_final: 0.7748 (tt0) REVERT: 6 68 LYS cc_start: 0.9232 (mttt) cc_final: 0.8919 (mttp) REVERT: 6 88 THR cc_start: 0.9497 (m) cc_final: 0.9194 (p) REVERT: 6 97 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8590 (tttm) REVERT: 6 117 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.7980 (pp) REVERT: 6 133 ASN cc_start: 0.8878 (m-40) cc_final: 0.8142 (t0) REVERT: 6 144 ASN cc_start: 0.8565 (t0) cc_final: 0.8284 (t0) REVERT: 8 48 PHE cc_start: 0.9028 (t80) cc_final: 0.8795 (t80) REVERT: 8 65 GLN cc_start: 0.8313 (tt0) cc_final: 0.7951 (tt0) REVERT: 8 70 ARG cc_start: 0.8933 (mmt90) cc_final: 0.8699 (mmt90) REVERT: 8 74 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6969 (tm-30) REVERT: 8 85 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7981 (tm-30) REVERT: 8 88 THR cc_start: 0.9559 (m) cc_final: 0.9266 (p) REVERT: 8 97 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8754 (tttp) REVERT: 8 128 TYR cc_start: 0.9156 (t80) cc_final: 0.8881 (t80) REVERT: 8 133 ASN cc_start: 0.8922 (m-40) cc_final: 0.8601 (t0) REVERT: 8 138 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7651 (mtp85) REVERT: x 65 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8501 (tm-30) REVERT: x 70 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8381 (mtt-85) REVERT: x 74 GLU cc_start: 0.7604 (tt0) cc_final: 0.7119 (tt0) REVERT: x 81 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7526 (tm-30) REVERT: x 82 GLU cc_start: 0.8203 (mp0) cc_final: 0.7756 (mp0) REVERT: x 86 LYS cc_start: 0.9149 (ttpt) cc_final: 0.8608 (ttpp) REVERT: x 97 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8419 (tttp) REVERT: x 106 ASP cc_start: 0.8081 (t0) cc_final: 0.7653 (t0) REVERT: x 117 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8123 (pp) REVERT: x 138 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8192 (mtm-85) REVERT: y 58 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6434 (m-10) REVERT: y 65 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8710 (tm-30) REVERT: y 85 GLU cc_start: 0.8009 (tp30) cc_final: 0.7746 (tm-30) REVERT: y 86 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8386 (ttpp) REVERT: y 97 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8573 (tttm) REVERT: y 117 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8184 (pp) REVERT: y 127 GLN cc_start: 0.8952 (tp40) cc_final: 0.8684 (tp40) REVERT: y 148 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8971 (mtmt) REVERT: z 65 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8665 (tm-30) REVERT: z 85 GLU cc_start: 0.8016 (tp30) cc_final: 0.7635 (tm-30) REVERT: z 86 LYS cc_start: 0.9128 (ttpt) cc_final: 0.8797 (mmtm) REVERT: z 97 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8419 (tttp) REVERT: z 109 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7748 (mt-10) REVERT: z 117 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8330 (pp) REVERT: z 138 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8054 (mtm-85) REVERT: 1 52 PHE cc_start: 0.8959 (t80) cc_final: 0.8616 (t80) REVERT: 1 58 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6440 (m-10) REVERT: 1 65 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8685 (tm-30) REVERT: 1 85 GLU cc_start: 0.8012 (tp30) cc_final: 0.7739 (tm-30) REVERT: 1 86 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8370 (mtpt) REVERT: 1 97 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8577 (tttm) REVERT: 1 117 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8179 (pp) REVERT: 1 127 GLN cc_start: 0.8946 (tp40) cc_final: 0.8678 (tp40) REVERT: 1 148 LYS cc_start: 0.9273 (mtpt) cc_final: 0.8976 (mtmt) REVERT: 3 70 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8415 (mtt-85) REVERT: 3 74 GLU cc_start: 0.7580 (tt0) cc_final: 0.7322 (tt0) REVERT: 3 86 LYS cc_start: 0.9234 (ttpt) cc_final: 0.8558 (ttpp) REVERT: 3 97 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8400 (tttp) REVERT: 3 109 GLU cc_start: 0.8302 (mp0) cc_final: 0.7886 (mt-10) REVERT: 3 117 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8127 (pp) REVERT: 5 52 PHE cc_start: 0.8926 (t80) cc_final: 0.8598 (t80) REVERT: 5 58 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: 5 65 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8689 (tm-30) REVERT: 5 85 GLU cc_start: 0.8011 (tp30) cc_final: 0.7735 (tm-30) REVERT: 5 86 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8617 (mtpt) REVERT: 5 97 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8582 (tttm) REVERT: 5 117 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8185 (pp) REVERT: 5 127 GLN cc_start: 0.8944 (tp40) cc_final: 0.8682 (tp40) REVERT: 5 148 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8976 (mtmt) REVERT: 7 47 SER cc_start: 0.8026 (t) cc_final: 0.6970 (p) REVERT: 7 51 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: 7 70 ARG cc_start: 0.8612 (mtt-85) cc_final: 0.8395 (mtt-85) REVERT: 7 74 GLU cc_start: 0.7466 (tt0) cc_final: 0.7199 (tt0) REVERT: 7 81 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7424 (tm-30) REVERT: 7 82 GLU cc_start: 0.8292 (mp0) cc_final: 0.7828 (mp0) REVERT: 7 86 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8551 (ttpp) REVERT: 7 97 LYS cc_start: 0.9217 (ttpt) cc_final: 0.8585 (tttp) REVERT: 7 117 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8152 (pp) REVERT: 9 52 PHE cc_start: 0.8929 (t80) cc_final: 0.8609 (t80) REVERT: 9 58 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6412 (m-10) REVERT: 9 65 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8699 (tm-30) REVERT: 9 85 GLU cc_start: 0.8022 (tp30) cc_final: 0.7717 (tm-30) REVERT: 9 86 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8410 (ttpp) REVERT: 9 97 LYS cc_start: 0.9154 (ttmt) cc_final: 0.8573 (tttm) REVERT: 9 117 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8183 (pp) REVERT: 9 127 GLN cc_start: 0.8954 (tp40) cc_final: 0.8691 (tp40) REVERT: 9 128 TYR cc_start: 0.9186 (t80) cc_final: 0.8940 (t80) REVERT: 9 148 LYS cc_start: 0.9264 (mtpt) cc_final: 0.8972 (mtmt) REVERT: A 345 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8198 (mmmt) REVERT: A 354 ASP cc_start: 0.7878 (m-30) cc_final: 0.7580 (m-30) REVERT: A 359 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7511 (pp) REVERT: D 359 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7897 (pp) REVERT: G 345 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8193 (mmmt) REVERT: G 358 MET cc_start: 0.7823 (tpp) cc_final: 0.7542 (tpp) REVERT: G 359 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7502 (pp) REVERT: J 342 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8396 (p0) REVERT: M 345 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8359 (mmmt) REVERT: M 359 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7609 (pp) REVERT: P 354 ASP cc_start: 0.7917 (m-30) cc_final: 0.7125 (m-30) REVERT: S 345 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8480 (mmmt) REVERT: S 354 ASP cc_start: 0.7821 (m-30) cc_final: 0.7605 (m-30) REVERT: S 358 MET cc_start: 0.7854 (tpp) cc_final: 0.7521 (tpp) REVERT: S 359 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7514 (pp) REVERT: U 354 ASP cc_start: 0.7999 (m-30) cc_final: 0.7673 (m-30) REVERT: U 359 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7902 (pp) REVERT: B 343 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7600 (p0) REVERT: B 358 MET cc_start: 0.8623 (tpp) cc_final: 0.8413 (tpp) REVERT: H 343 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7658 (p0) REVERT: H 358 MET cc_start: 0.8618 (tpp) cc_final: 0.8396 (tpp) REVERT: K 339 LEU cc_start: 0.8953 (mt) cc_final: 0.8531 (tt) REVERT: K 353 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8654 (mttt) REVERT: K 365 PHE cc_start: 0.8869 (t80) cc_final: 0.8639 (t80) REVERT: Q 358 MET cc_start: 0.8713 (tpp) cc_final: 0.8504 (tpp) REVERT: V 353 LYS cc_start: 0.8973 (pttt) cc_final: 0.8655 (mmmt) REVERT: V 358 MET cc_start: 0.8754 (tpp) cc_final: 0.8427 (tpp) outliers start: 140 outliers final: 57 residues processed: 1095 average time/residue: 0.1546 time to fit residues: 252.9953 Evaluate side-chains 1022 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 939 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 126 ILE Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 77 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 126 ILE Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 126 ILE Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 126 ILE Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 165 THR Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 126 ILE Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 126 ILE Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 165 THR Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 126 ILE Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 126 ILE Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 165 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain V residue 359 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 156 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 198 optimal weight: 0.0000 chunk 207 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 79 ASN 4 79 ASN J 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.082280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.071758 restraints weight = 55070.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.074089 restraints weight = 28316.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.075678 restraints weight = 17702.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.076812 restraints weight = 12410.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.077606 restraints weight = 9368.898| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 22224 Z= 0.206 Angle : 0.670 7.763 30080 Z= 0.356 Chirality : 0.046 0.184 3392 Planarity : 0.005 0.060 3744 Dihedral : 8.283 58.433 3036 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 6.21 % Allowed : 20.75 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2624 helix: -0.05 (0.18), residues: 960 sheet: -1.17 (0.19), residues: 752 loop : -3.39 (0.16), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 138 TYR 0.018 0.002 TYR P 349 PHE 0.019 0.002 PHE z 48 TRP 0.007 0.001 TRP A 364 HIS 0.003 0.001 HIS H 363 Details of bonding type rmsd covalent geometry : bond 0.00478 (22224) covalent geometry : angle 0.66972 (30080) hydrogen bonds : bond 0.03855 ( 1021) hydrogen bonds : angle 5.44586 ( 2784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 917 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8117 (tm-30) REVERT: X 88 THR cc_start: 0.9481 (m) cc_final: 0.9208 (p) REVERT: X 97 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8691 (tttm) REVERT: X 117 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8124 (pp) REVERT: X 133 ASN cc_start: 0.8875 (m-40) cc_final: 0.8204 (t0) REVERT: X 144 ASN cc_start: 0.8547 (t0) cc_final: 0.8286 (t0) REVERT: Y 37 LYS cc_start: 0.9129 (mttt) cc_final: 0.8830 (ttmm) REVERT: Y 65 GLN cc_start: 0.8331 (tt0) cc_final: 0.8045 (tt0) REVERT: Y 74 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6868 (tm-30) REVERT: Y 85 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8008 (tm-30) REVERT: Y 88 THR cc_start: 0.9581 (m) cc_final: 0.9266 (p) REVERT: Y 133 ASN cc_start: 0.8894 (m-40) cc_final: 0.8517 (t0) REVERT: Z 68 LYS cc_start: 0.9233 (mttt) cc_final: 0.8969 (mttp) REVERT: Z 85 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8222 (tm-30) REVERT: Z 88 THR cc_start: 0.9487 (m) cc_final: 0.9191 (p) REVERT: Z 97 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8685 (tttm) REVERT: Z 117 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8138 (pp) REVERT: Z 133 ASN cc_start: 0.8879 (m-40) cc_final: 0.8232 (t0) REVERT: Z 144 ASN cc_start: 0.8538 (t0) cc_final: 0.8293 (t0) REVERT: 0 65 GLN cc_start: 0.8353 (tt0) cc_final: 0.7753 (tm-30) REVERT: 0 74 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7005 (tm-30) REVERT: 0 88 THR cc_start: 0.9566 (m) cc_final: 0.9246 (p) REVERT: 0 117 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8135 (pp) REVERT: 0 133 ASN cc_start: 0.8932 (m-40) cc_final: 0.8559 (t0) REVERT: 0 144 ASN cc_start: 0.8207 (t0) cc_final: 0.7422 (p0) REVERT: 2 65 GLN cc_start: 0.8165 (tt0) cc_final: 0.7749 (tt0) REVERT: 2 79 ASN cc_start: 0.9032 (p0) cc_final: 0.8818 (p0) REVERT: 2 81 GLU cc_start: 0.8229 (pm20) cc_final: 0.8001 (pm20) REVERT: 2 85 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8034 (tm-30) REVERT: 2 88 THR cc_start: 0.9508 (m) cc_final: 0.9212 (p) REVERT: 2 97 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8709 (tttm) REVERT: 2 117 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8116 (pp) REVERT: 2 133 ASN cc_start: 0.8880 (m-40) cc_final: 0.8192 (t0) REVERT: 2 144 ASN cc_start: 0.8549 (t0) cc_final: 0.8283 (t0) REVERT: 4 37 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.7791 (tptm) REVERT: 4 48 PHE cc_start: 0.9012 (t80) cc_final: 0.8782 (t80) REVERT: 4 65 GLN cc_start: 0.8442 (tt0) cc_final: 0.8172 (tt0) REVERT: 4 85 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8067 (tm-30) REVERT: 4 88 THR cc_start: 0.9558 (m) cc_final: 0.9273 (p) REVERT: 4 133 ASN cc_start: 0.8924 (m-40) cc_final: 0.8572 (t0) REVERT: 4 144 ASN cc_start: 0.8204 (t0) cc_final: 0.7404 (p0) REVERT: 4 165 THR cc_start: 0.9445 (m) cc_final: 0.9161 (t) REVERT: 6 65 GLN cc_start: 0.8171 (tt0) cc_final: 0.7721 (tt0) REVERT: 6 68 LYS cc_start: 0.9207 (mttt) cc_final: 0.8951 (mttp) REVERT: 6 79 ASN cc_start: 0.9029 (p0) cc_final: 0.8814 (p0) REVERT: 6 81 GLU cc_start: 0.8254 (pm20) cc_final: 0.8018 (pm20) REVERT: 6 85 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8034 (tm-30) REVERT: 6 88 THR cc_start: 0.9532 (m) cc_final: 0.9232 (p) REVERT: 6 97 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8704 (tttm) REVERT: 6 117 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8130 (pp) REVERT: 6 133 ASN cc_start: 0.8885 (m-40) cc_final: 0.8185 (t0) REVERT: 6 144 ASN cc_start: 0.8546 (t0) cc_final: 0.8284 (t0) REVERT: 8 37 LYS cc_start: 0.9087 (tptm) cc_final: 0.8794 (tptp) REVERT: 8 65 GLN cc_start: 0.8283 (tt0) cc_final: 0.7983 (tt0) REVERT: 8 70 ARG cc_start: 0.8940 (mmt90) cc_final: 0.8728 (mmt90) REVERT: 8 74 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6859 (tm-30) REVERT: 8 85 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8118 (tm-30) REVERT: 8 88 THR cc_start: 0.9570 (m) cc_final: 0.9224 (p) REVERT: 8 117 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8162 (pp) REVERT: 8 133 ASN cc_start: 0.8931 (m-40) cc_final: 0.8588 (t0) REVERT: 8 136 ASP cc_start: 0.7898 (p0) cc_final: 0.7669 (p0) REVERT: 8 144 ASN cc_start: 0.8195 (t0) cc_final: 0.7459 (p0) REVERT: 8 165 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9305 (t) REVERT: x 65 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8427 (tm-30) REVERT: x 70 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8377 (mtt-85) REVERT: x 86 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8331 (ttpp) REVERT: x 97 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8422 (tttp) REVERT: x 102 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8267 (tp) REVERT: x 117 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7987 (pp) REVERT: x 171 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6904 (pmtt) REVERT: y 58 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: y 65 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8701 (tm-30) REVERT: y 85 GLU cc_start: 0.8040 (tp30) cc_final: 0.7614 (tm-30) REVERT: y 86 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8328 (ttpp) REVERT: y 97 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8621 (tttm) REVERT: y 106 ASP cc_start: 0.8199 (t0) cc_final: 0.7897 (t0) REVERT: y 117 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8126 (pp) REVERT: y 127 GLN cc_start: 0.8987 (tp40) cc_final: 0.8719 (tp40) REVERT: y 148 LYS cc_start: 0.9312 (mtpt) cc_final: 0.9057 (mtmt) REVERT: y 171 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6880 (pmtt) REVERT: z 52 PHE cc_start: 0.9182 (t80) cc_final: 0.8943 (t80) REVERT: z 65 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8458 (tm-30) REVERT: z 81 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7441 (tm-30) REVERT: z 82 GLU cc_start: 0.8270 (mp0) cc_final: 0.7785 (mp0) REVERT: z 85 GLU cc_start: 0.7950 (tp30) cc_final: 0.7631 (tm-30) REVERT: z 86 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8778 (mmtm) REVERT: z 97 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8388 (tttp) REVERT: z 102 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8290 (tp) REVERT: z 106 ASP cc_start: 0.8027 (t0) cc_final: 0.7499 (t0) REVERT: z 117 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8098 (pp) REVERT: z 171 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6968 (pmtt) REVERT: 1 58 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6526 (m-10) REVERT: 1 65 GLN cc_start: 0.9383 (tm-30) cc_final: 0.8808 (tm-30) REVERT: 1 85 GLU cc_start: 0.8140 (tp30) cc_final: 0.7716 (tm-30) REVERT: 1 86 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8237 (mtpt) REVERT: 1 97 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8564 (tttm) REVERT: 1 117 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8117 (pp) REVERT: 1 127 GLN cc_start: 0.8971 (tp40) cc_final: 0.8705 (tp40) REVERT: 1 148 LYS cc_start: 0.9313 (mtpt) cc_final: 0.9073 (mtmt) REVERT: 1 171 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6933 (pmtt) REVERT: 3 65 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8492 (tm-30) REVERT: 3 70 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8480 (mtt-85) REVERT: 3 86 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8455 (ttpp) REVERT: 3 97 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8403 (tttp) REVERT: 3 102 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8162 (tp) REVERT: 3 106 ASP cc_start: 0.8255 (t0) cc_final: 0.7992 (t0) REVERT: 3 171 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6982 (pmtt) REVERT: 5 58 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: 5 65 GLN cc_start: 0.9380 (tm-30) cc_final: 0.8799 (tm-30) REVERT: 5 85 GLU cc_start: 0.8133 (tp30) cc_final: 0.7688 (tm-30) REVERT: 5 86 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8362 (ttpp) REVERT: 5 97 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8630 (tttm) REVERT: 5 117 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8128 (pp) REVERT: 5 127 GLN cc_start: 0.8980 (tp40) cc_final: 0.8723 (tp40) REVERT: 5 148 LYS cc_start: 0.9316 (mtpt) cc_final: 0.9074 (mtmt) REVERT: 5 171 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7037 (pmtt) REVERT: 7 52 PHE cc_start: 0.9240 (t80) cc_final: 0.8832 (t80) REVERT: 7 65 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8756 (tm-30) REVERT: 7 70 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8418 (mtt-85) REVERT: 7 74 GLU cc_start: 0.7563 (tt0) cc_final: 0.7307 (tt0) REVERT: 7 86 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7990 (ttpt) REVERT: 7 97 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8652 (tttp) REVERT: 7 102 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8343 (tp) REVERT: 7 139 TYR cc_start: 0.8335 (m-80) cc_final: 0.8062 (m-80) REVERT: 7 171 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7001 (pmtt) REVERT: 9 58 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6503 (m-10) REVERT: 9 65 GLN cc_start: 0.9350 (tm-30) cc_final: 0.8676 (tm-30) REVERT: 9 85 GLU cc_start: 0.8121 (tp30) cc_final: 0.7691 (tm-30) REVERT: 9 86 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8263 (ttpp) REVERT: 9 97 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8565 (tttm) REVERT: 9 106 ASP cc_start: 0.8181 (t0) cc_final: 0.7885 (t0) REVERT: 9 117 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8121 (pp) REVERT: 9 127 GLN cc_start: 0.8978 (tp40) cc_final: 0.8715 (tp40) REVERT: 9 148 LYS cc_start: 0.9311 (mtpt) cc_final: 0.9070 (mtmt) REVERT: 9 171 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6961 (pmtt) REVERT: A 354 ASP cc_start: 0.7817 (m-30) cc_final: 0.7338 (m-30) REVERT: A 359 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7681 (pp) REVERT: D 359 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (pp) REVERT: G 359 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7666 (pp) REVERT: M 359 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7734 (pp) REVERT: P 342 ASP cc_start: 0.8820 (p0) cc_final: 0.8413 (p0) REVERT: P 345 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8337 (tppt) REVERT: P 354 ASP cc_start: 0.7889 (m-30) cc_final: 0.7117 (m-30) REVERT: S 354 ASP cc_start: 0.7774 (m-30) cc_final: 0.7572 (m-30) REVERT: S 358 MET cc_start: 0.7981 (tpp) cc_final: 0.7557 (tpp) REVERT: S 359 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7618 (pp) REVERT: U 354 ASP cc_start: 0.7915 (m-30) cc_final: 0.7355 (m-30) REVERT: U 359 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 358 MET cc_start: 0.8555 (tpp) cc_final: 0.8290 (tpp) REVERT: K 353 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8665 (mttt) REVERT: N 358 MET cc_start: 0.8629 (tpp) cc_final: 0.8308 (tpp) REVERT: Q 353 LYS cc_start: 0.9117 (pttt) cc_final: 0.8804 (mmmt) REVERT: Q 358 MET cc_start: 0.8754 (tpp) cc_final: 0.8398 (tpp) REVERT: T 362 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8563 (mmtt) REVERT: V 353 LYS cc_start: 0.8971 (pttt) cc_final: 0.8496 (mmmt) REVERT: V 358 MET cc_start: 0.8736 (tpp) cc_final: 0.8372 (tpp) outliers start: 149 outliers final: 77 residues processed: 1002 average time/residue: 0.1572 time to fit residues: 233.8217 Evaluate side-chains 1005 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 891 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 43 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 120 ILE Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain 8 residue 165 THR Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 77 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 112 SER Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 112 SER Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 165 THR Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 112 SER Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 165 THR Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 112 SER Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 165 THR Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain V residue 359 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 170 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 79 ASN 0 65 GLN 8 79 ASN y 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.083500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.072950 restraints weight = 54474.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.075279 restraints weight = 28008.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.076883 restraints weight = 17548.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078010 restraints weight = 12326.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.078788 restraints weight = 9331.059| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22224 Z= 0.161 Angle : 0.639 7.505 30080 Z= 0.339 Chirality : 0.046 0.160 3392 Planarity : 0.004 0.048 3744 Dihedral : 8.080 59.483 3020 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 6.25 % Allowed : 22.46 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2624 helix: 0.10 (0.18), residues: 976 sheet: -0.77 (0.19), residues: 752 loop : -3.21 (0.16), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 0 138 TYR 0.021 0.002 TYR 2 96 PHE 0.019 0.002 PHE 2 48 TRP 0.008 0.001 TRP J 364 HIS 0.002 0.001 HIS T 363 Details of bonding type rmsd covalent geometry : bond 0.00370 (22224) covalent geometry : angle 0.63883 (30080) hydrogen bonds : bond 0.03469 ( 1021) hydrogen bonds : angle 5.23825 ( 2784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 950 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8131 (tm-30) REVERT: X 88 THR cc_start: 0.9483 (m) cc_final: 0.9155 (p) REVERT: X 117 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8057 (pp) REVERT: X 133 ASN cc_start: 0.8846 (m-40) cc_final: 0.8278 (t0) REVERT: X 144 ASN cc_start: 0.8478 (t0) cc_final: 0.8277 (t0) REVERT: Y 37 LYS cc_start: 0.9100 (mttt) cc_final: 0.8721 (tptm) REVERT: Y 43 ASP cc_start: 0.8282 (m-30) cc_final: 0.7894 (m-30) REVERT: Y 65 GLN cc_start: 0.8310 (tt0) cc_final: 0.7898 (tt0) REVERT: Y 74 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6691 (tm-30) REVERT: Y 85 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7990 (tm-30) REVERT: Y 88 THR cc_start: 0.9559 (m) cc_final: 0.9256 (p) REVERT: Y 106 ASP cc_start: 0.8075 (t70) cc_final: 0.7815 (t70) REVERT: Y 133 ASN cc_start: 0.8887 (m-40) cc_final: 0.8534 (t0) REVERT: Z 43 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: Z 65 GLN cc_start: 0.8027 (tt0) cc_final: 0.7826 (tm-30) REVERT: Z 68 LYS cc_start: 0.9232 (mttt) cc_final: 0.8989 (mttp) REVERT: Z 85 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Z 88 THR cc_start: 0.9456 (m) cc_final: 0.9132 (p) REVERT: Z 97 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8692 (tttm) REVERT: Z 117 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8078 (pp) REVERT: Z 133 ASN cc_start: 0.8854 (m-40) cc_final: 0.8308 (t0) REVERT: Z 144 ASN cc_start: 0.8508 (t0) cc_final: 0.8284 (t0) REVERT: 0 37 LYS cc_start: 0.8934 (tppt) cc_final: 0.8534 (tptp) REVERT: 0 65 GLN cc_start: 0.8314 (tt0) cc_final: 0.7739 (tm-30) REVERT: 0 85 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8068 (tm-30) REVERT: 0 88 THR cc_start: 0.9555 (m) cc_final: 0.9284 (p) REVERT: 0 117 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7984 (pp) REVERT: 0 133 ASN cc_start: 0.8897 (m-40) cc_final: 0.8537 (t0) REVERT: 2 65 GLN cc_start: 0.8031 (tt0) cc_final: 0.7712 (tt0) REVERT: 2 85 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8076 (tm-30) REVERT: 2 88 THR cc_start: 0.9507 (m) cc_final: 0.9187 (p) REVERT: 2 117 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8045 (pp) REVERT: 2 133 ASN cc_start: 0.8858 (m-40) cc_final: 0.8279 (t0) REVERT: 4 37 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8957 (tptp) REVERT: 4 74 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7231 (tm-30) REVERT: 4 85 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8075 (tm-30) REVERT: 4 88 THR cc_start: 0.9557 (m) cc_final: 0.9288 (p) REVERT: 4 133 ASN cc_start: 0.8898 (m-40) cc_final: 0.8506 (t0) REVERT: 4 165 THR cc_start: 0.9409 (m) cc_final: 0.9128 (t) REVERT: 6 65 GLN cc_start: 0.8079 (tt0) cc_final: 0.7665 (tt0) REVERT: 6 68 LYS cc_start: 0.9208 (mttt) cc_final: 0.8943 (mttp) REVERT: 6 85 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8048 (tm-30) REVERT: 6 88 THR cc_start: 0.9501 (m) cc_final: 0.9164 (p) REVERT: 6 117 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8047 (pp) REVERT: 6 133 ASN cc_start: 0.8857 (m-40) cc_final: 0.8275 (t0) REVERT: 6 144 ASN cc_start: 0.8503 (t0) cc_final: 0.8284 (t0) REVERT: 8 65 GLN cc_start: 0.8297 (tt0) cc_final: 0.7848 (tt0) REVERT: 8 74 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6772 (tm-30) REVERT: 8 85 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8082 (tm-30) REVERT: 8 88 THR cc_start: 0.9544 (m) cc_final: 0.9220 (p) REVERT: 8 106 ASP cc_start: 0.8089 (t70) cc_final: 0.7815 (t70) REVERT: 8 117 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7943 (pp) REVERT: 8 133 ASN cc_start: 0.8889 (m-40) cc_final: 0.8543 (t0) REVERT: x 65 GLN cc_start: 0.9162 (tm-30) cc_final: 0.7947 (tm-30) REVERT: x 86 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8251 (ttpp) REVERT: x 97 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8351 (tttp) REVERT: x 102 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8232 (tp) REVERT: x 171 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6658 (pmtt) REVERT: y 58 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6488 (m-10) REVERT: y 65 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8553 (tm-30) REVERT: y 85 GLU cc_start: 0.7899 (tp30) cc_final: 0.7603 (tm-30) REVERT: y 86 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8429 (mtpt) REVERT: y 97 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8549 (tttm) REVERT: y 106 ASP cc_start: 0.8109 (t0) cc_final: 0.7711 (t0) REVERT: y 127 GLN cc_start: 0.8944 (tp40) cc_final: 0.8690 (tp40) REVERT: y 147 ASP cc_start: 0.8429 (t0) cc_final: 0.8097 (m-30) REVERT: y 148 LYS cc_start: 0.9288 (mtpt) cc_final: 0.8949 (mtmt) REVERT: y 171 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6804 (pmtt) REVERT: z 65 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8088 (tm-30) REVERT: z 82 GLU cc_start: 0.8222 (mp0) cc_final: 0.7748 (mp0) REVERT: z 86 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8505 (ttpp) REVERT: z 97 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8443 (tttp) REVERT: z 147 ASP cc_start: 0.8219 (t0) cc_final: 0.7762 (m-30) REVERT: z 171 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6739 (pmtt) REVERT: 1 58 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: 1 65 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8594 (tm-30) REVERT: 1 85 GLU cc_start: 0.8058 (tp30) cc_final: 0.7641 (tm-30) REVERT: 1 86 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8419 (mtpt) REVERT: 1 97 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8584 (tttm) REVERT: 1 127 GLN cc_start: 0.8931 (tp40) cc_final: 0.8685 (tp40) REVERT: 1 147 ASP cc_start: 0.8426 (t0) cc_final: 0.8122 (m-30) REVERT: 1 148 LYS cc_start: 0.9288 (mtpt) cc_final: 0.8950 (mtmt) REVERT: 1 171 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6479 (pmtt) REVERT: 3 65 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8782 (tm-30) REVERT: 3 70 ARG cc_start: 0.8677 (mtt-85) cc_final: 0.8439 (mtt-85) REVERT: 3 86 LYS cc_start: 0.8436 (ttpt) cc_final: 0.7972 (ttpp) REVERT: 3 97 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8387 (tttp) REVERT: 3 109 GLU cc_start: 0.8284 (mp0) cc_final: 0.8017 (mt-10) REVERT: 3 147 ASP cc_start: 0.8052 (t0) cc_final: 0.7530 (m-30) REVERT: 3 171 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6750 (pmtt) REVERT: 5 58 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: 5 65 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8587 (tm-30) REVERT: 5 85 GLU cc_start: 0.7961 (tp30) cc_final: 0.7591 (tm-30) REVERT: 5 86 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8460 (mtpt) REVERT: 5 97 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8556 (tttm) REVERT: 5 127 GLN cc_start: 0.8943 (tp40) cc_final: 0.8516 (tp40) REVERT: 5 147 ASP cc_start: 0.8439 (t0) cc_final: 0.8124 (m-30) REVERT: 5 148 LYS cc_start: 0.9287 (mtpt) cc_final: 0.8950 (mtmt) REVERT: 5 171 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6450 (pmtt) REVERT: 7 70 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.8450 (mtt-85) REVERT: 7 86 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8184 (ttpp) REVERT: 7 97 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8632 (tttp) REVERT: 7 139 TYR cc_start: 0.8349 (m-80) cc_final: 0.8115 (m-80) REVERT: 7 171 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6746 (pmtt) REVERT: 9 58 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: 9 65 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8534 (tm-30) REVERT: 9 85 GLU cc_start: 0.8064 (tp30) cc_final: 0.7669 (tm-30) REVERT: 9 86 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8379 (mtpt) REVERT: 9 97 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8490 (tttm) REVERT: 9 106 ASP cc_start: 0.8107 (t0) cc_final: 0.7730 (t0) REVERT: 9 127 GLN cc_start: 0.8948 (tp40) cc_final: 0.8694 (tp40) REVERT: 9 148 LYS cc_start: 0.9274 (mtpt) cc_final: 0.9014 (mtmt) REVERT: 9 171 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6589 (pmtt) REVERT: A 354 ASP cc_start: 0.7879 (m-30) cc_final: 0.7572 (m-30) REVERT: D 359 LEU cc_start: 0.8023 (pp) cc_final: 0.7597 (pp) REVERT: G 359 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7758 (pp) REVERT: J 345 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8268 (tppt) REVERT: P 342 ASP cc_start: 0.8758 (p0) cc_final: 0.8444 (p0) REVERT: P 345 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8219 (tppt) REVERT: P 354 ASP cc_start: 0.7893 (m-30) cc_final: 0.7161 (m-30) REVERT: S 345 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8367 (mmmt) REVERT: S 358 MET cc_start: 0.8001 (tpp) cc_final: 0.7597 (tpp) REVERT: S 359 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7751 (pp) REVERT: U 354 ASP cc_start: 0.7842 (m-30) cc_final: 0.7458 (m-30) REVERT: U 359 LEU cc_start: 0.8128 (pp) cc_final: 0.7775 (pp) REVERT: B 343 ASP cc_start: 0.7661 (p0) cc_final: 0.7458 (p0) REVERT: B 358 MET cc_start: 0.8534 (tpp) cc_final: 0.8303 (tpp) REVERT: H 343 ASP cc_start: 0.7651 (p0) cc_final: 0.7441 (p0) REVERT: N 358 MET cc_start: 0.8544 (tpp) cc_final: 0.8238 (tpp) REVERT: Q 353 LYS cc_start: 0.9006 (pttt) cc_final: 0.8749 (mmmt) REVERT: Q 358 MET cc_start: 0.8731 (tpp) cc_final: 0.8167 (tpp) REVERT: T 358 MET cc_start: 0.8462 (mmm) cc_final: 0.7920 (tpp) REVERT: V 353 LYS cc_start: 0.9013 (pttt) cc_final: 0.8532 (mmmt) REVERT: V 358 MET cc_start: 0.8787 (tpp) cc_final: 0.8416 (tpp) outliers start: 150 outliers final: 80 residues processed: 1028 average time/residue: 0.1556 time to fit residues: 238.5265 Evaluate side-chains 1021 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 918 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 120 ILE Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 118 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 118 GLU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain V residue 359 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 91 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 145 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 79 ASN ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN 1 41 GLN Q 363 HIS V 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.075388 restraints weight = 53987.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077747 restraints weight = 27706.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.079350 restraints weight = 17280.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080484 restraints weight = 12064.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.081303 restraints weight = 9093.678| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22224 Z= 0.126 Angle : 0.638 8.543 30080 Z= 0.338 Chirality : 0.045 0.157 3392 Planarity : 0.004 0.045 3744 Dihedral : 7.743 59.705 3004 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.62 % Allowed : 24.54 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.16), residues: 2624 helix: 0.40 (0.18), residues: 976 sheet: -0.39 (0.21), residues: 672 loop : -3.04 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 138 TYR 0.021 0.001 TYR P 349 PHE 0.021 0.001 PHE 2 48 TRP 0.007 0.001 TRP J 364 HIS 0.002 0.000 HIS T 363 Details of bonding type rmsd covalent geometry : bond 0.00284 (22224) covalent geometry : angle 0.63792 (30080) hydrogen bonds : bond 0.03164 ( 1021) hydrogen bonds : angle 5.00785 ( 2784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 967 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8268 (tm-30) REVERT: X 88 THR cc_start: 0.9409 (m) cc_final: 0.9105 (p) REVERT: X 117 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8095 (pp) REVERT: X 133 ASN cc_start: 0.8847 (m-40) cc_final: 0.8327 (t0) REVERT: X 151 TYR cc_start: 0.9119 (t80) cc_final: 0.8750 (t80) REVERT: Y 65 GLN cc_start: 0.8221 (tt0) cc_final: 0.7912 (tt0) REVERT: Y 85 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8128 (tm-30) REVERT: Y 88 THR cc_start: 0.9525 (m) cc_final: 0.9211 (p) REVERT: Y 106 ASP cc_start: 0.7985 (t70) cc_final: 0.7731 (t70) REVERT: Y 133 ASN cc_start: 0.8869 (m-40) cc_final: 0.8402 (t0) REVERT: Y 144 ASN cc_start: 0.8169 (t0) cc_final: 0.7382 (p0) REVERT: Z 65 GLN cc_start: 0.8117 (tt0) cc_final: 0.7828 (tm-30) REVERT: Z 85 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8257 (tm-30) REVERT: Z 88 THR cc_start: 0.9406 (m) cc_final: 0.9091 (p) REVERT: Z 117 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7964 (pp) REVERT: Z 133 ASN cc_start: 0.8871 (m-40) cc_final: 0.8311 (t0) REVERT: Z 151 TYR cc_start: 0.9123 (t80) cc_final: 0.8736 (t80) REVERT: 0 37 LYS cc_start: 0.9005 (tppt) cc_final: 0.8598 (tptp) REVERT: 0 85 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8083 (tm-30) REVERT: 0 88 THR cc_start: 0.9527 (m) cc_final: 0.9236 (p) REVERT: 0 117 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7988 (pp) REVERT: 0 133 ASN cc_start: 0.8879 (m-40) cc_final: 0.8508 (t0) REVERT: 0 144 ASN cc_start: 0.8236 (t0) cc_final: 0.7418 (p0) REVERT: 2 85 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8064 (tm-30) REVERT: 2 88 THR cc_start: 0.9457 (m) cc_final: 0.9156 (p) REVERT: 2 117 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (pp) REVERT: 2 133 ASN cc_start: 0.8832 (m-40) cc_final: 0.8274 (t0) REVERT: 2 151 TYR cc_start: 0.9137 (t80) cc_final: 0.8723 (t80) REVERT: 4 37 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9024 (tmtt) REVERT: 4 65 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8102 (tm-30) REVERT: 4 85 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8036 (tm-30) REVERT: 4 88 THR cc_start: 0.9509 (m) cc_final: 0.9223 (p) REVERT: 4 106 ASP cc_start: 0.8304 (t0) cc_final: 0.7956 (t0) REVERT: 4 133 ASN cc_start: 0.8887 (m-40) cc_final: 0.8520 (t0) REVERT: 4 144 ASN cc_start: 0.8248 (t0) cc_final: 0.7423 (p0) REVERT: 6 68 LYS cc_start: 0.9139 (mttt) cc_final: 0.8934 (mttp) REVERT: 6 85 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8084 (tm-30) REVERT: 6 88 THR cc_start: 0.9467 (m) cc_final: 0.9149 (p) REVERT: 6 117 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7939 (pp) REVERT: 6 133 ASN cc_start: 0.8835 (m-40) cc_final: 0.8276 (t0) REVERT: 6 151 TYR cc_start: 0.9120 (t80) cc_final: 0.8713 (t80) REVERT: 8 37 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8397 (tptp) REVERT: 8 65 GLN cc_start: 0.8214 (tt0) cc_final: 0.7834 (tt0) REVERT: 8 76 ASP cc_start: 0.8113 (t0) cc_final: 0.7892 (t0) REVERT: 8 84 LEU cc_start: 0.9392 (tp) cc_final: 0.9191 (tp) REVERT: 8 85 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8148 (tm-30) REVERT: 8 88 THR cc_start: 0.9554 (m) cc_final: 0.9198 (p) REVERT: 8 106 ASP cc_start: 0.8063 (t70) cc_final: 0.7789 (t70) REVERT: 8 117 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7828 (pp) REVERT: 8 133 ASN cc_start: 0.8902 (m-40) cc_final: 0.8465 (t0) REVERT: 8 144 ASN cc_start: 0.8196 (t0) cc_final: 0.7439 (p0) REVERT: x 65 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8159 (tm-30) REVERT: x 81 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7448 (tm-30) REVERT: x 82 GLU cc_start: 0.8211 (mp0) cc_final: 0.7707 (mp0) REVERT: x 86 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8164 (ttpp) REVERT: x 97 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8396 (tttp) REVERT: x 109 GLU cc_start: 0.8019 (mp0) cc_final: 0.7374 (mp0) REVERT: x 171 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6274 (pmtt) REVERT: y 58 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6325 (m-10) REVERT: y 65 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8536 (tm-30) REVERT: y 86 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8399 (ttpp) REVERT: y 97 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8536 (tttm) REVERT: y 106 ASP cc_start: 0.7987 (t0) cc_final: 0.7621 (t0) REVERT: y 127 GLN cc_start: 0.8904 (tp40) cc_final: 0.8453 (tp40) REVERT: y 147 ASP cc_start: 0.8235 (t0) cc_final: 0.8010 (m-30) REVERT: y 148 LYS cc_start: 0.9262 (mtpt) cc_final: 0.8874 (mtmt) REVERT: y 171 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6254 (pmtt) REVERT: z 65 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8381 (tm-30) REVERT: z 82 GLU cc_start: 0.8206 (mp0) cc_final: 0.7928 (mp0) REVERT: z 86 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8217 (ttpp) REVERT: z 97 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8398 (tttp) REVERT: z 102 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8205 (tp) REVERT: z 106 ASP cc_start: 0.8224 (t0) cc_final: 0.7931 (t0) REVERT: z 147 ASP cc_start: 0.7989 (t0) cc_final: 0.7604 (m-30) REVERT: z 171 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6388 (pmtt) REVERT: 1 52 PHE cc_start: 0.9192 (t80) cc_final: 0.8798 (t80) REVERT: 1 58 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6266 (m-10) REVERT: 1 65 GLN cc_start: 0.9315 (tm-30) cc_final: 0.8623 (tm-30) REVERT: 1 85 GLU cc_start: 0.8012 (tp30) cc_final: 0.7668 (tm-30) REVERT: 1 86 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8490 (mtpt) REVERT: 1 97 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8550 (tttm) REVERT: 1 127 GLN cc_start: 0.8899 (tp40) cc_final: 0.8458 (tp40) REVERT: 1 147 ASP cc_start: 0.8235 (t0) cc_final: 0.8033 (m-30) REVERT: 1 148 LYS cc_start: 0.9262 (mtpt) cc_final: 0.8880 (mtmt) REVERT: 1 171 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6314 (pmtt) REVERT: 3 65 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8738 (tm-30) REVERT: 3 70 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8451 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7389 (tm-30) REVERT: 3 82 GLU cc_start: 0.8297 (mp0) cc_final: 0.7784 (mp0) REVERT: 3 86 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8156 (ttpp) REVERT: 3 97 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8372 (tttp) REVERT: 3 109 GLU cc_start: 0.8326 (mp0) cc_final: 0.7935 (mt-10) REVERT: 3 147 ASP cc_start: 0.7959 (t0) cc_final: 0.7597 (m-30) REVERT: 3 171 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6337 (pmtt) REVERT: 5 58 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6254 (m-10) REVERT: 5 65 GLN cc_start: 0.9307 (tm-30) cc_final: 0.8617 (tm-30) REVERT: 5 85 GLU cc_start: 0.7871 (tp30) cc_final: 0.7580 (tm-30) REVERT: 5 86 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8466 (mtpt) REVERT: 5 97 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8558 (tttp) REVERT: 5 127 GLN cc_start: 0.8909 (tp40) cc_final: 0.8459 (tp40) REVERT: 5 147 ASP cc_start: 0.8238 (t0) cc_final: 0.8030 (m-30) REVERT: 5 148 LYS cc_start: 0.9260 (mtpt) cc_final: 0.8881 (mtmt) REVERT: 5 171 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6086 (pmtt) REVERT: 7 81 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7345 (tm-30) REVERT: 7 82 GLU cc_start: 0.8448 (mp0) cc_final: 0.7921 (mp0) REVERT: 7 86 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8047 (ttpp) REVERT: 7 97 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8457 (tttp) REVERT: 7 102 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8257 (tp) REVERT: 7 147 ASP cc_start: 0.8019 (t0) cc_final: 0.7464 (m-30) REVERT: 7 171 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6418 (pmtt) REVERT: 9 37 LYS cc_start: 0.8966 (tttt) cc_final: 0.8653 (ttmt) REVERT: 9 52 PHE cc_start: 0.9180 (t80) cc_final: 0.8925 (t80) REVERT: 9 58 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6265 (m-10) REVERT: 9 65 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8520 (tm-30) REVERT: 9 86 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8453 (ttpp) REVERT: 9 97 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8543 (tttp) REVERT: 9 106 ASP cc_start: 0.7978 (t0) cc_final: 0.7601 (t0) REVERT: 9 127 GLN cc_start: 0.8905 (tp40) cc_final: 0.8457 (tp40) REVERT: 9 147 ASP cc_start: 0.8352 (t0) cc_final: 0.7831 (m-30) REVERT: 9 148 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8862 (mtmt) REVERT: 9 171 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6329 (pmtt) REVERT: A 347 LYS cc_start: 0.9097 (mmtp) cc_final: 0.8873 (mmtt) REVERT: D 359 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7655 (pp) REVERT: J 345 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8222 (tppt) REVERT: P 345 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8216 (tppt) REVERT: P 354 ASP cc_start: 0.7823 (m-30) cc_final: 0.7300 (m-30) REVERT: S 358 MET cc_start: 0.7875 (tpp) cc_final: 0.7578 (tpp) REVERT: U 359 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7679 (pp) REVERT: B 343 ASP cc_start: 0.7653 (p0) cc_final: 0.7233 (p0) REVERT: E 341 ASP cc_start: 0.7983 (p0) cc_final: 0.7761 (p0) REVERT: H 343 ASP cc_start: 0.7643 (p0) cc_final: 0.7235 (p0) REVERT: H 358 MET cc_start: 0.8628 (tpp) cc_final: 0.8177 (tpp) REVERT: N 358 MET cc_start: 0.8457 (tpp) cc_final: 0.8219 (tpp) REVERT: Q 353 LYS cc_start: 0.8946 (pttt) cc_final: 0.8555 (mmmt) REVERT: Q 358 MET cc_start: 0.8629 (tpp) cc_final: 0.8230 (tpp) REVERT: T 339 LEU cc_start: 0.8916 (mt) cc_final: 0.8534 (tt) REVERT: T 358 MET cc_start: 0.8472 (mmm) cc_final: 0.7938 (tpp) REVERT: T 361 ASP cc_start: 0.7933 (t0) cc_final: 0.7661 (t0) REVERT: V 353 LYS cc_start: 0.9002 (pttt) cc_final: 0.8504 (mmmt) REVERT: V 358 MET cc_start: 0.8524 (tpp) cc_final: 0.8311 (tpp) outliers start: 135 outliers final: 74 residues processed: 1041 average time/residue: 0.1502 time to fit residues: 235.2858 Evaluate side-chains 1017 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 919 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 78 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 102 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain T residue 355 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 173 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 192 optimal weight: 0.0040 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN 5 41 GLN A 360 ASN D 360 ASN P 360 ASN S 360 ASN U 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.075609 restraints weight = 54188.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.077996 restraints weight = 27952.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079628 restraints weight = 17508.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.080758 restraints weight = 12266.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.081595 restraints weight = 9251.476| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22224 Z= 0.139 Angle : 0.654 8.319 30080 Z= 0.348 Chirality : 0.045 0.156 3392 Planarity : 0.004 0.047 3744 Dihedral : 7.443 59.894 2986 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 6.21 % Allowed : 25.46 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2624 helix: 0.48 (0.17), residues: 976 sheet: -0.25 (0.21), residues: 672 loop : -3.00 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 4 138 TYR 0.021 0.001 TYR U 349 PHE 0.022 0.002 PHE 2 48 TRP 0.009 0.001 TRP U 364 HIS 0.002 0.001 HIS N 363 Details of bonding type rmsd covalent geometry : bond 0.00318 (22224) covalent geometry : angle 0.65437 (30080) hydrogen bonds : bond 0.03243 ( 1021) hydrogen bonds : angle 4.96493 ( 2784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 950 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8181 (tm-30) REVERT: X 88 THR cc_start: 0.9395 (m) cc_final: 0.9057 (p) REVERT: X 117 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8139 (pp) REVERT: X 133 ASN cc_start: 0.8835 (m-40) cc_final: 0.8323 (t0) REVERT: X 144 ASN cc_start: 0.8022 (t0) cc_final: 0.7807 (p0) REVERT: X 151 TYR cc_start: 0.9130 (t80) cc_final: 0.8703 (t80) REVERT: Y 37 LYS cc_start: 0.9076 (mttt) cc_final: 0.8775 (ttmm) REVERT: Y 65 GLN cc_start: 0.8285 (tt0) cc_final: 0.7849 (tt0) REVERT: Y 85 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8157 (tm-30) REVERT: Y 88 THR cc_start: 0.9510 (m) cc_final: 0.9219 (p) REVERT: Y 106 ASP cc_start: 0.7944 (t70) cc_final: 0.7588 (t70) REVERT: Y 133 ASN cc_start: 0.8843 (m-40) cc_final: 0.8411 (t0) REVERT: Y 138 ARG cc_start: 0.8500 (ptp-110) cc_final: 0.8280 (mtm110) REVERT: Y 144 ASN cc_start: 0.8221 (t0) cc_final: 0.7233 (p0) REVERT: Z 85 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8238 (tm-30) REVERT: Z 88 THR cc_start: 0.9396 (m) cc_final: 0.9085 (p) REVERT: Z 117 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8091 (pp) REVERT: Z 133 ASN cc_start: 0.8853 (m-40) cc_final: 0.8318 (t0) REVERT: Z 151 TYR cc_start: 0.9117 (t80) cc_final: 0.8705 (t80) REVERT: 0 74 GLU cc_start: 0.6661 (tp30) cc_final: 0.6193 (tp30) REVERT: 0 85 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8056 (tm-30) REVERT: 0 88 THR cc_start: 0.9540 (m) cc_final: 0.9239 (p) REVERT: 0 96 TYR cc_start: 0.8810 (t80) cc_final: 0.8522 (t80) REVERT: 0 117 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8042 (pp) REVERT: 0 133 ASN cc_start: 0.8889 (m-40) cc_final: 0.8389 (t0) REVERT: 2 85 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8076 (tm-30) REVERT: 2 88 THR cc_start: 0.9453 (m) cc_final: 0.9121 (p) REVERT: 2 106 ASP cc_start: 0.8071 (t0) cc_final: 0.7827 (t0) REVERT: 2 117 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8123 (pp) REVERT: 2 133 ASN cc_start: 0.8827 (m-40) cc_final: 0.8284 (t0) REVERT: 2 151 TYR cc_start: 0.9127 (t80) cc_final: 0.8704 (t80) REVERT: 4 85 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8069 (tm-30) REVERT: 4 88 THR cc_start: 0.9533 (m) cc_final: 0.9220 (p) REVERT: 4 96 TYR cc_start: 0.8819 (t80) cc_final: 0.8531 (t80) REVERT: 4 106 ASP cc_start: 0.8208 (t0) cc_final: 0.7997 (t0) REVERT: 4 133 ASN cc_start: 0.8886 (m-40) cc_final: 0.8405 (t0) REVERT: 6 68 LYS cc_start: 0.9158 (mttt) cc_final: 0.8923 (mttm) REVERT: 6 85 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8054 (tm-30) REVERT: 6 88 THR cc_start: 0.9457 (m) cc_final: 0.9146 (p) REVERT: 6 106 ASP cc_start: 0.8102 (t0) cc_final: 0.7869 (t0) REVERT: 6 133 ASN cc_start: 0.8847 (m-40) cc_final: 0.8314 (t0) REVERT: 6 151 TYR cc_start: 0.9132 (t80) cc_final: 0.8692 (t80) REVERT: 8 37 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8473 (tptp) REVERT: 8 65 GLN cc_start: 0.8235 (tt0) cc_final: 0.7877 (tt0) REVERT: 8 85 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8141 (tm-30) REVERT: 8 88 THR cc_start: 0.9531 (m) cc_final: 0.9179 (p) REVERT: 8 106 ASP cc_start: 0.8008 (t70) cc_final: 0.7744 (t70) REVERT: 8 117 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8049 (pp) REVERT: 8 133 ASN cc_start: 0.8888 (m-40) cc_final: 0.8446 (t0) REVERT: x 65 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8033 (tm-30) REVERT: x 81 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7376 (tm-30) REVERT: x 82 GLU cc_start: 0.8297 (mp0) cc_final: 0.7836 (mp0) REVERT: x 97 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8276 (tttp) REVERT: x 109 GLU cc_start: 0.7987 (mp0) cc_final: 0.7429 (mp0) REVERT: x 138 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7979 (mtm-85) REVERT: x 171 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6443 (pmtt) REVERT: y 37 LYS cc_start: 0.9003 (tttt) cc_final: 0.8431 (ttmt) REVERT: y 58 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: y 65 GLN cc_start: 0.9376 (tm-30) cc_final: 0.8988 (tm-30) REVERT: y 97 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8451 (tttp) REVERT: y 127 GLN cc_start: 0.8925 (tp40) cc_final: 0.8483 (tp40) REVERT: y 148 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8868 (mtmt) REVERT: y 171 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6278 (pmtt) REVERT: z 52 PHE cc_start: 0.9105 (t80) cc_final: 0.8886 (t80) REVERT: z 65 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8081 (tm-30) REVERT: z 97 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8397 (tttp) REVERT: z 102 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8201 (tp) REVERT: z 106 ASP cc_start: 0.8080 (t0) cc_final: 0.7531 (t0) REVERT: z 128 TYR cc_start: 0.9263 (t80) cc_final: 0.9060 (t80) REVERT: z 147 ASP cc_start: 0.7975 (t0) cc_final: 0.7674 (m-30) REVERT: z 171 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6445 (pmtt) REVERT: 1 37 LYS cc_start: 0.8999 (tttt) cc_final: 0.8499 (ttmt) REVERT: 1 58 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6264 (m-10) REVERT: 1 85 GLU cc_start: 0.8115 (tp30) cc_final: 0.7602 (tm-30) REVERT: 1 86 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8441 (mtpt) REVERT: 1 97 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8453 (tttp) REVERT: 1 106 ASP cc_start: 0.7586 (t0) cc_final: 0.7357 (t0) REVERT: 1 127 GLN cc_start: 0.8914 (tp40) cc_final: 0.8482 (tp40) REVERT: 1 147 ASP cc_start: 0.8352 (t0) cc_final: 0.7855 (m-30) REVERT: 1 148 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8878 (mtmt) REVERT: 1 171 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6392 (pmtt) REVERT: 3 65 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8764 (tm-30) REVERT: 3 70 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8363 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7336 (tm-30) REVERT: 3 82 GLU cc_start: 0.8326 (mp0) cc_final: 0.7851 (mp0) REVERT: 3 97 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8421 (tttp) REVERT: 3 109 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: 3 128 TYR cc_start: 0.9269 (t80) cc_final: 0.9043 (t80) REVERT: 3 147 ASP cc_start: 0.7967 (t0) cc_final: 0.7646 (m-30) REVERT: 3 171 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6350 (pmtt) REVERT: 5 37 LYS cc_start: 0.9021 (tttt) cc_final: 0.8545 (ttmt) REVERT: 5 58 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6248 (m-10) REVERT: 5 65 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9113 (tm-30) REVERT: 5 85 GLU cc_start: 0.8054 (tp30) cc_final: 0.7637 (tm-30) REVERT: 5 86 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8423 (mtpt) REVERT: 5 97 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8449 (tttp) REVERT: 5 106 ASP cc_start: 0.7708 (t0) cc_final: 0.7470 (t0) REVERT: 5 127 GLN cc_start: 0.8931 (tp40) cc_final: 0.8500 (tp40) REVERT: 5 147 ASP cc_start: 0.8291 (t0) cc_final: 0.8010 (m-30) REVERT: 5 148 LYS cc_start: 0.9272 (mtpt) cc_final: 0.8878 (mtmt) REVERT: 5 171 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6428 (pmtt) REVERT: 7 79 ASN cc_start: 0.8543 (p0) cc_final: 0.8162 (p0) REVERT: 7 81 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7190 (tm-30) REVERT: 7 82 GLU cc_start: 0.8506 (mp0) cc_final: 0.7490 (mp0) REVERT: 7 86 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8118 (ttpp) REVERT: 7 97 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8392 (tttp) REVERT: 7 102 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8199 (tp) REVERT: 7 138 ARG cc_start: 0.8409 (mtp85) cc_final: 0.7998 (mtm-85) REVERT: 7 147 ASP cc_start: 0.7992 (t0) cc_final: 0.7506 (m-30) REVERT: 7 171 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6544 (pmtt) REVERT: 9 58 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6251 (m-10) REVERT: 9 65 GLN cc_start: 0.9372 (tm-30) cc_final: 0.8975 (tm-30) REVERT: 9 97 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8453 (tttm) REVERT: 9 127 GLN cc_start: 0.8917 (tp40) cc_final: 0.8482 (tp40) REVERT: 9 147 ASP cc_start: 0.8331 (t0) cc_final: 0.7832 (m-30) REVERT: 9 148 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8858 (mtmt) REVERT: 9 171 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6356 (pmtt) REVERT: A 347 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8870 (mmtt) REVERT: D 359 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7555 (pp) REVERT: P 345 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8225 (tppt) REVERT: P 354 ASP cc_start: 0.7959 (m-30) cc_final: 0.7461 (m-30) REVERT: S 358 MET cc_start: 0.7772 (tpp) cc_final: 0.7301 (tpp) REVERT: U 354 ASP cc_start: 0.7799 (m-30) cc_final: 0.7280 (m-30) REVERT: U 359 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7552 (pp) REVERT: B 343 ASP cc_start: 0.7609 (p0) cc_final: 0.7201 (p0) REVERT: H 343 ASP cc_start: 0.7601 (p0) cc_final: 0.7194 (p0) REVERT: H 358 MET cc_start: 0.8651 (tpp) cc_final: 0.8172 (tpp) REVERT: N 358 MET cc_start: 0.8454 (tpp) cc_final: 0.8194 (tpp) REVERT: Q 353 LYS cc_start: 0.8968 (pttt) cc_final: 0.8691 (mmmt) REVERT: Q 358 MET cc_start: 0.8660 (tpp) cc_final: 0.8239 (tpp) REVERT: T 358 MET cc_start: 0.8469 (mmm) cc_final: 0.7817 (tpp) REVERT: T 361 ASP cc_start: 0.7812 (t0) cc_final: 0.7603 (t0) REVERT: V 341 ASP cc_start: 0.8087 (p0) cc_final: 0.7863 (p0) REVERT: V 353 LYS cc_start: 0.8995 (pttt) cc_final: 0.8484 (mmmt) REVERT: V 358 MET cc_start: 0.8531 (tpp) cc_final: 0.8120 (tpp) outliers start: 149 outliers final: 91 residues processed: 1032 average time/residue: 0.1511 time to fit residues: 234.3049 Evaluate side-chains 1021 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 907 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 78 SER Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 43 ASP Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 109 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 112 SER Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 112 SER Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 355 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 169 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 152 optimal weight: 0.1980 chunk 186 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN 1 41 GLN 5 41 GLN D 360 ASN J 360 ASN P 360 ASN S 360 ASN U 360 ASN E 363 HIS K 363 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.085664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.075077 restraints weight = 54543.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.077451 restraints weight = 28158.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079085 restraints weight = 17624.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080211 restraints weight = 12335.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.081040 restraints weight = 9325.636| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22224 Z= 0.162 Angle : 0.685 8.562 30080 Z= 0.365 Chirality : 0.046 0.160 3392 Planarity : 0.004 0.043 3744 Dihedral : 7.295 59.809 2978 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 5.50 % Allowed : 28.04 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2624 helix: 0.49 (0.17), residues: 976 sheet: 0.06 (0.21), residues: 640 loop : -3.07 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 5 51 TYR 0.025 0.002 TYR Z 96 PHE 0.025 0.002 PHE z 48 TRP 0.008 0.001 TRP D 364 HIS 0.002 0.001 HIS T 363 Details of bonding type rmsd covalent geometry : bond 0.00373 (22224) covalent geometry : angle 0.68450 (30080) hydrogen bonds : bond 0.03398 ( 1021) hydrogen bonds : angle 5.07519 ( 2784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 919 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8237 (tm-30) REVERT: X 88 THR cc_start: 0.9390 (m) cc_final: 0.9098 (p) REVERT: X 133 ASN cc_start: 0.8863 (m-40) cc_final: 0.8380 (t0) REVERT: X 144 ASN cc_start: 0.8018 (t0) cc_final: 0.7757 (p0) REVERT: Y 37 LYS cc_start: 0.9106 (mttt) cc_final: 0.8807 (ttmm) REVERT: Y 65 GLN cc_start: 0.8328 (tt0) cc_final: 0.7934 (tt0) REVERT: Y 74 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7237 (tm-30) REVERT: Y 85 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8157 (tm-30) REVERT: Y 88 THR cc_start: 0.9511 (m) cc_final: 0.9199 (p) REVERT: Y 133 ASN cc_start: 0.8844 (m-40) cc_final: 0.8438 (t0) REVERT: Y 138 ARG cc_start: 0.8473 (ptp-110) cc_final: 0.8206 (mtm110) REVERT: Y 144 ASN cc_start: 0.8306 (t0) cc_final: 0.7290 (p0) REVERT: Z 85 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8229 (tm-30) REVERT: Z 88 THR cc_start: 0.9407 (m) cc_final: 0.9067 (p) REVERT: Z 117 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8117 (pp) REVERT: Z 133 ASN cc_start: 0.8886 (m-40) cc_final: 0.8400 (t0) REVERT: 0 85 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8145 (tm-30) REVERT: 0 88 THR cc_start: 0.9511 (m) cc_final: 0.9211 (p) REVERT: 0 117 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8112 (pp) REVERT: 0 133 ASN cc_start: 0.8881 (m-40) cc_final: 0.8410 (t0) REVERT: 2 85 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8090 (tm-30) REVERT: 2 88 THR cc_start: 0.9454 (m) cc_final: 0.9158 (p) REVERT: 2 117 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8159 (pp) REVERT: 2 133 ASN cc_start: 0.8861 (m-40) cc_final: 0.8363 (t0) REVERT: 4 37 LYS cc_start: 0.9253 (tmtt) cc_final: 0.8716 (tptp) REVERT: 4 85 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8238 (tm-30) REVERT: 4 88 THR cc_start: 0.9511 (m) cc_final: 0.9206 (p) REVERT: 4 96 TYR cc_start: 0.8791 (t80) cc_final: 0.8473 (t80) REVERT: 4 133 ASN cc_start: 0.8877 (m-40) cc_final: 0.8407 (t0) REVERT: 6 37 LYS cc_start: 0.9108 (tptm) cc_final: 0.8883 (mmmt) REVERT: 6 68 LYS cc_start: 0.9231 (mttt) cc_final: 0.8944 (mttm) REVERT: 6 85 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8075 (tm-30) REVERT: 6 88 THR cc_start: 0.9480 (m) cc_final: 0.9147 (p) REVERT: 6 133 ASN cc_start: 0.8862 (m-40) cc_final: 0.8361 (t0) REVERT: 8 37 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.7918 (tptp) REVERT: 8 65 GLN cc_start: 0.8318 (tt0) cc_final: 0.7881 (tt0) REVERT: 8 74 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6436 (tm-30) REVERT: 8 88 THR cc_start: 0.9541 (m) cc_final: 0.9196 (p) REVERT: 8 106 ASP cc_start: 0.8032 (t70) cc_final: 0.7732 (t70) REVERT: 8 117 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8085 (pp) REVERT: 8 133 ASN cc_start: 0.8835 (m-40) cc_final: 0.8400 (t0) REVERT: x 65 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8688 (tm-30) REVERT: x 70 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8468 (mtt-85) REVERT: x 81 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7403 (tm-30) REVERT: x 82 GLU cc_start: 0.8285 (mp0) cc_final: 0.7814 (mp0) REVERT: x 97 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8448 (tttp) REVERT: x 106 ASP cc_start: 0.7933 (t0) cc_final: 0.7728 (t0) REVERT: x 137 HIS cc_start: 0.7608 (p-80) cc_final: 0.7402 (p-80) REVERT: x 138 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8003 (mtm-85) REVERT: x 171 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6641 (pmtt) REVERT: y 58 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6284 (m-10) REVERT: y 65 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8879 (tm-30) REVERT: y 97 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8400 (tttm) REVERT: y 106 ASP cc_start: 0.7756 (t0) cc_final: 0.7203 (t0) REVERT: y 127 GLN cc_start: 0.8930 (tp40) cc_final: 0.8508 (tp40) REVERT: y 147 ASP cc_start: 0.8418 (m-30) cc_final: 0.7867 (t0) REVERT: y 148 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8664 (mtmt) REVERT: y 171 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6707 (pmtt) REVERT: z 65 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8108 (tm-30) REVERT: z 81 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7167 (pp20) REVERT: z 82 GLU cc_start: 0.8050 (mp0) cc_final: 0.6967 (mp0) REVERT: z 97 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8322 (tttp) REVERT: z 102 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8243 (tp) REVERT: z 106 ASP cc_start: 0.8064 (t0) cc_final: 0.7509 (t0) REVERT: z 128 TYR cc_start: 0.9247 (t80) cc_final: 0.9041 (t80) REVERT: z 147 ASP cc_start: 0.8021 (t0) cc_final: 0.7719 (m-30) REVERT: z 171 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6663 (pmtt) REVERT: 1 37 LYS cc_start: 0.8840 (tttt) cc_final: 0.8535 (tttp) REVERT: 1 58 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: 1 85 GLU cc_start: 0.8017 (tp30) cc_final: 0.7611 (tm-30) REVERT: 1 86 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8467 (mtpt) REVERT: 1 97 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8456 (tttm) REVERT: 1 127 GLN cc_start: 0.8925 (tp40) cc_final: 0.8519 (tp40) REVERT: 1 148 LYS cc_start: 0.9291 (mtpt) cc_final: 0.8886 (mtmt) REVERT: 1 171 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6793 (pmtt) REVERT: 3 70 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.8336 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7375 (tm-30) REVERT: 3 82 GLU cc_start: 0.8384 (mp0) cc_final: 0.7916 (mp0) REVERT: 3 97 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8437 (tttp) REVERT: 3 102 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8241 (tp) REVERT: 3 106 ASP cc_start: 0.8106 (t0) cc_final: 0.7850 (t0) REVERT: 3 109 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: 3 128 TYR cc_start: 0.9246 (t80) cc_final: 0.9039 (t80) REVERT: 3 147 ASP cc_start: 0.7989 (t0) cc_final: 0.7673 (m-30) REVERT: 3 171 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6660 (pmtt) REVERT: 5 37 LYS cc_start: 0.8841 (tttt) cc_final: 0.8620 (tttp) REVERT: 5 58 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6245 (m-10) REVERT: 5 85 GLU cc_start: 0.7955 (tp30) cc_final: 0.7593 (tm-30) REVERT: 5 86 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8406 (mtpt) REVERT: 5 97 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8453 (tttm) REVERT: 5 106 ASP cc_start: 0.7791 (t0) cc_final: 0.7268 (t0) REVERT: 5 127 GLN cc_start: 0.8936 (tp40) cc_final: 0.8526 (tp40) REVERT: 5 147 ASP cc_start: 0.8263 (t0) cc_final: 0.8059 (m-30) REVERT: 5 148 LYS cc_start: 0.9289 (mtpt) cc_final: 0.8881 (mtmt) REVERT: 5 171 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6702 (pmtt) REVERT: 7 65 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8587 (tm-30) REVERT: 7 79 ASN cc_start: 0.8531 (p0) cc_final: 0.8040 (p0) REVERT: 7 81 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7200 (tm-30) REVERT: 7 82 GLU cc_start: 0.8479 (mp0) cc_final: 0.7306 (mp0) REVERT: 7 97 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8425 (tttp) REVERT: 7 102 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8265 (tp) REVERT: 7 109 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7692 (mt-10) REVERT: 7 137 HIS cc_start: 0.7603 (p-80) cc_final: 0.7396 (p-80) REVERT: 7 138 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8025 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8021 (t0) cc_final: 0.7541 (m-30) REVERT: 7 171 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6851 (pmtt) REVERT: 9 58 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6345 (m-10) REVERT: 9 65 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8863 (tm-30) REVERT: 9 97 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8504 (tttm) REVERT: 9 106 ASP cc_start: 0.7797 (t0) cc_final: 0.7180 (t0) REVERT: 9 127 GLN cc_start: 0.8929 (tp40) cc_final: 0.8526 (tp40) REVERT: 9 138 ARG cc_start: 0.8250 (mtp85) cc_final: 0.8045 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8354 (t0) cc_final: 0.7861 (m-30) REVERT: 9 148 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8872 (mtmt) REVERT: 9 171 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6875 (pmtt) REVERT: A 347 LYS cc_start: 0.9106 (mmtp) cc_final: 0.8873 (mmtt) REVERT: D 359 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7267 (pp) REVERT: P 345 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8263 (tppt) REVERT: P 354 ASP cc_start: 0.7927 (m-30) cc_final: 0.7399 (m-30) REVERT: P 358 MET cc_start: 0.7531 (ttm) cc_final: 0.7264 (ttm) REVERT: S 358 MET cc_start: 0.7829 (tpp) cc_final: 0.7390 (tpp) REVERT: U 354 ASP cc_start: 0.7828 (m-30) cc_final: 0.7363 (m-30) REVERT: B 343 ASP cc_start: 0.7666 (p0) cc_final: 0.7274 (p0) REVERT: H 343 ASP cc_start: 0.7625 (p0) cc_final: 0.7240 (p0) REVERT: H 358 MET cc_start: 0.8666 (tpp) cc_final: 0.8076 (tpp) REVERT: N 358 MET cc_start: 0.8454 (tpp) cc_final: 0.8141 (tpp) REVERT: Q 353 LYS cc_start: 0.9044 (pttt) cc_final: 0.8783 (mmmt) REVERT: Q 358 MET cc_start: 0.8649 (tpp) cc_final: 0.8196 (tpp) REVERT: T 358 MET cc_start: 0.8565 (mmm) cc_final: 0.7842 (tpp) REVERT: V 353 LYS cc_start: 0.9011 (pttt) cc_final: 0.8572 (mmmt) REVERT: V 358 MET cc_start: 0.8568 (tpp) cc_final: 0.8225 (tpp) outliers start: 132 outliers final: 94 residues processed: 1001 average time/residue: 0.1476 time to fit residues: 223.2801 Evaluate side-chains 1007 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 891 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 144 ASN Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 78 SER Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 43 ASP Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 109 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 43 ASP Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 102 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain T residue 353 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 142 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 225 optimal weight: 0.1980 chunk 253 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN z 79 ASN 5 41 GLN A 360 ASN G 360 ASN J 360 ASN M 360 ASN S 360 ASN U 360 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.075701 restraints weight = 54330.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078074 restraints weight = 27895.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.079695 restraints weight = 17395.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.080807 restraints weight = 12183.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.081633 restraints weight = 9215.281| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22224 Z= 0.141 Angle : 0.707 9.044 30080 Z= 0.375 Chirality : 0.046 0.183 3392 Planarity : 0.005 0.053 3744 Dihedral : 7.215 59.642 2976 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.88 % Favored : 91.08 % Rotamer: Outliers : 5.17 % Allowed : 29.00 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2624 helix: 0.52 (0.17), residues: 976 sheet: -0.02 (0.21), residues: 672 loop : -2.88 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 5 51 TYR 0.022 0.001 TYR U 349 PHE 0.022 0.002 PHE 2 48 TRP 0.010 0.001 TRP K 364 HIS 0.002 0.001 HIS T 363 Details of bonding type rmsd covalent geometry : bond 0.00322 (22224) covalent geometry : angle 0.70743 (30080) hydrogen bonds : bond 0.03184 ( 1021) hydrogen bonds : angle 4.96326 ( 2784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 925 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 41 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8460 (mm-40) REVERT: X 85 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8186 (tm-30) REVERT: X 88 THR cc_start: 0.9415 (m) cc_final: 0.9105 (p) REVERT: X 131 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7601 (t0) REVERT: X 133 ASN cc_start: 0.8957 (m-40) cc_final: 0.8427 (t0) REVERT: X 144 ASN cc_start: 0.8024 (t0) cc_final: 0.7592 (p0) REVERT: X 151 TYR cc_start: 0.9013 (t80) cc_final: 0.8674 (t80) REVERT: Y 74 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7282 (tm-30) REVERT: Y 85 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8288 (tm-30) REVERT: Y 88 THR cc_start: 0.9521 (m) cc_final: 0.9206 (p) REVERT: Y 133 ASN cc_start: 0.8888 (m-40) cc_final: 0.8571 (t0) REVERT: Y 138 ARG cc_start: 0.8363 (ptp-110) cc_final: 0.8146 (mtm110) REVERT: Z 85 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8240 (tm-30) REVERT: Z 88 THR cc_start: 0.9372 (m) cc_final: 0.9082 (p) REVERT: Z 133 ASN cc_start: 0.8889 (m-40) cc_final: 0.8255 (t0) REVERT: Z 151 TYR cc_start: 0.9056 (t80) cc_final: 0.8697 (t80) REVERT: 0 85 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8281 (tm-30) REVERT: 0 88 THR cc_start: 0.9535 (m) cc_final: 0.9217 (p) REVERT: 0 117 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7981 (pp) REVERT: 0 133 ASN cc_start: 0.8844 (m-40) cc_final: 0.8337 (t0) REVERT: 2 85 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8089 (tm-30) REVERT: 2 88 THR cc_start: 0.9467 (m) cc_final: 0.9133 (p) REVERT: 2 131 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7534 (t70) REVERT: 2 133 ASN cc_start: 0.8951 (m-40) cc_final: 0.8398 (t0) REVERT: 2 151 TYR cc_start: 0.9055 (t80) cc_final: 0.8692 (t80) REVERT: 4 37 LYS cc_start: 0.9312 (tmtt) cc_final: 0.8668 (tptp) REVERT: 4 85 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8261 (tm-30) REVERT: 4 88 THR cc_start: 0.9532 (m) cc_final: 0.9224 (p) REVERT: 4 133 ASN cc_start: 0.8831 (m-40) cc_final: 0.8357 (t0) REVERT: 6 37 LYS cc_start: 0.8914 (tptm) cc_final: 0.8484 (mmmt) REVERT: 6 68 LYS cc_start: 0.9280 (mttt) cc_final: 0.8988 (mttp) REVERT: 6 85 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8094 (tm-30) REVERT: 6 88 THR cc_start: 0.9445 (m) cc_final: 0.9148 (p) REVERT: 6 131 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7616 (t0) REVERT: 6 133 ASN cc_start: 0.8956 (m-40) cc_final: 0.8406 (t0) REVERT: 8 37 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8076 (tptp) REVERT: 8 65 GLN cc_start: 0.8266 (tt0) cc_final: 0.7875 (tt0) REVERT: 8 85 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8286 (tm-30) REVERT: 8 86 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8775 (ttpt) REVERT: 8 88 THR cc_start: 0.9519 (m) cc_final: 0.9174 (p) REVERT: 8 106 ASP cc_start: 0.8073 (t70) cc_final: 0.7784 (t70) REVERT: 8 117 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7957 (pp) REVERT: 8 133 ASN cc_start: 0.8878 (m-40) cc_final: 0.8505 (t0) REVERT: 8 138 ARG cc_start: 0.8519 (ptp-110) cc_final: 0.8279 (mtm110) REVERT: x 65 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8161 (tm-30) REVERT: x 81 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7426 (tm-30) REVERT: x 82 GLU cc_start: 0.8367 (mp0) cc_final: 0.7919 (mp0) REVERT: x 97 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8327 (tttp) REVERT: x 102 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8118 (tp) REVERT: x 137 HIS cc_start: 0.7618 (p-80) cc_final: 0.7413 (p-80) REVERT: x 138 ARG cc_start: 0.8422 (mtp85) cc_final: 0.7972 (mtm-85) REVERT: x 171 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6507 (pmtt) REVERT: y 37 LYS cc_start: 0.8792 (tttt) cc_final: 0.8581 (ttmt) REVERT: y 58 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6178 (m-10) REVERT: y 65 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8848 (tm-30) REVERT: y 74 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7424 (tm-30) REVERT: y 97 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8376 (tttm) REVERT: y 109 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7347 (mt-10) REVERT: y 127 GLN cc_start: 0.8918 (tp40) cc_final: 0.8487 (tp40) REVERT: y 147 ASP cc_start: 0.8490 (m-30) cc_final: 0.7893 (t0) REVERT: y 148 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8621 (mtmt) REVERT: y 171 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6442 (pmtt) REVERT: z 65 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8175 (tm-30) REVERT: z 97 LYS cc_start: 0.9063 (ttpt) cc_final: 0.8387 (tttp) REVERT: z 102 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8155 (tp) REVERT: z 106 ASP cc_start: 0.8114 (t0) cc_final: 0.7556 (t0) REVERT: z 128 TYR cc_start: 0.9253 (t80) cc_final: 0.9040 (t80) REVERT: z 147 ASP cc_start: 0.8263 (t0) cc_final: 0.7883 (m-30) REVERT: z 171 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6422 (pmtt) REVERT: 1 37 LYS cc_start: 0.8921 (tttt) cc_final: 0.8713 (tttp) REVERT: 1 58 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: 1 85 GLU cc_start: 0.7832 (tp30) cc_final: 0.7529 (tm-30) REVERT: 1 86 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8485 (mtpt) REVERT: 1 97 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8406 (tttp) REVERT: 1 106 ASP cc_start: 0.7532 (t0) cc_final: 0.7166 (t0) REVERT: 1 127 GLN cc_start: 0.8921 (tp40) cc_final: 0.8465 (tp-100) REVERT: 1 147 ASP cc_start: 0.8476 (m-30) cc_final: 0.7718 (t0) REVERT: 1 148 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8684 (mtmt) REVERT: 1 171 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6580 (pmtt) REVERT: 3 37 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8767 (tttt) REVERT: 3 70 ARG cc_start: 0.8704 (mtt-85) cc_final: 0.8489 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7287 (tm-30) REVERT: 3 82 GLU cc_start: 0.8357 (mp0) cc_final: 0.7889 (mp0) REVERT: 3 97 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8427 (tttp) REVERT: 3 102 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8152 (tp) REVERT: 3 128 TYR cc_start: 0.9251 (t80) cc_final: 0.9036 (t80) REVERT: 3 139 TYR cc_start: 0.8469 (m-80) cc_final: 0.8242 (m-80) REVERT: 3 147 ASP cc_start: 0.7999 (t0) cc_final: 0.7688 (m-30) REVERT: 3 171 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6513 (pmtt) REVERT: 5 37 LYS cc_start: 0.8951 (tttt) cc_final: 0.8735 (tttp) REVERT: 5 58 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.6117 (m-10) REVERT: 5 85 GLU cc_start: 0.7984 (tp30) cc_final: 0.7659 (tm-30) REVERT: 5 86 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8487 (mtpt) REVERT: 5 97 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8421 (tttp) REVERT: 5 109 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7400 (mt-10) REVERT: 5 127 GLN cc_start: 0.8919 (tp40) cc_final: 0.8501 (tp40) REVERT: 5 147 ASP cc_start: 0.8415 (t0) cc_final: 0.7883 (m-30) REVERT: 5 148 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8838 (mtmt) REVERT: 5 171 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6538 (pmtt) REVERT: 7 65 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8694 (tm-30) REVERT: 7 79 ASN cc_start: 0.8505 (p0) cc_final: 0.8155 (p0) REVERT: 7 81 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7200 (tm-30) REVERT: 7 82 GLU cc_start: 0.8447 (mp0) cc_final: 0.7536 (mp0) REVERT: 7 97 LYS cc_start: 0.9163 (ttpt) cc_final: 0.8510 (tttp) REVERT: 7 102 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8131 (tp) REVERT: 7 109 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7706 (mt-10) REVERT: 7 138 ARG cc_start: 0.8403 (mtp85) cc_final: 0.7939 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8053 (t0) cc_final: 0.7579 (m-30) REVERT: 7 171 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6500 (pmtt) REVERT: 9 58 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6281 (m-10) REVERT: 9 65 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8826 (tm-30) REVERT: 9 97 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8435 (tttm) REVERT: 9 109 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7356 (mt-10) REVERT: 9 127 GLN cc_start: 0.8917 (tp40) cc_final: 0.8495 (tp40) REVERT: 9 138 ARG cc_start: 0.8262 (mtp85) cc_final: 0.8015 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8408 (t0) cc_final: 0.7887 (m-30) REVERT: 9 148 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8835 (mtmt) REVERT: 9 171 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6685 (pmtt) REVERT: A 347 LYS cc_start: 0.9054 (mmtp) cc_final: 0.8799 (mmtt) REVERT: G 359 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7540 (pp) REVERT: P 354 ASP cc_start: 0.8070 (m-30) cc_final: 0.7527 (m-30) REVERT: S 358 MET cc_start: 0.7802 (tpp) cc_final: 0.7373 (tpp) REVERT: U 354 ASP cc_start: 0.7768 (m-30) cc_final: 0.7466 (m-30) REVERT: B 343 ASP cc_start: 0.7760 (p0) cc_final: 0.7408 (p0) REVERT: H 343 ASP cc_start: 0.7714 (p0) cc_final: 0.7362 (p0) REVERT: H 358 MET cc_start: 0.8653 (tpp) cc_final: 0.8211 (tpp) REVERT: K 365 PHE cc_start: 0.8844 (t80) cc_final: 0.8541 (t80) REVERT: N 343 ASP cc_start: 0.7719 (p0) cc_final: 0.7450 (p0) REVERT: N 358 MET cc_start: 0.8414 (tpp) cc_final: 0.8157 (tpp) REVERT: Q 353 LYS cc_start: 0.8989 (pttt) cc_final: 0.8686 (mmtt) REVERT: Q 358 MET cc_start: 0.8624 (tpp) cc_final: 0.8156 (tpp) REVERT: T 339 LEU cc_start: 0.8885 (mt) cc_final: 0.8490 (tt) REVERT: T 343 ASP cc_start: 0.7757 (p0) cc_final: 0.7544 (p0) REVERT: V 358 MET cc_start: 0.8504 (tpp) cc_final: 0.8079 (tpp) outliers start: 124 outliers final: 89 residues processed: 1000 average time/residue: 0.1479 time to fit residues: 224.3940 Evaluate side-chains 1009 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 897 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 43 ASP Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 79 ASN Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 43 ASP Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain S residue 342 ASP Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 355 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 28 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 177 optimal weight: 0.1980 chunk 139 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 79 ASN z 79 ASN 1 41 GLN 5 79 ASN A 360 ASN G 360 ASN M 360 ASN S 360 ASN U 360 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.075497 restraints weight = 55088.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.077865 restraints weight = 28232.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.079484 restraints weight = 17613.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.080600 restraints weight = 12321.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.081433 restraints weight = 9325.855| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22224 Z= 0.152 Angle : 0.732 9.079 30080 Z= 0.392 Chirality : 0.046 0.193 3392 Planarity : 0.005 0.066 3744 Dihedral : 7.179 59.754 2976 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.29 % Allowed : 29.50 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.16), residues: 2624 helix: 0.57 (0.17), residues: 976 sheet: 0.07 (0.21), residues: 672 loop : -2.82 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 8 70 TYR 0.019 0.001 TYR 2 96 PHE 0.023 0.002 PHE 2 48 TRP 0.011 0.001 TRP K 364 HIS 0.002 0.001 HIS T 363 Details of bonding type rmsd covalent geometry : bond 0.00349 (22224) covalent geometry : angle 0.73248 (30080) hydrogen bonds : bond 0.03236 ( 1021) hydrogen bonds : angle 4.99562 ( 2784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 907 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 41 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8449 (mm-40) REVERT: X 85 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8182 (tm-30) REVERT: X 88 THR cc_start: 0.9411 (m) cc_final: 0.9104 (p) REVERT: X 133 ASN cc_start: 0.8920 (m-40) cc_final: 0.8399 (t0) REVERT: X 144 ASN cc_start: 0.8041 (t0) cc_final: 0.7539 (p0) REVERT: Y 65 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8056 (tm-30) REVERT: Y 85 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8286 (tm-30) REVERT: Y 88 THR cc_start: 0.9517 (m) cc_final: 0.9203 (p) REVERT: Y 96 TYR cc_start: 0.8885 (t80) cc_final: 0.8597 (t80) REVERT: Y 133 ASN cc_start: 0.8917 (m-40) cc_final: 0.8648 (t0) REVERT: Y 138 ARG cc_start: 0.8437 (ptp-110) cc_final: 0.8225 (mtm110) REVERT: Z 85 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8246 (tm-30) REVERT: Z 88 THR cc_start: 0.9415 (m) cc_final: 0.9118 (p) REVERT: Z 133 ASN cc_start: 0.8856 (m-40) cc_final: 0.8240 (t0) REVERT: Z 151 TYR cc_start: 0.9051 (t80) cc_final: 0.8699 (t80) REVERT: 0 37 LYS cc_start: 0.9196 (tptp) cc_final: 0.8976 (tppt) REVERT: 0 85 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8298 (tm-30) REVERT: 0 88 THR cc_start: 0.9518 (m) cc_final: 0.9165 (p) REVERT: 0 117 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7991 (pp) REVERT: 0 133 ASN cc_start: 0.8836 (m-40) cc_final: 0.8350 (t0) REVERT: 2 41 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8501 (mm-40) REVERT: 2 85 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8078 (tm-30) REVERT: 2 88 THR cc_start: 0.9442 (m) cc_final: 0.9159 (p) REVERT: 2 131 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7555 (t70) REVERT: 2 133 ASN cc_start: 0.8940 (m-40) cc_final: 0.8403 (t0) REVERT: 2 151 TYR cc_start: 0.9044 (t80) cc_final: 0.8700 (t80) REVERT: 4 37 LYS cc_start: 0.9318 (tmtt) cc_final: 0.8670 (tptp) REVERT: 4 85 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8270 (tm-30) REVERT: 4 88 THR cc_start: 0.9499 (m) cc_final: 0.9205 (p) REVERT: 4 133 ASN cc_start: 0.8825 (m-40) cc_final: 0.8475 (t0) REVERT: 4 138 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.8302 (mtm110) REVERT: 6 37 LYS cc_start: 0.9089 (tptm) cc_final: 0.8401 (tptp) REVERT: 6 68 LYS cc_start: 0.9297 (mttt) cc_final: 0.9010 (mttp) REVERT: 6 85 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8101 (tm-30) REVERT: 6 88 THR cc_start: 0.9475 (m) cc_final: 0.9178 (p) REVERT: 6 133 ASN cc_start: 0.8946 (m-40) cc_final: 0.8383 (t0) REVERT: 8 37 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8094 (tptp) REVERT: 8 65 GLN cc_start: 0.8293 (tt0) cc_final: 0.7889 (tt0) REVERT: 8 85 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8182 (tm-30) REVERT: 8 86 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8854 (ttpt) REVERT: 8 88 THR cc_start: 0.9512 (m) cc_final: 0.9201 (p) REVERT: 8 106 ASP cc_start: 0.8041 (t70) cc_final: 0.7742 (t70) REVERT: 8 117 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7994 (pp) REVERT: 8 133 ASN cc_start: 0.8852 (m-40) cc_final: 0.8550 (t0) REVERT: 8 138 ARG cc_start: 0.8524 (ptp-110) cc_final: 0.8282 (mtm110) REVERT: x 65 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8210 (tm-30) REVERT: x 81 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7428 (tm-30) REVERT: x 82 GLU cc_start: 0.8347 (mp0) cc_final: 0.7928 (mp0) REVERT: x 97 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8353 (tttp) REVERT: x 138 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7939 (mtm-85) REVERT: x 171 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6601 (pmtt) REVERT: y 37 LYS cc_start: 0.8892 (tttt) cc_final: 0.8627 (ttmt) REVERT: y 58 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: y 65 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8773 (tm-30) REVERT: y 97 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8370 (tttm) REVERT: y 109 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7321 (mt-10) REVERT: y 127 GLN cc_start: 0.8928 (tp40) cc_final: 0.8502 (tp40) REVERT: y 147 ASP cc_start: 0.8438 (m-30) cc_final: 0.7821 (t0) REVERT: y 148 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8638 (mtmt) REVERT: y 171 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6491 (pmtt) REVERT: z 65 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8117 (tm-30) REVERT: z 97 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8320 (tttp) REVERT: z 102 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8283 (tp) REVERT: z 106 ASP cc_start: 0.8334 (t0) cc_final: 0.7793 (t0) REVERT: z 128 TYR cc_start: 0.9255 (t80) cc_final: 0.9045 (t80) REVERT: z 147 ASP cc_start: 0.8248 (t0) cc_final: 0.7905 (m-30) REVERT: z 171 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6472 (pmtt) REVERT: 1 37 LYS cc_start: 0.8879 (tttt) cc_final: 0.8661 (ttmt) REVERT: 1 58 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6115 (m-10) REVERT: 1 79 ASN cc_start: 0.8509 (p0) cc_final: 0.8300 (p0) REVERT: 1 85 GLU cc_start: 0.7851 (tp30) cc_final: 0.7553 (tm-30) REVERT: 1 86 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8532 (mtpt) REVERT: 1 97 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8408 (tttm) REVERT: 1 109 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7385 (mt-10) REVERT: 1 127 GLN cc_start: 0.8935 (tp40) cc_final: 0.8487 (tp-100) REVERT: 1 148 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8541 (mtmt) REVERT: 1 171 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6596 (pmtt) REVERT: 3 70 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8513 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7323 (tm-30) REVERT: 3 82 GLU cc_start: 0.8312 (mp0) cc_final: 0.7895 (mp0) REVERT: 3 97 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8406 (tttp) REVERT: 3 147 ASP cc_start: 0.7989 (t0) cc_final: 0.7705 (m-30) REVERT: 3 171 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6434 (pmtt) REVERT: 5 58 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6162 (m-10) REVERT: 5 85 GLU cc_start: 0.8003 (tp30) cc_final: 0.7650 (tm-30) REVERT: 5 86 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8567 (mtpt) REVERT: 5 97 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8433 (tttp) REVERT: 5 109 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7400 (mt-10) REVERT: 5 127 GLN cc_start: 0.8932 (tp40) cc_final: 0.8517 (tp40) REVERT: 5 147 ASP cc_start: 0.8417 (t0) cc_final: 0.7910 (m-30) REVERT: 5 148 LYS cc_start: 0.9279 (mtpt) cc_final: 0.8858 (mtmt) REVERT: 5 171 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6400 (pmtt) REVERT: 7 65 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8682 (tm-30) REVERT: 7 79 ASN cc_start: 0.8469 (p0) cc_final: 0.7978 (p0) REVERT: 7 81 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7205 (tm-30) REVERT: 7 82 GLU cc_start: 0.8425 (mp0) cc_final: 0.7504 (mp0) REVERT: 7 97 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8174 (tttp) REVERT: 7 102 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8149 (tp) REVERT: 7 109 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7662 (mt-10) REVERT: 7 138 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7957 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8052 (t0) cc_final: 0.7617 (m-30) REVERT: 7 171 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6531 (pmtt) REVERT: 9 37 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8555 (tttp) REVERT: 9 58 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.6124 (m-10) REVERT: 9 65 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8761 (tm-30) REVERT: 9 97 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8417 (tttm) REVERT: 9 109 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7341 (mt-10) REVERT: 9 127 GLN cc_start: 0.8930 (tp40) cc_final: 0.8474 (tp-100) REVERT: 9 147 ASP cc_start: 0.8393 (t0) cc_final: 0.7888 (m-30) REVERT: 9 148 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8836 (mtmt) REVERT: 9 171 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6557 (pmtt) REVERT: A 347 LYS cc_start: 0.9072 (mmtp) cc_final: 0.8826 (mmtt) REVERT: D 358 MET cc_start: 0.8136 (tmm) cc_final: 0.7432 (tmm) REVERT: J 358 MET cc_start: 0.7992 (tmm) cc_final: 0.7407 (tmm) REVERT: P 354 ASP cc_start: 0.8110 (m-30) cc_final: 0.7747 (m-30) REVERT: S 358 MET cc_start: 0.7720 (tpp) cc_final: 0.7269 (tpp) REVERT: U 354 ASP cc_start: 0.7766 (m-30) cc_final: 0.7486 (m-30) REVERT: B 343 ASP cc_start: 0.7726 (p0) cc_final: 0.7372 (p0) REVERT: B 358 MET cc_start: 0.8528 (mmm) cc_final: 0.8002 (tpp) REVERT: H 343 ASP cc_start: 0.7748 (p0) cc_final: 0.7400 (p0) REVERT: H 358 MET cc_start: 0.8620 (tpp) cc_final: 0.8092 (tpp) REVERT: K 365 PHE cc_start: 0.8846 (t80) cc_final: 0.8548 (t80) REVERT: N 343 ASP cc_start: 0.7711 (p0) cc_final: 0.7445 (p0) REVERT: N 358 MET cc_start: 0.8420 (tpp) cc_final: 0.8158 (tpp) REVERT: Q 353 LYS cc_start: 0.9004 (pttt) cc_final: 0.8680 (mmtt) REVERT: Q 358 MET cc_start: 0.8618 (tpp) cc_final: 0.8147 (tpp) REVERT: T 358 MET cc_start: 0.8688 (tpp) cc_final: 0.7982 (tpp) REVERT: V 358 MET cc_start: 0.8513 (tpp) cc_final: 0.8055 (tpp) outliers start: 127 outliers final: 94 residues processed: 985 average time/residue: 0.1465 time to fit residues: 218.5266 Evaluate side-chains 1004 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 892 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 79 ASN Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 43 ASP Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 79 ASN Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 ASN Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 43 ASP Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 102 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain J residue 362 LYS Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain M residue 360 ASN Chi-restraints excluded: chain S residue 342 ASP Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 355 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 ASN ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 79 ASN y 79 ASN z 79 ASN 5 79 ASN 9 79 ASN A 360 ASN G 360 ASN M 360 ASN S 360 ASN U 360 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.073801 restraints weight = 55187.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.076092 restraints weight = 28921.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.077656 restraints weight = 18256.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.078770 restraints weight = 12881.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.079568 restraints weight = 9761.237| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22224 Z= 0.200 Angle : 0.769 11.842 30080 Z= 0.410 Chirality : 0.048 0.366 3392 Planarity : 0.005 0.062 3744 Dihedral : 7.203 59.643 2976 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.38 % Favored : 90.59 % Rotamer: Outliers : 5.33 % Allowed : 30.21 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2624 helix: 0.47 (0.17), residues: 976 sheet: -0.11 (0.19), residues: 752 loop : -2.94 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 70 TYR 0.040 0.002 TYR 6 96 PHE 0.025 0.002 PHE 2 48 TRP 0.007 0.001 TRP K 364 HIS 0.003 0.001 HIS T 363 Details of bonding type rmsd covalent geometry : bond 0.00464 (22224) covalent geometry : angle 0.76921 (30080) hydrogen bonds : bond 0.03639 ( 1021) hydrogen bonds : angle 5.20102 ( 2784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 864 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8173 (tm-30) REVERT: X 88 THR cc_start: 0.9427 (m) cc_final: 0.9114 (p) REVERT: X 133 ASN cc_start: 0.8967 (m-40) cc_final: 0.8469 (t0) REVERT: Y 85 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8281 (tm-30) REVERT: Y 88 THR cc_start: 0.9503 (m) cc_final: 0.9182 (p) REVERT: Y 96 TYR cc_start: 0.8850 (t80) cc_final: 0.8552 (t80) REVERT: Y 133 ASN cc_start: 0.8876 (m-40) cc_final: 0.8512 (t0) REVERT: Y 138 ARG cc_start: 0.8509 (ptp-110) cc_final: 0.8268 (mtm110) REVERT: Z 85 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8243 (tm-30) REVERT: Z 88 THR cc_start: 0.9433 (m) cc_final: 0.9121 (p) REVERT: Z 133 ASN cc_start: 0.8901 (m-40) cc_final: 0.8319 (t0) REVERT: 0 37 LYS cc_start: 0.9294 (tptp) cc_final: 0.8990 (tppt) REVERT: 0 96 TYR cc_start: 0.8763 (t80) cc_final: 0.8461 (t80) REVERT: 0 117 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8126 (pp) REVERT: 0 133 ASN cc_start: 0.8864 (m-40) cc_final: 0.8425 (t0) REVERT: 2 85 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8028 (tm-30) REVERT: 2 88 THR cc_start: 0.9447 (m) cc_final: 0.9139 (p) REVERT: 2 133 ASN cc_start: 0.8967 (m-40) cc_final: 0.8475 (t0) REVERT: 4 37 LYS cc_start: 0.9326 (tmtt) cc_final: 0.8683 (tptp) REVERT: 4 85 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8270 (tm-30) REVERT: 4 88 THR cc_start: 0.9483 (m) cc_final: 0.9200 (p) REVERT: 4 96 TYR cc_start: 0.8841 (t80) cc_final: 0.8551 (t80) REVERT: 4 133 ASN cc_start: 0.8830 (m-40) cc_final: 0.8501 (t0) REVERT: 4 138 ARG cc_start: 0.8683 (ptp-110) cc_final: 0.8250 (mtm110) REVERT: 6 37 LYS cc_start: 0.9089 (tptm) cc_final: 0.8882 (tptp) REVERT: 6 68 LYS cc_start: 0.9311 (mttt) cc_final: 0.9042 (mttp) REVERT: 6 85 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8057 (tm-30) REVERT: 6 88 THR cc_start: 0.9463 (m) cc_final: 0.9156 (p) REVERT: 6 133 ASN cc_start: 0.8971 (m-40) cc_final: 0.8437 (t0) REVERT: 8 37 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8161 (tptp) REVERT: 8 65 GLN cc_start: 0.8298 (tt0) cc_final: 0.7867 (tt0) REVERT: 8 85 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8133 (tm-30) REVERT: 8 88 THR cc_start: 0.9498 (m) cc_final: 0.9180 (p) REVERT: 8 106 ASP cc_start: 0.8018 (t70) cc_final: 0.7713 (t70) REVERT: 8 117 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8100 (pp) REVERT: 8 133 ASN cc_start: 0.8838 (m-40) cc_final: 0.8446 (t0) REVERT: 8 138 ARG cc_start: 0.8643 (ptp-110) cc_final: 0.8318 (mtm110) REVERT: x 65 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8693 (tm-30) REVERT: x 81 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7488 (tm-30) REVERT: x 82 GLU cc_start: 0.8403 (mp0) cc_final: 0.7992 (mp0) REVERT: x 97 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8443 (tttp) REVERT: x 102 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8258 (tp) REVERT: x 138 ARG cc_start: 0.8487 (mtp85) cc_final: 0.7990 (mtm-85) REVERT: x 171 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7066 (pmtt) REVERT: y 58 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6255 (m-10) REVERT: y 74 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7484 (tm-30) REVERT: y 97 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8414 (tttm) REVERT: y 127 GLN cc_start: 0.8982 (tp40) cc_final: 0.8563 (tp40) REVERT: y 147 ASP cc_start: 0.8417 (m-30) cc_final: 0.7821 (t0) REVERT: y 148 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8680 (mtmt) REVERT: y 171 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7401 (pmtt) REVERT: z 65 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8680 (tm-30) REVERT: z 97 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8335 (tttp) REVERT: z 102 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8321 (tp) REVERT: z 147 ASP cc_start: 0.8085 (t0) cc_final: 0.7763 (m-30) REVERT: z 171 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7030 (pmtt) REVERT: 1 58 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6228 (m-10) REVERT: 1 74 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7501 (tm-30) REVERT: 1 78 SER cc_start: 0.8961 (m) cc_final: 0.8547 (p) REVERT: 1 79 ASN cc_start: 0.8580 (p0) cc_final: 0.8249 (p0) REVERT: 1 85 GLU cc_start: 0.7832 (tp30) cc_final: 0.7541 (tm-30) REVERT: 1 86 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8530 (mtpt) REVERT: 1 97 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8438 (tttm) REVERT: 1 127 GLN cc_start: 0.8981 (tp40) cc_final: 0.8565 (tp40) REVERT: 1 148 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8534 (mtmt) REVERT: 1 171 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7454 (pmtt) REVERT: 3 65 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8790 (tm-30) REVERT: 3 70 ARG cc_start: 0.8734 (mtt-85) cc_final: 0.8501 (mtt-85) REVERT: 3 97 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8463 (tttp) REVERT: 3 147 ASP cc_start: 0.8065 (t0) cc_final: 0.7756 (m-30) REVERT: 3 171 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7251 (pmtt) REVERT: 5 58 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6220 (m-10) REVERT: 5 85 GLU cc_start: 0.7942 (tp30) cc_final: 0.7573 (tm-30) REVERT: 5 86 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8586 (mtpt) REVERT: 5 97 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8453 (tttm) REVERT: 5 109 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7448 (mt-10) REVERT: 5 127 GLN cc_start: 0.8983 (tp40) cc_final: 0.8572 (tp40) REVERT: 5 147 ASP cc_start: 0.8330 (t0) cc_final: 0.8094 (m-30) REVERT: 5 148 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8874 (mtmt) REVERT: 5 171 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7361 (pmtt) REVERT: 7 65 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8436 (tm-30) REVERT: 7 79 ASN cc_start: 0.8407 (p0) cc_final: 0.7962 (p0) REVERT: 7 81 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7275 (tm-30) REVERT: 7 82 GLU cc_start: 0.8350 (mp0) cc_final: 0.7481 (mp0) REVERT: 7 97 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8370 (tttp) REVERT: 7 102 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8348 (tp) REVERT: 7 138 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8011 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8119 (t0) cc_final: 0.7645 (m-30) REVERT: 7 171 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6885 (pmtt) REVERT: 9 58 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6201 (m-10) REVERT: 9 97 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8448 (tttm) REVERT: 9 109 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7456 (mt-10) REVERT: 9 127 GLN cc_start: 0.8975 (tp40) cc_final: 0.8567 (tp40) REVERT: 9 147 ASP cc_start: 0.8444 (t0) cc_final: 0.7912 (m-30) REVERT: 9 148 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8868 (mtmt) REVERT: 9 171 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7503 (pmtt) REVERT: A 347 LYS cc_start: 0.9120 (mmtp) cc_final: 0.8868 (mmtt) REVERT: D 358 MET cc_start: 0.8394 (tmm) cc_final: 0.7843 (tmm) REVERT: J 358 MET cc_start: 0.8094 (tmm) cc_final: 0.7544 (tmm) REVERT: P 354 ASP cc_start: 0.7977 (m-30) cc_final: 0.7593 (m-30) REVERT: U 354 ASP cc_start: 0.7689 (m-30) cc_final: 0.7487 (m-30) REVERT: U 362 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8106 (mmpt) REVERT: B 343 ASP cc_start: 0.7762 (p0) cc_final: 0.7402 (p0) REVERT: B 358 MET cc_start: 0.8628 (mmm) cc_final: 0.8208 (tpp) REVERT: H 343 ASP cc_start: 0.7751 (p0) cc_final: 0.7390 (p0) REVERT: H 358 MET cc_start: 0.8639 (tpp) cc_final: 0.8104 (tpp) REVERT: K 358 MET cc_start: 0.8103 (ttm) cc_final: 0.7731 (ttm) REVERT: N 343 ASP cc_start: 0.7776 (p0) cc_final: 0.7555 (p0) REVERT: N 358 MET cc_start: 0.8462 (tpp) cc_final: 0.8176 (tpp) REVERT: Q 353 LYS cc_start: 0.8995 (pttt) cc_final: 0.8642 (mmtt) REVERT: Q 358 MET cc_start: 0.8689 (tpp) cc_final: 0.8102 (tpp) REVERT: T 358 MET cc_start: 0.8590 (tpp) cc_final: 0.8296 (mmm) REVERT: V 358 MET cc_start: 0.8546 (tpp) cc_final: 0.8203 (tpp) outliers start: 128 outliers final: 95 residues processed: 945 average time/residue: 0.1513 time to fit residues: 215.4351 Evaluate side-chains 973 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 860 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 78 SER Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 171 LYS Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 79 ASN Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 171 LYS Chi-restraints excluded: chain z residue 43 ASP Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 79 ASN Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 171 LYS Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 171 LYS Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 ASN Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 43 ASP Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 102 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain S residue 342 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 355 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 185 optimal weight: 0.4980 chunk 88 optimal weight: 0.0070 chunk 237 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 ASN ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 79 ASN z 79 ASN 5 79 ASN 9 79 ASN A 360 ASN G 360 ASN J 360 ASN S 360 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076312 restraints weight = 54523.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.078645 restraints weight = 28315.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080246 restraints weight = 17782.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081346 restraints weight = 12461.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082153 restraints weight = 9427.977| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22224 Z= 0.149 Angle : 0.766 12.117 30080 Z= 0.408 Chirality : 0.047 0.355 3392 Planarity : 0.005 0.067 3744 Dihedral : 7.232 59.925 2976 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.08 % Allowed : 30.92 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2624 helix: 0.56 (0.17), residues: 976 sheet: 0.19 (0.19), residues: 720 loop : -2.93 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 70 TYR 0.035 0.001 TYR Z 96 PHE 0.022 0.001 PHE Z 48 TRP 0.009 0.001 TRP B 364 HIS 0.002 0.001 HIS x 137 Details of bonding type rmsd covalent geometry : bond 0.00341 (22224) covalent geometry : angle 0.76597 (30080) hydrogen bonds : bond 0.03229 ( 1021) hydrogen bonds : angle 5.04298 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4378.60 seconds wall clock time: 76 minutes 7.66 seconds (4567.66 seconds total)