Starting phenix.real_space_refine on Sun Jun 22 11:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui2_42286/06_2025/8ui2_42286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui2_42286/06_2025/8ui2_42286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ui2_42286/06_2025/8ui2_42286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui2_42286/06_2025/8ui2_42286.map" model { file = "/net/cci-nas-00/data/ceres_data/8ui2_42286/06_2025/8ui2_42286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui2_42286/06_2025/8ui2_42286.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.147 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 48 5.16 5 C 17052 2.51 5 N 4668 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26568 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "B" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Restraints were copied for chains: D, F, H, J, L, N, P, R, T, V, X, C, E, G, I, K, M, O, Q, S, U, W Time building chain proxies: 6.96, per 1000 atoms: 0.26 Number of scatterers: 26568 At special positions: 0 Unit cell: (135.3, 138.6, 133.1, 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 48 16.00 O 4800 8.00 N 4668 7.00 C 17052 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: 6.10 Conformation dependent library (CDL) restraints added in 3.5 seconds 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 36 sheets defined 40.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 167 through 183 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.645A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 23 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 128 through 143 Processing helix chain 'I' and resid 167 through 183 Processing helix chain 'I' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 11 No H-bonds generated for 'chain 'J' and resid 9 through 11' Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'K' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 106 Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 167 through 183 Processing helix chain 'K' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 11 No H-bonds generated for 'chain 'L' and resid 9 through 11' Processing helix chain 'L' and resid 12 through 23 Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 90 through 101 Processing helix chain 'M' and resid 29 through 44 removed outlier: 3.645A pdb=" N ALA M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 106 Processing helix chain 'M' and resid 128 through 143 Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'M' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 11 No H-bonds generated for 'chain 'N' and resid 9 through 11' Processing helix chain 'N' and resid 12 through 23 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 90 through 101 Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS O 82 " --> pdb=" O LEU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 128 through 143 Processing helix chain 'O' and resid 167 through 183 Processing helix chain 'O' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY O 201 " --> pdb=" O GLU O 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG O 202 " --> pdb=" O ALA O 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 11 No H-bonds generated for 'chain 'P' and resid 9 through 11' Processing helix chain 'P' and resid 12 through 23 Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 90 through 101 Processing helix chain 'Q' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS Q 82 " --> pdb=" O LEU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 106 Processing helix chain 'Q' and resid 128 through 143 Processing helix chain 'Q' and resid 167 through 183 Processing helix chain 'Q' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY Q 201 " --> pdb=" O GLU Q 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG Q 202 " --> pdb=" O ALA Q 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 11 No H-bonds generated for 'chain 'R' and resid 9 through 11' Processing helix chain 'R' and resid 12 through 23 Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 90 through 101 Processing helix chain 'S' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 106 Processing helix chain 'S' and resid 128 through 143 Processing helix chain 'S' and resid 167 through 183 Processing helix chain 'S' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY S 201 " --> pdb=" O GLU S 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG S 202 " --> pdb=" O ALA S 198 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 11 No H-bonds generated for 'chain 'T' and resid 9 through 11' Processing helix chain 'T' and resid 12 through 23 Processing helix chain 'T' and resid 60 through 70 Processing helix chain 'T' and resid 90 through 101 Processing helix chain 'U' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS U 82 " --> pdb=" O LEU U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 101 through 106 Processing helix chain 'U' and resid 128 through 143 Processing helix chain 'U' and resid 167 through 183 Processing helix chain 'U' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY U 201 " --> pdb=" O GLU U 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG U 202 " --> pdb=" O ALA U 198 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 11 No H-bonds generated for 'chain 'V' and resid 9 through 11' Processing helix chain 'V' and resid 12 through 23 Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 90 through 101 Processing helix chain 'W' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS W 82 " --> pdb=" O LEU W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 106 Processing helix chain 'W' and resid 128 through 143 Processing helix chain 'W' and resid 167 through 183 Processing helix chain 'W' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY W 201 " --> pdb=" O GLU W 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG W 202 " --> pdb=" O ALA W 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 11 No H-bonds generated for 'chain 'X' and resid 9 through 11' Processing helix chain 'X' and resid 12 through 23 Processing helix chain 'X' and resid 60 through 70 Processing helix chain 'X' and resid 90 through 101 Processing sheet with id=1, first strand: chain 'A' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET A 62 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 51 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 60 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS A 58 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 22 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A 93 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 24 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS A 91 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU A 26 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU A 147 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 165 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 149 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 121 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 191 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 123 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 189 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A 125 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU B 28 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 38 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 3 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'C' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET C 62 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS C 51 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 60 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS C 58 " --> pdb=" O PRO C 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 22 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C 93 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 24 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS C 91 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C 26 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU C 147 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 165 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 149 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C 121 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C 191 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 123 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 189 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU C 125 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'D' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU D 28 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 38 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 3 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 47 through 54 removed outlier: 5.955A pdb=" N MET E 62 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS E 51 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 60 " --> pdb=" O CYS E 51 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS E 58 " --> pdb=" O PRO E 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU E 22 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE E 93 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 24 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS E 91 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU E 26 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'E' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU E 147 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA E 165 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 149 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL E 121 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE E 191 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 123 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU E 189 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU E 125 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'F' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU F 28 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 38 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE F 3 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'G' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET G 62 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS G 51 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU G 60 " --> pdb=" O CYS G 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS G 58 " --> pdb=" O PRO G 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU G 22 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE G 93 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL G 24 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS G 91 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU G 26 " --> pdb=" O ILE G 89 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'G' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU G 147 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 149 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 121 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE G 191 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL G 123 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU G 189 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU G 125 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU H 28 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR H 38 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 3 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET I 62 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS I 51 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU I 60 " --> pdb=" O CYS I 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS I 58 " --> pdb=" O PRO I 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU I 22 " --> pdb=" O PHE I 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE I 93 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL I 24 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS I 91 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU I 26 " --> pdb=" O ILE I 89 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'I' and resid 146 through 152 removed outlier: 5.577A pdb=" N LEU I 147 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA I 165 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG I 149 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL I 121 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE I 191 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL I 123 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU I 189 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU I 125 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'J' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU J 28 " --> pdb=" O LEU J 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR J 38 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE J 3 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'K' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET K 62 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS K 51 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU K 60 " --> pdb=" O CYS K 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS K 58 " --> pdb=" O PRO K 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU K 22 " --> pdb=" O PHE K 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE K 93 " --> pdb=" O LEU K 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL K 24 " --> pdb=" O HIS K 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS K 91 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU K 26 " --> pdb=" O ILE K 89 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'K' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU K 147 " --> pdb=" O ALA K 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA K 165 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG K 149 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL K 121 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE K 191 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 123 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU K 189 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU K 125 " --> pdb=" O ILE K 187 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'L' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU L 28 " --> pdb=" O LEU L 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR L 38 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE L 3 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'M' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET M 62 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS M 51 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU M 60 " --> pdb=" O CYS M 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS M 58 " --> pdb=" O PRO M 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU M 22 " --> pdb=" O PHE M 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE M 93 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL M 24 " --> pdb=" O HIS M 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS M 91 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU M 26 " --> pdb=" O ILE M 89 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'M' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU M 147 " --> pdb=" O ALA M 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA M 165 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG M 149 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL M 121 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE M 191 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL M 123 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU M 189 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU M 125 " --> pdb=" O ILE M 187 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'N' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU N 28 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR N 38 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 3 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET O 62 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS O 51 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU O 60 " --> pdb=" O CYS O 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS O 58 " --> pdb=" O PRO O 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU O 22 " --> pdb=" O PHE O 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE O 93 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL O 24 " --> pdb=" O HIS O 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS O 91 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU O 26 " --> pdb=" O ILE O 89 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'O' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU O 147 " --> pdb=" O ALA O 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA O 165 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG O 149 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL O 121 " --> pdb=" O ILE O 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE O 191 " --> pdb=" O VAL O 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL O 123 " --> pdb=" O LEU O 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU O 189 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU O 125 " --> pdb=" O ILE O 187 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'P' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU P 28 " --> pdb=" O LEU P 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR P 38 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 3 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 47 through 54 removed outlier: 5.955A pdb=" N MET Q 62 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS Q 51 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU Q 60 " --> pdb=" O CYS Q 51 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS Q 58 " --> pdb=" O PRO Q 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU Q 22 " --> pdb=" O PHE Q 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE Q 93 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL Q 24 " --> pdb=" O HIS Q 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS Q 91 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU Q 26 " --> pdb=" O ILE Q 89 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'Q' and resid 146 through 152 removed outlier: 5.577A pdb=" N LEU Q 147 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA Q 165 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG Q 149 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL Q 121 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE Q 191 " --> pdb=" O VAL Q 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL Q 123 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU Q 189 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU Q 125 " --> pdb=" O ILE Q 187 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'R' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU R 28 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR R 38 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE R 3 " --> pdb=" O LEU R 82 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET S 62 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS S 51 " --> pdb=" O LEU S 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU S 60 " --> pdb=" O CYS S 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS S 58 " --> pdb=" O PRO S 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU S 22 " --> pdb=" O PHE S 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE S 93 " --> pdb=" O LEU S 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL S 24 " --> pdb=" O HIS S 91 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS S 91 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU S 26 " --> pdb=" O ILE S 89 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'S' and resid 146 through 152 removed outlier: 5.577A pdb=" N LEU S 147 " --> pdb=" O ALA S 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG S 149 " --> pdb=" O VAL S 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 121 " --> pdb=" O ILE S 191 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE S 191 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL S 123 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU S 189 " --> pdb=" O VAL S 123 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU S 125 " --> pdb=" O ILE S 187 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'T' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU T 28 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR T 38 " --> pdb=" O ARG T 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE T 3 " --> pdb=" O LEU T 82 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET U 62 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS U 51 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU U 60 " --> pdb=" O CYS U 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS U 58 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU U 22 " --> pdb=" O PHE U 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE U 93 " --> pdb=" O LEU U 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL U 24 " --> pdb=" O HIS U 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS U 91 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU U 26 " --> pdb=" O ILE U 89 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'U' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU U 147 " --> pdb=" O ALA U 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA U 165 " --> pdb=" O LEU U 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG U 149 " --> pdb=" O VAL U 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL U 121 " --> pdb=" O ILE U 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE U 191 " --> pdb=" O VAL U 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL U 123 " --> pdb=" O LEU U 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU U 189 " --> pdb=" O VAL U 123 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU U 125 " --> pdb=" O ILE U 187 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'V' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU V 28 " --> pdb=" O LEU V 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR V 38 " --> pdb=" O ARG V 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE V 3 " --> pdb=" O LEU V 82 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'W' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET W 62 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS W 51 " --> pdb=" O LEU W 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU W 60 " --> pdb=" O CYS W 51 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS W 58 " --> pdb=" O PRO W 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU W 22 " --> pdb=" O PHE W 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE W 93 " --> pdb=" O LEU W 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL W 24 " --> pdb=" O HIS W 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS W 91 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU W 26 " --> pdb=" O ILE W 89 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'W' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU W 147 " --> pdb=" O ALA W 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA W 165 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG W 149 " --> pdb=" O VAL W 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL W 121 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE W 191 " --> pdb=" O VAL W 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL W 123 " --> pdb=" O LEU W 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU W 189 " --> pdb=" O VAL W 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU W 125 " --> pdb=" O ILE W 187 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'X' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU X 28 " --> pdb=" O LEU X 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR X 38 " --> pdb=" O ARG X 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE X 3 " --> pdb=" O LEU X 82 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4140 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: 10.17 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9072 1.34 - 1.46: 4075 1.46 - 1.58: 13805 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 27036 Sorted by residual: bond pdb=" C ARG M 96 " pdb=" N ILE M 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 7.12e-01 bond pdb=" C ARG C 96 " pdb=" N ILE C 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.99e-01 bond pdb=" C ARG I 96 " pdb=" N ILE I 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.92e-01 bond pdb=" C ARG Q 96 " pdb=" N ILE Q 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.91e-01 bond pdb=" C ARG G 96 " pdb=" N ILE G 97 " ideal model delta sigma weight residual 1.334 1.323 0.010 1.29e-02 6.01e+03 6.61e-01 ... (remaining 27031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 35214 1.03 - 2.06: 1186 2.06 - 3.09: 236 3.09 - 4.11: 132 4.11 - 5.14: 24 Bond angle restraints: 36792 Sorted by residual: angle pdb=" C HIS H 72 " pdb=" N PRO H 73 " pdb=" CA PRO H 73 " ideal model delta sigma weight residual 118.97 120.62 -1.65 1.04e+00 9.25e-01 2.53e+00 angle pdb=" C HIS P 72 " pdb=" N PRO P 73 " pdb=" CA PRO P 73 " ideal model delta sigma weight residual 118.97 120.62 -1.65 1.04e+00 9.25e-01 2.51e+00 angle pdb=" C HIS R 72 " pdb=" N PRO R 73 " pdb=" CA PRO R 73 " ideal model delta sigma weight residual 118.97 120.61 -1.64 1.04e+00 9.25e-01 2.49e+00 angle pdb=" C HIS T 72 " pdb=" N PRO T 73 " pdb=" CA PRO T 73 " ideal model delta sigma weight residual 118.97 120.61 -1.64 1.04e+00 9.25e-01 2.48e+00 angle pdb=" C HIS F 72 " pdb=" N PRO F 73 " pdb=" CA PRO F 73 " ideal model delta sigma weight residual 118.97 120.60 -1.63 1.04e+00 9.25e-01 2.45e+00 ... (remaining 36787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 14393 17.02 - 34.03: 1534 34.03 - 51.05: 657 51.05 - 68.06: 180 68.06 - 85.08: 36 Dihedral angle restraints: 16800 sinusoidal: 6660 harmonic: 10140 Sorted by residual: dihedral pdb=" CA ARG L 35 " pdb=" C ARG L 35 " pdb=" N ARG L 36 " pdb=" CA ARG L 36 " ideal model delta harmonic sigma weight residual -180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CB GLU G 134 " pdb=" CG GLU G 134 " pdb=" CD GLU G 134 " pdb=" OE1 GLU G 134 " ideal model delta sinusoidal sigma weight residual 0.00 -85.08 85.08 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU M 134 " pdb=" CG GLU M 134 " pdb=" CD GLU M 134 " pdb=" OE1 GLU M 134 " ideal model delta sinusoidal sigma weight residual 0.00 -85.03 85.03 1 3.00e+01 1.11e-03 9.74e+00 ... (remaining 16797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2388 0.027 - 0.053: 1274 0.053 - 0.080: 297 0.080 - 0.107: 223 0.107 - 0.133: 222 Chirality restraints: 4404 Sorted by residual: chirality pdb=" CA VAL C 124 " pdb=" N VAL C 124 " pdb=" C VAL C 124 " pdb=" CB VAL C 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL O 124 " pdb=" N VAL O 124 " pdb=" C VAL O 124 " pdb=" CB VAL O 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA VAL E 124 " pdb=" N VAL E 124 " pdb=" C VAL E 124 " pdb=" CB VAL E 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 4401 not shown) Planarity restraints: 4788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 14 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO F 15 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 15 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 15 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 14 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO D 15 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 15 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 15 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 14 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO J 15 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 15 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 15 " 0.020 5.00e-02 4.00e+02 ... (remaining 4785 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1226 2.73 - 3.27: 23700 3.27 - 3.81: 41074 3.81 - 4.36: 50133 4.36 - 4.90: 93374 Nonbonded interactions: 209507 Sorted by model distance: nonbonded pdb=" OE2 GLU K 125 " pdb=" OG SER M 29 " model vdw 2.187 3.040 nonbonded pdb=" OG SER G 29 " pdb=" OE2 GLU Q 125 " model vdw 2.187 3.040 nonbonded pdb=" OE2 GLU M 125 " pdb=" OG SER U 29 " model vdw 2.187 3.040 nonbonded pdb=" OG SER O 29 " pdb=" OE2 GLU S 125 " model vdw 2.187 3.040 nonbonded pdb=" OG SER K 29 " pdb=" OE2 GLU U 125 " model vdw 2.187 3.040 ... (remaining 209502 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: 0.24 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 50.710 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.004 0.023 27036 Z= 0.156 Angle : 0.516 5.142 36792 Z= 0.256 Chirality : 0.044 0.133 4404 Planarity : 0.005 0.035 4788 Dihedral : 17.613 85.075 10200 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.35 % Allowed : 24.32 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3444 helix: -0.36 (0.13), residues: 1380 sheet: 0.67 (0.18), residues: 972 loop : -0.75 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 67 HIS 0.003 0.001 HIS W 196 PHE 0.017 0.002 PHE E 93 TYR 0.008 0.002 TYR K 161 ARG 0.003 0.000 ARG N 58 Details of bonding type rmsd hydrogen bonds : bond 0.21969 ( 1452) hydrogen bonds : angle 7.56641 ( 4140) covalent geometry : bond 0.00394 (27036) covalent geometry : angle 0.51601 (36792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 2.697 Fit side-chains REVERT: A 150 MET cc_start: 0.8854 (tpt) cc_final: 0.8401 (tpp) REVERT: A 185 LYS cc_start: 0.8918 (mttm) cc_final: 0.8396 (mptt) REVERT: B 58 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7580 (mtp180) REVERT: B 90 ASN cc_start: 0.8779 (t160) cc_final: 0.8558 (t0) REVERT: C 150 MET cc_start: 0.8741 (tpt) cc_final: 0.8433 (tpp) REVERT: D 58 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7563 (mtp180) REVERT: E 62 MET cc_start: 0.9072 (mtt) cc_final: 0.8851 (mtm) REVERT: E 150 MET cc_start: 0.8796 (tpt) cc_final: 0.8522 (tpp) REVERT: E 185 LYS cc_start: 0.8874 (mttm) cc_final: 0.8528 (mmtp) REVERT: F 58 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7584 (mtp180) REVERT: G 185 LYS cc_start: 0.8965 (mttm) cc_final: 0.8620 (mmtp) REVERT: H 58 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7608 (mtp-110) REVERT: H 76 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6396 (mt) REVERT: I 185 LYS cc_start: 0.8895 (mttm) cc_final: 0.8654 (mttp) REVERT: K 185 LYS cc_start: 0.8951 (mttm) cc_final: 0.8646 (mmtm) REVERT: O 74 MET cc_start: 0.8208 (mmm) cc_final: 0.7794 (mmm) REVERT: O 150 MET cc_start: 0.8835 (tpt) cc_final: 0.8042 (tpt) REVERT: O 185 LYS cc_start: 0.9011 (mttm) cc_final: 0.8637 (mttp) REVERT: P 18 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7653 (mtt90) REVERT: P 58 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7795 (mtp180) REVERT: Q 28 LYS cc_start: 0.8479 (mttp) cc_final: 0.8172 (mttp) REVERT: R 58 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7443 (tpp-160) REVERT: S 185 LYS cc_start: 0.8824 (mttm) cc_final: 0.8277 (mptt) REVERT: U 185 LYS cc_start: 0.8881 (mttm) cc_final: 0.8666 (mmtm) REVERT: V 76 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6532 (mt) REVERT: V 90 ASN cc_start: 0.8700 (t160) cc_final: 0.8468 (t0) REVERT: V 93 TYR cc_start: 0.8664 (t80) cc_final: 0.8437 (t80) REVERT: W 28 LYS cc_start: 0.8539 (mttp) cc_final: 0.8319 (mttp) REVERT: W 185 LYS cc_start: 0.8881 (mttm) cc_final: 0.8669 (mtpt) REVERT: X 18 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7633 (mtt90) REVERT: X 58 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7491 (mtp180) outliers start: 36 outliers final: 6 residues processed: 335 average time/residue: 1.8761 time to fit residues: 702.7611 Evaluate side-chains 276 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 268 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain V residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 72 HIS B 90 ASN C 196 HIS D 72 HIS D 90 ASN E 196 HIS F 72 HIS F 90 ASN G 196 HIS H 72 HIS H 90 ASN I 196 HIS J 72 HIS J 90 ASN K 196 HIS L 72 HIS L 90 ASN M 196 HIS N 72 HIS N 90 ASN O 196 HIS P 72 HIS P 90 ASN Q 196 HIS R 72 HIS R 90 ASN S 196 HIS T 72 HIS T 90 ASN U 196 HIS V 72 HIS V 90 ASN W 196 HIS X 72 HIS X 90 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119290 restraints weight = 27713.835| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.13 r_work: 0.3216 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 27036 Z= 0.190 Angle : 0.629 6.333 36792 Z= 0.309 Chirality : 0.046 0.128 4404 Planarity : 0.006 0.038 4788 Dihedral : 4.720 40.211 3852 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.34 % Allowed : 22.15 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3444 helix: 0.35 (0.13), residues: 1404 sheet: 0.77 (0.17), residues: 984 loop : -0.96 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 67 HIS 0.004 0.001 HIS C 91 PHE 0.014 0.002 PHE W 162 TYR 0.018 0.002 TYR L 93 ARG 0.006 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.05934 ( 1452) hydrogen bonds : angle 4.91183 ( 4140) covalent geometry : bond 0.00472 (27036) covalent geometry : angle 0.62910 (36792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 282 time to evaluate : 3.156 Fit side-chains REVERT: A 149 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8171 (ttp80) REVERT: A 150 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: A 185 LYS cc_start: 0.8525 (mttm) cc_final: 0.8323 (mmmt) REVERT: C 150 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8602 (tpp) REVERT: D 39 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.4704 (ttm110) REVERT: D 58 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7788 (mtp180) REVERT: D 69 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: E 66 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: E 93 PHE cc_start: 0.8772 (t80) cc_final: 0.8348 (t80) REVERT: E 150 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8599 (tpp) REVERT: E 185 LYS cc_start: 0.8455 (mttm) cc_final: 0.7959 (mmtp) REVERT: F 6 THR cc_start: 0.8833 (p) cc_final: 0.8577 (m) REVERT: F 69 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: G 66 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: G 185 LYS cc_start: 0.8518 (mttm) cc_final: 0.8082 (mmtp) REVERT: H 39 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.5007 (ttp-170) REVERT: H 58 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7882 (mtp180) REVERT: I 185 LYS cc_start: 0.8492 (mttm) cc_final: 0.8211 (mmtp) REVERT: J 87 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6717 (mp0) REVERT: K 28 LYS cc_start: 0.8551 (mttp) cc_final: 0.8267 (mttp) REVERT: K 52 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: K 185 LYS cc_start: 0.8553 (mttm) cc_final: 0.8140 (mmtm) REVERT: L 36 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7910 (ttt180) REVERT: M 66 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: M 90 ASP cc_start: 0.8674 (t0) cc_final: 0.8262 (t70) REVERT: N 18 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7006 (mtt180) REVERT: O 52 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: O 150 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8248 (tpt) REVERT: O 185 LYS cc_start: 0.8598 (mttm) cc_final: 0.8124 (mttp) REVERT: P 18 ARG cc_start: 0.7443 (mtt90) cc_final: 0.7019 (mtt90) REVERT: Q 52 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: Q 184 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7714 (pp20) REVERT: R 58 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7209 (tpp-160) REVERT: S 184 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: S 185 LYS cc_start: 0.8355 (mttm) cc_final: 0.7999 (mmmm) REVERT: U 66 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: U 150 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8558 (tpt) REVERT: U 185 LYS cc_start: 0.8495 (mttm) cc_final: 0.8174 (mmtm) REVERT: V 28 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: W 28 LYS cc_start: 0.8560 (mttp) cc_final: 0.8318 (mttp) REVERT: W 52 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: W 185 LYS cc_start: 0.8472 (mttm) cc_final: 0.8104 (mmtp) REVERT: X 18 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7056 (mtt90) REVERT: X 58 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7798 (mtp180) REVERT: X 87 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6858 (mp0) outliers start: 89 outliers final: 18 residues processed: 350 average time/residue: 2.2388 time to fit residues: 870.5129 Evaluate side-chains 313 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 184 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain W residue 52 GLU Chi-restraints excluded: chain W residue 171 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 288 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 chunk 180 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117406 restraints weight = 27834.619| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.14 r_work: 0.3195 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 27036 Z= 0.259 Angle : 0.719 8.395 36792 Z= 0.346 Chirality : 0.049 0.140 4404 Planarity : 0.007 0.045 4788 Dihedral : 4.938 49.933 3840 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.69 % Allowed : 22.45 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3444 helix: 0.19 (0.13), residues: 1404 sheet: 0.53 (0.17), residues: 996 loop : -1.12 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 67 HIS 0.005 0.002 HIS G 196 PHE 0.018 0.003 PHE W 162 TYR 0.017 0.003 TYR L 93 ARG 0.005 0.001 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.06580 ( 1452) hydrogen bonds : angle 4.84937 ( 4140) covalent geometry : bond 0.00672 (27036) covalent geometry : angle 0.71937 (36792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 283 time to evaluate : 3.131 Fit side-chains REVERT: A 47 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: A 150 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: A 169 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: B 28 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: B 69 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: C 150 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8605 (tpp) REVERT: C 185 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8554 (mtpp) REVERT: D 69 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: D 93 TYR cc_start: 0.8637 (t80) cc_final: 0.8256 (t80) REVERT: E 93 PHE cc_start: 0.8799 (t80) cc_final: 0.8504 (t80) REVERT: E 150 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8570 (tpp) REVERT: E 185 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8085 (mmtp) REVERT: F 39 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.4676 (ttp80) REVERT: F 69 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: G 47 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: G 169 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: G 184 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: G 185 LYS cc_start: 0.8549 (mttm) cc_final: 0.8047 (mmtp) REVERT: H 39 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4833 (ttp-170) REVERT: H 58 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7942 (mtp180) REVERT: I 184 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: I 185 LYS cc_start: 0.8520 (mttm) cc_final: 0.7960 (mptt) REVERT: J 39 ARG cc_start: 0.5093 (OUTLIER) cc_final: 0.4879 (ttp-170) REVERT: K 28 LYS cc_start: 0.8535 (mttp) cc_final: 0.8273 (mttp) REVERT: K 52 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: K 66 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: K 169 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: K 185 LYS cc_start: 0.8569 (mttm) cc_final: 0.8228 (mmtm) REVERT: L 36 ARG cc_start: 0.8209 (ttt180) cc_final: 0.7971 (ttt180) REVERT: M 47 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: M 52 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: M 66 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: M 169 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: M 184 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: M 185 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8471 (mmtm) REVERT: N 18 ARG cc_start: 0.7334 (mtt90) cc_final: 0.6872 (mtt180) REVERT: O 150 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8335 (tpt) REVERT: O 184 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: O 185 LYS cc_start: 0.8642 (mttm) cc_final: 0.8237 (mmtp) REVERT: P 18 ARG cc_start: 0.7355 (mtt90) cc_final: 0.6943 (mtt90) REVERT: Q 28 LYS cc_start: 0.8468 (mttp) cc_final: 0.8226 (mttp) REVERT: Q 52 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: Q 169 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: Q 185 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8002 (mttm) REVERT: R 48 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7760 (mm-30) REVERT: R 58 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7186 (tpp-160) REVERT: R 87 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6834 (mp0) REVERT: S 47 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: S 169 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: S 184 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: S 185 LYS cc_start: 0.8399 (mttm) cc_final: 0.8025 (mmmm) REVERT: T 28 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: T 74 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6980 (p0) REVERT: U 66 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: U 150 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8561 (tpt) REVERT: U 169 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: U 184 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7432 (pp20) REVERT: V 69 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: W 28 LYS cc_start: 0.8575 (mttp) cc_final: 0.8268 (mttp) REVERT: W 47 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6712 (mt-10) REVERT: W 66 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: W 184 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7431 (pp20) REVERT: W 185 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8268 (mmtp) REVERT: X 18 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7188 (mtt90) REVERT: X 39 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4868 (ttp80) REVERT: X 58 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7828 (mtp180) outliers start: 125 outliers final: 26 residues processed: 379 average time/residue: 2.1230 time to fit residues: 894.5159 Evaluate side-chains 345 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain J residue 39 ARG Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 38 TYR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 185 LYS Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 169 GLU Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 28 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 169 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain W residue 185 LYS Chi-restraints excluded: chain X residue 39 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 96 optimal weight: 0.2980 chunk 200 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 0.0470 chunk 312 optimal weight: 10.0000 chunk 236 optimal weight: 0.3980 chunk 258 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123050 restraints weight = 27903.501| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.14 r_work: 0.3277 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27036 Z= 0.106 Angle : 0.495 5.230 36792 Z= 0.249 Chirality : 0.043 0.127 4404 Planarity : 0.005 0.040 4788 Dihedral : 4.317 51.671 3840 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.12 % Allowed : 25.15 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3444 helix: 0.92 (0.14), residues: 1392 sheet: 0.66 (0.17), residues: 972 loop : -1.04 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 67 HIS 0.003 0.001 HIS K 91 PHE 0.011 0.001 PHE M 162 TYR 0.010 0.001 TYR T 93 ARG 0.005 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1452) hydrogen bonds : angle 4.31286 ( 4140) covalent geometry : bond 0.00246 (27036) covalent geometry : angle 0.49516 (36792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 292 time to evaluate : 3.246 Fit side-chains REVERT: A 47 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: A 150 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: A 185 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8008 (mptt) REVERT: B 69 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: C 38 ASP cc_start: 0.8117 (t0) cc_final: 0.7893 (t0) REVERT: C 150 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8501 (tpp) REVERT: D 69 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: D 87 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7011 (mp0) REVERT: E 93 PHE cc_start: 0.8789 (t80) cc_final: 0.8434 (t80) REVERT: E 184 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7319 (pp20) REVERT: E 185 LYS cc_start: 0.8481 (mttm) cc_final: 0.8119 (mmtp) REVERT: F 69 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.5848 (mp0) REVERT: G 47 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: G 184 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: G 185 LYS cc_start: 0.8585 (mttm) cc_final: 0.8092 (mmtm) REVERT: H 39 ARG cc_start: 0.5286 (OUTLIER) cc_final: 0.5077 (ttp-170) REVERT: H 58 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7944 (mtp180) REVERT: H 74 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7477 (p0) REVERT: I 28 LYS cc_start: 0.8654 (mttp) cc_final: 0.8437 (mttt) REVERT: I 185 LYS cc_start: 0.8570 (mttm) cc_final: 0.8030 (mptt) REVERT: K 28 LYS cc_start: 0.8616 (mttp) cc_final: 0.8366 (mttp) REVERT: K 52 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: K 184 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: K 185 LYS cc_start: 0.8560 (mttm) cc_final: 0.8207 (mmtm) REVERT: L 69 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: L 87 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6792 (mp0) REVERT: M 47 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: M 184 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: N 18 ARG cc_start: 0.7402 (mtt90) cc_final: 0.6743 (mtt-85) REVERT: O 150 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: O 184 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: O 185 LYS cc_start: 0.8644 (mttm) cc_final: 0.8242 (mmtp) REVERT: Q 52 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: R 58 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7244 (tpp-160) REVERT: R 87 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6933 (mp0) REVERT: S 52 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: S 184 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: S 185 LYS cc_start: 0.8440 (mttm) cc_final: 0.7816 (mptt) REVERT: U 185 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8171 (mmtp) REVERT: V 69 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: W 47 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: W 185 LYS cc_start: 0.8553 (mttm) cc_final: 0.8273 (mmtp) REVERT: X 87 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6855 (mp0) outliers start: 83 outliers final: 6 residues processed: 351 average time/residue: 1.8628 time to fit residues: 731.8647 Evaluate side-chains 299 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 131 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 290 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121158 restraints weight = 27795.676| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.14 r_work: 0.3251 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 27036 Z= 0.138 Angle : 0.547 5.185 36792 Z= 0.268 Chirality : 0.044 0.127 4404 Planarity : 0.005 0.039 4788 Dihedral : 4.328 53.017 3840 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.97 % Allowed : 26.20 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3444 helix: 0.95 (0.14), residues: 1404 sheet: 0.55 (0.17), residues: 1008 loop : -0.92 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 67 HIS 0.003 0.001 HIS U 91 PHE 0.012 0.002 PHE W 162 TYR 0.012 0.002 TYR I 161 ARG 0.005 0.000 ARG N 58 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 1452) hydrogen bonds : angle 4.31600 ( 4140) covalent geometry : bond 0.00342 (27036) covalent geometry : angle 0.54707 (36792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 270 time to evaluate : 2.992 Fit side-chains REVERT: A 47 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: A 150 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8430 (tpp) REVERT: A 185 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8028 (mptt) REVERT: B 69 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: C 38 ASP cc_start: 0.8317 (t0) cc_final: 0.8075 (t0) REVERT: C 47 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: C 150 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8517 (tpp) REVERT: D 69 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: D 87 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7032 (mp0) REVERT: D 93 TYR cc_start: 0.8621 (t80) cc_final: 0.8290 (t80) REVERT: E 93 PHE cc_start: 0.8789 (t80) cc_final: 0.8498 (t80) REVERT: E 185 LYS cc_start: 0.8556 (mttm) cc_final: 0.8153 (mmtp) REVERT: F 69 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: G 47 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: G 185 LYS cc_start: 0.8591 (mttm) cc_final: 0.8089 (mmtm) REVERT: H 39 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4952 (ttp-170) REVERT: H 58 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7947 (mtp180) REVERT: I 185 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8034 (mptt) REVERT: J 87 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6657 (mp0) REVERT: K 28 LYS cc_start: 0.8611 (mttp) cc_final: 0.8372 (mttp) REVERT: K 47 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: K 184 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: K 185 LYS cc_start: 0.8576 (mttm) cc_final: 0.8221 (mmtm) REVERT: L 39 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.4372 (tpp80) REVERT: L 69 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: L 87 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6805 (mp0) REVERT: M 47 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: M 66 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: M 184 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: N 18 ARG cc_start: 0.7422 (mtt90) cc_final: 0.6776 (mtt-85) REVERT: O 87 ASN cc_start: 0.8037 (m-40) cc_final: 0.7558 (m-40) REVERT: O 150 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: O 184 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: O 185 LYS cc_start: 0.8655 (mttm) cc_final: 0.8245 (mmtp) REVERT: P 69 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: Q 52 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: R 58 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7232 (tpp-160) REVERT: R 69 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: R 87 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6968 (mp0) REVERT: S 47 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: S 184 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: S 185 LYS cc_start: 0.8407 (mttm) cc_final: 0.8003 (mmmm) REVERT: V 69 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: W 185 LYS cc_start: 0.8611 (mttm) cc_final: 0.8284 (mmtp) REVERT: X 39 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.4797 (ttp80) REVERT: X 87 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6863 (mp0) outliers start: 79 outliers final: 14 residues processed: 330 average time/residue: 2.2417 time to fit residues: 831.3125 Evaluate side-chains 309 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 185 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain X residue 39 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 242 optimal weight: 0.0370 chunk 216 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 149 optimal weight: 0.0070 chunk 221 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 overall best weight: 2.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.154024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120977 restraints weight = 27915.089| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.14 r_work: 0.3248 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 27036 Z= 0.144 Angle : 0.553 5.497 36792 Z= 0.270 Chirality : 0.044 0.127 4404 Planarity : 0.005 0.037 4788 Dihedral : 4.337 54.657 3840 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.30 % Allowed : 25.68 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3444 helix: 0.97 (0.14), residues: 1404 sheet: 0.52 (0.17), residues: 1008 loop : -0.92 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 67 HIS 0.003 0.001 HIS U 91 PHE 0.013 0.002 PHE W 162 TYR 0.013 0.002 TYR I 161 ARG 0.007 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 1452) hydrogen bonds : angle 4.30954 ( 4140) covalent geometry : bond 0.00358 (27036) covalent geometry : angle 0.55277 (36792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 3.154 Fit side-chains REVERT: A 47 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: A 150 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8348 (tpp) REVERT: A 184 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: A 185 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7929 (mptt) REVERT: B 69 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: C 38 ASP cc_start: 0.8185 (t0) cc_final: 0.7954 (t0) REVERT: C 47 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: C 150 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8488 (tpp) REVERT: D 69 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: D 87 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6959 (mp0) REVERT: D 93 TYR cc_start: 0.8553 (t80) cc_final: 0.8208 (t80) REVERT: E 93 PHE cc_start: 0.8727 (t80) cc_final: 0.8442 (t80) REVERT: E 185 LYS cc_start: 0.8452 (mttm) cc_final: 0.8036 (mmtp) REVERT: F 69 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.5711 (mp0) REVERT: G 47 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: G 66 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: G 184 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: G 185 LYS cc_start: 0.8514 (mttm) cc_final: 0.8033 (mmtp) REVERT: H 39 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.4890 (ttp-170) REVERT: H 58 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7905 (mtp180) REVERT: I 185 LYS cc_start: 0.8514 (mttm) cc_final: 0.7949 (mptt) REVERT: J 39 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.4645 (ttp-170) REVERT: J 87 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6619 (mp0) REVERT: K 28 LYS cc_start: 0.8557 (mttp) cc_final: 0.8315 (mttp) REVERT: K 47 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: K 52 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: K 184 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: K 185 LYS cc_start: 0.8488 (mttm) cc_final: 0.8123 (mmtm) REVERT: L 69 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: L 87 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6692 (mp0) REVERT: M 47 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: M 66 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: M 184 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: N 18 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6655 (mtt-85) REVERT: O 87 ASN cc_start: 0.7937 (m-40) cc_final: 0.7458 (m-40) REVERT: O 150 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8390 (tpt) REVERT: O 185 LYS cc_start: 0.8570 (mttm) cc_final: 0.8171 (mmtp) REVERT: P 69 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6003 (mp0) REVERT: Q 47 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: Q 52 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: R 58 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7195 (tpp-160) REVERT: R 69 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.5799 (mp0) REVERT: R 87 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6655 (mp0) REVERT: S 47 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: S 52 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: S 184 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: S 185 LYS cc_start: 0.8308 (mttm) cc_final: 0.7897 (mmmm) REVERT: U 169 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: U 184 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: V 69 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: W 184 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: W 185 LYS cc_start: 0.8489 (mttm) cc_final: 0.8158 (mmtp) REVERT: X 39 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.4681 (ttp80) REVERT: X 87 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6716 (mp0) outliers start: 88 outliers final: 15 residues processed: 340 average time/residue: 1.9451 time to fit residues: 736.2061 Evaluate side-chains 318 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain J residue 39 ARG Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain U residue 169 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain X residue 39 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 321 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120390 restraints weight = 27959.795| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.14 r_work: 0.3240 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27036 Z= 0.156 Angle : 0.577 6.462 36792 Z= 0.280 Chirality : 0.045 0.129 4404 Planarity : 0.005 0.037 4788 Dihedral : 4.438 58.025 3840 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.00 % Allowed : 26.16 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3444 helix: 0.93 (0.14), residues: 1404 sheet: 0.49 (0.17), residues: 1008 loop : -0.95 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 67 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.002 PHE W 162 TYR 0.013 0.002 TYR I 161 ARG 0.006 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 1452) hydrogen bonds : angle 4.35255 ( 4140) covalent geometry : bond 0.00391 (27036) covalent geometry : angle 0.57675 (36792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 2.976 Fit side-chains REVERT: A 47 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: A 150 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8404 (tpp) REVERT: A 184 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7798 (pt0) REVERT: A 185 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7959 (mptt) REVERT: B 69 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6095 (mp0) REVERT: C 38 ASP cc_start: 0.8287 (t0) cc_final: 0.8046 (t0) REVERT: C 47 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: C 150 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8534 (tpp) REVERT: D 69 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: D 87 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7008 (mp0) REVERT: D 93 TYR cc_start: 0.8596 (t80) cc_final: 0.8325 (t80) REVERT: E 93 PHE cc_start: 0.8745 (t80) cc_final: 0.8473 (t80) REVERT: E 185 LYS cc_start: 0.8426 (mttm) cc_final: 0.7990 (mmtp) REVERT: F 69 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: G 47 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: G 66 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: G 184 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: G 185 LYS cc_start: 0.8563 (mttm) cc_final: 0.8080 (mmtp) REVERT: H 39 ARG cc_start: 0.5172 (OUTLIER) cc_final: 0.4937 (ttp-170) REVERT: H 58 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7954 (mtp180) REVERT: I 185 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7985 (mptt) REVERT: J 39 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.4674 (ttp-170) REVERT: J 87 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6651 (mp0) REVERT: K 28 LYS cc_start: 0.8586 (mttp) cc_final: 0.8347 (mttp) REVERT: K 47 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: K 52 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: K 184 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: K 185 LYS cc_start: 0.8543 (mttm) cc_final: 0.8174 (mmtm) REVERT: L 28 GLU cc_start: 0.8414 (tt0) cc_final: 0.8211 (tt0) REVERT: L 69 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: L 87 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6741 (mp0) REVERT: M 47 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: M 66 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: M 184 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7398 (pp20) REVERT: N 18 ARG cc_start: 0.7325 (mtt90) cc_final: 0.6671 (mtt-85) REVERT: O 52 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: O 150 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8390 (tpt) REVERT: O 185 LYS cc_start: 0.8623 (mttm) cc_final: 0.8223 (mmtp) REVERT: P 69 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: Q 47 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: Q 52 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: Q 185 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: R 58 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7189 (tpp-160) REVERT: R 69 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: R 87 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6817 (mp0) REVERT: S 47 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: S 184 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: S 185 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7995 (mmmm) REVERT: U 150 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (tpt) REVERT: U 169 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: U 184 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7444 (pp20) REVERT: V 69 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: W 184 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7266 (pp20) REVERT: W 185 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8176 (mmtp) REVERT: X 39 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.4743 (ttp80) outliers start: 80 outliers final: 17 residues processed: 324 average time/residue: 1.9407 time to fit residues: 701.3018 Evaluate side-chains 324 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 185 LYS Chi-restraints excluded: chain J residue 39 ARG Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 185 LYS Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain S residue 185 LYS Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 169 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain W residue 185 LYS Chi-restraints excluded: chain X residue 39 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 264 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123468 restraints weight = 27822.595| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.15 r_work: 0.3277 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27036 Z= 0.104 Angle : 0.490 5.255 36792 Z= 0.245 Chirality : 0.043 0.127 4404 Planarity : 0.005 0.036 4788 Dihedral : 4.173 57.886 3840 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.44 % Allowed : 26.61 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3444 helix: 1.23 (0.14), residues: 1404 sheet: 0.76 (0.18), residues: 960 loop : -1.18 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 67 HIS 0.002 0.000 HIS E 91 PHE 0.010 0.001 PHE O 162 TYR 0.010 0.001 TYR H 93 ARG 0.009 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 1452) hydrogen bonds : angle 4.17379 ( 4140) covalent geometry : bond 0.00245 (27036) covalent geometry : angle 0.49037 (36792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 3.110 Fit side-chains REVERT: A 47 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: A 150 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8351 (tpp) REVERT: A 184 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: A 185 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7939 (mptt) REVERT: B 58 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7760 (mtp180) REVERT: B 69 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: C 38 ASP cc_start: 0.8242 (t0) cc_final: 0.7998 (t0) REVERT: C 47 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: C 150 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8483 (tpp) REVERT: D 69 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: D 87 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6968 (mp0) REVERT: E 93 PHE cc_start: 0.8696 (t80) cc_final: 0.8476 (t80) REVERT: E 185 LYS cc_start: 0.8418 (mttm) cc_final: 0.8005 (mmtp) REVERT: F 69 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.5769 (mp0) REVERT: G 47 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: G 74 MET cc_start: 0.7911 (mmm) cc_final: 0.7531 (mmm) REVERT: G 184 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: G 185 LYS cc_start: 0.8506 (mttm) cc_final: 0.8037 (mmtp) REVERT: H 39 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.4816 (ttp-170) REVERT: H 58 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7983 (mtp180) REVERT: I 185 LYS cc_start: 0.8525 (mttm) cc_final: 0.7964 (mptt) REVERT: J 87 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6632 (mp0) REVERT: K 28 LYS cc_start: 0.8528 (mttp) cc_final: 0.8291 (mttp) REVERT: K 52 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: K 184 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: K 185 LYS cc_start: 0.8483 (mttm) cc_final: 0.8111 (mmtm) REVERT: L 28 GLU cc_start: 0.8340 (tt0) cc_final: 0.8121 (tt0) REVERT: L 69 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: L 87 GLU cc_start: 0.7634 (mm-30) cc_final: 0.6688 (mp0) REVERT: M 47 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: M 184 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7359 (pp20) REVERT: N 18 ARG cc_start: 0.7317 (mtt90) cc_final: 0.6669 (mtt-85) REVERT: N 86 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7626 (mt-10) REVERT: O 146 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8190 (mtp-110) REVERT: O 150 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8405 (tpt) REVERT: O 184 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: O 185 LYS cc_start: 0.8589 (mttm) cc_final: 0.8169 (mmtp) REVERT: P 69 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: Q 47 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: Q 49 LEU cc_start: 0.8687 (mt) cc_final: 0.8479 (mt) REVERT: Q 52 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: R 58 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7195 (tpp-160) REVERT: R 69 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6019 (mp0) REVERT: R 87 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6782 (mp0) REVERT: S 47 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: S 52 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: S 184 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: S 185 LYS cc_start: 0.8360 (mttm) cc_final: 0.8020 (mmtm) REVERT: U 150 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8471 (tpt) REVERT: U 184 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: V 69 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: W 184 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7068 (pp20) REVERT: X 87 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6719 (mp0) outliers start: 65 outliers final: 7 residues processed: 332 average time/residue: 1.9760 time to fit residues: 732.0082 Evaluate side-chains 318 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 290 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 322 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123013 restraints weight = 27981.364| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.15 r_work: 0.3270 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 27036 Z= 0.113 Angle : 0.510 5.321 36792 Z= 0.251 Chirality : 0.043 0.125 4404 Planarity : 0.005 0.036 4788 Dihedral : 4.144 59.762 3840 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 27.36 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3444 helix: 1.27 (0.14), residues: 1404 sheet: 0.69 (0.17), residues: 972 loop : -1.13 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 67 HIS 0.002 0.001 HIS U 91 PHE 0.011 0.001 PHE G 162 TYR 0.011 0.001 TYR H 93 ARG 0.008 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 1452) hydrogen bonds : angle 4.15691 ( 4140) covalent geometry : bond 0.00274 (27036) covalent geometry : angle 0.51005 (36792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 3.400 Fit side-chains REVERT: A 47 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: A 150 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8330 (tpp) REVERT: A 184 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: A 185 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7927 (mptt) REVERT: B 69 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: C 38 ASP cc_start: 0.8255 (t0) cc_final: 0.8005 (t0) REVERT: C 47 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: C 150 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8459 (tpp) REVERT: D 69 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: D 87 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6976 (mp0) REVERT: E 185 LYS cc_start: 0.8399 (mttm) cc_final: 0.7984 (mmtp) REVERT: F 69 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.5814 (mp0) REVERT: G 47 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: G 184 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: G 185 LYS cc_start: 0.8497 (mttm) cc_final: 0.8023 (mmtp) REVERT: H 39 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.4814 (ttp-170) REVERT: H 58 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7882 (mtp180) REVERT: I 185 LYS cc_start: 0.8499 (mttm) cc_final: 0.7946 (mptt) REVERT: J 87 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6544 (mp0) REVERT: K 28 LYS cc_start: 0.8514 (mttp) cc_final: 0.8303 (mttp) REVERT: K 47 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: K 52 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: K 184 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: K 185 LYS cc_start: 0.8513 (mttm) cc_final: 0.8152 (mmtm) REVERT: L 28 GLU cc_start: 0.8359 (tt0) cc_final: 0.8131 (tt0) REVERT: L 69 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: L 87 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6679 (mp0) REVERT: M 47 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: N 18 ARG cc_start: 0.7334 (mtt90) cc_final: 0.6677 (mtt-85) REVERT: N 86 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7638 (mt-10) REVERT: O 146 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8207 (mtp-110) REVERT: O 150 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8395 (tpt) REVERT: O 184 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: O 185 LYS cc_start: 0.8577 (mttm) cc_final: 0.8167 (mmtp) REVERT: P 69 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: Q 47 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: Q 49 LEU cc_start: 0.8683 (mt) cc_final: 0.8454 (mt) REVERT: Q 52 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: R 58 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7189 (tpp-160) REVERT: R 69 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6037 (mp0) REVERT: R 87 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6900 (mp0) REVERT: S 47 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: S 52 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: S 184 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: S 185 LYS cc_start: 0.8367 (mttm) cc_final: 0.8029 (mmtm) REVERT: U 150 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8478 (tpt) REVERT: U 184 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: V 69 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: W 184 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7110 (pp20) REVERT: X 39 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.4631 (ttp80) REVERT: X 87 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6727 (mp0) outliers start: 52 outliers final: 6 residues processed: 313 average time/residue: 1.9772 time to fit residues: 689.9958 Evaluate side-chains 312 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain X residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 19 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 221 optimal weight: 0.0670 chunk 139 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121022 restraints weight = 27808.265| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.14 r_work: 0.3248 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27036 Z= 0.154 Angle : 0.575 6.042 36792 Z= 0.279 Chirality : 0.045 0.127 4404 Planarity : 0.005 0.038 4788 Dihedral : 4.340 61.592 3840 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.69 % Allowed : 27.67 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3444 helix: 1.11 (0.14), residues: 1404 sheet: 0.50 (0.18), residues: 1008 loop : -0.92 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 67 HIS 0.003 0.001 HIS E 91 PHE 0.013 0.002 PHE W 162 TYR 0.014 0.002 TYR H 93 ARG 0.007 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 1452) hydrogen bonds : angle 4.28975 ( 4140) covalent geometry : bond 0.00387 (27036) covalent geometry : angle 0.57504 (36792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 3.023 Fit side-chains REVERT: A 47 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: A 150 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8250 (tpp) REVERT: A 184 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: A 185 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7906 (mptt) REVERT: B 69 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.5892 (mp0) REVERT: C 38 ASP cc_start: 0.8241 (t0) cc_final: 0.7969 (t0) REVERT: C 47 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: C 150 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8496 (tpp) REVERT: D 69 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: D 87 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6956 (mp0) REVERT: E 185 LYS cc_start: 0.8371 (mttm) cc_final: 0.7953 (mmtp) REVERT: F 69 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.5826 (mp0) REVERT: G 47 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: G 185 LYS cc_start: 0.8505 (mttm) cc_final: 0.8043 (mmtp) REVERT: H 39 ARG cc_start: 0.5017 (OUTLIER) cc_final: 0.4797 (ttp-170) REVERT: H 58 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7873 (mtp180) REVERT: I 185 LYS cc_start: 0.8495 (mttm) cc_final: 0.7929 (mptt) REVERT: J 87 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6555 (mp0) REVERT: K 28 LYS cc_start: 0.8495 (mttp) cc_final: 0.8258 (mttp) REVERT: K 47 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: K 52 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: K 184 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: K 185 LYS cc_start: 0.8484 (mttm) cc_final: 0.8108 (mmtm) REVERT: L 69 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: L 87 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6688 (mp0) REVERT: M 47 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: N 18 ARG cc_start: 0.7321 (mtt90) cc_final: 0.6645 (mtt-85) REVERT: N 86 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7635 (mt-10) REVERT: O 146 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8204 (mtp-110) REVERT: O 150 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8392 (tpt) REVERT: O 184 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: O 185 LYS cc_start: 0.8575 (mttm) cc_final: 0.8172 (mmtp) REVERT: P 69 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: Q 47 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: Q 52 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: R 58 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7161 (tpp-160) REVERT: R 69 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: R 87 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6672 (mp0) REVERT: S 47 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: S 52 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: S 184 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: S 185 LYS cc_start: 0.8359 (mttm) cc_final: 0.8033 (mmtm) REVERT: U 150 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8514 (tpt) REVERT: U 184 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7418 (pp20) REVERT: V 69 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: W 184 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: X 39 ARG cc_start: 0.5481 (OUTLIER) cc_final: 0.4685 (ttp80) outliers start: 45 outliers final: 6 residues processed: 303 average time/residue: 2.0062 time to fit residues: 681.2668 Evaluate side-chains 305 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain X residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 30 optimal weight: 0.0770 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 177 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121270 restraints weight = 27967.846| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.14 r_work: 0.3251 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27036 Z= 0.143 Angle : 0.558 5.994 36792 Z= 0.272 Chirality : 0.044 0.128 4404 Planarity : 0.005 0.036 4788 Dihedral : 4.337 62.209 3840 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.95 % Allowed : 27.70 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3444 helix: 1.11 (0.14), residues: 1404 sheet: 0.49 (0.17), residues: 1008 loop : -0.94 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 67 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.002 PHE W 162 TYR 0.013 0.002 TYR H 93 ARG 0.007 0.000 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1452) hydrogen bonds : angle 4.27749 ( 4140) covalent geometry : bond 0.00356 (27036) covalent geometry : angle 0.55827 (36792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19750.52 seconds wall clock time: 341 minutes 16.22 seconds (20476.22 seconds total)