Starting phenix.real_space_refine on Sun Oct 12 16:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui2_42286/10_2025/8ui2_42286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui2_42286/10_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_42286/10_2025/8ui2_42286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui2_42286/10_2025/8ui2_42286.map" model { file = "/net/cci-nas-00/data/ceres_data/8ui2_42286/10_2025/8ui2_42286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui2_42286/10_2025/8ui2_42286.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 2.93, per 1000 atoms: 0.11 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: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.91 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: 5.06 Time building geometry restraints manager: 2.97 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } 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' } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 21.720 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (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 ARG 0.003 0.000 ARG N 58 TYR 0.008 0.002 TYR K 161 PHE 0.017 0.002 PHE E 93 TRP 0.008 0.002 TRP D 67 HIS 0.003 0.001 HIS W 196 Details of bonding type rmsd covalent geometry : bond 0.00394 (27036) covalent geometry : angle 0.51601 (36792) hydrogen bonds : bond 0.21969 ( 1452) hydrogen bonds : angle 7.56641 ( 4140) *********************** 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 : 0.858 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: 0.9430 time to fit residues: 351.8539 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 : 0.969 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.154566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121439 restraints weight = 27800.801| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.13 r_work: 0.3246 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1045 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= 0.132 Angle : 0.552 5.184 36792 Z= 0.277 Chirality : 0.044 0.128 4404 Planarity : 0.005 0.033 4788 Dihedral : 4.447 38.952 3852 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.08 % Allowed : 22.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.14), residues: 3444 helix: 0.66 (0.14), residues: 1404 sheet: 0.71 (0.18), residues: 1008 loop : -0.75 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 58 TYR 0.015 0.002 TYR L 93 PHE 0.013 0.002 PHE M 93 TRP 0.005 0.001 TRP B 67 HIS 0.003 0.001 HIS S 196 Details of bonding type rmsd covalent geometry : bond 0.00309 (27036) covalent geometry : angle 0.55240 (36792) hydrogen bonds : bond 0.04903 ( 1452) hydrogen bonds : angle 4.73840 ( 4140) *********************** 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 370 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 288 time to evaluate : 1.046 Fit side-chains REVERT: A 150 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8279 (tpp) REVERT: C 150 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8430 (tpp) REVERT: D 69 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: E 66 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: E 93 PHE cc_start: 0.8730 (t80) cc_final: 0.8319 (t80) REVERT: E 150 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8537 (tpp) REVERT: E 185 LYS cc_start: 0.8413 (mttm) cc_final: 0.8023 (mmtp) REVERT: G 66 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: G 185 LYS cc_start: 0.8494 (mttm) cc_final: 0.8031 (mmtm) REVERT: H 39 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.5023 (ttp-170) REVERT: H 58 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7849 (mtp180) REVERT: I 185 LYS cc_start: 0.8452 (mttm) cc_final: 0.8127 (mmtp) REVERT: J 46 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: J 87 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6684 (mp0) REVERT: K 28 LYS cc_start: 0.8557 (mttp) cc_final: 0.8272 (mttp) REVERT: K 52 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: K 185 LYS cc_start: 0.8487 (mttm) cc_final: 0.8073 (mmtm) REVERT: L 6 THR cc_start: 0.8546 (p) cc_final: 0.8329 (m) REVERT: M 66 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: M 90 ASP cc_start: 0.8525 (t0) cc_final: 0.8078 (t70) REVERT: N 86 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7751 (mt-10) REVERT: O 150 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8218 (tpt) REVERT: O 185 LYS cc_start: 0.8583 (mttm) cc_final: 0.8115 (mttp) REVERT: P 18 ARG cc_start: 0.7460 (mtt90) cc_final: 0.7144 (mtt90) REVERT: Q 52 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: R 58 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7224 (tpp-160) REVERT: R 87 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7007 (mp0) REVERT: S 52 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: S 185 LYS cc_start: 0.8342 (mttm) cc_final: 0.7815 (mptt) REVERT: U 66 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: U 150 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8481 (tpt) REVERT: U 185 LYS cc_start: 0.8441 (mttm) cc_final: 0.8165 (mmtm) REVERT: V 69 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.5831 (mp0) REVERT: W 28 LYS cc_start: 0.8537 (mttp) cc_final: 0.8315 (mttp) REVERT: X 18 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7235 (mtt90) REVERT: X 58 ARG cc_start: 0.7969 (mtp-110) cc_final: 0.7756 (mtp180) REVERT: X 87 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6912 (mp0) outliers start: 82 outliers final: 12 residues processed: 355 average time/residue: 0.9605 time to fit residues: 377.2592 Evaluate side-chains 296 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 C residue 150 MET 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 G residue 66 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain O residue 150 MET 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 S residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain V residue 69 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 183 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 300 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 155 optimal weight: 0.0980 chunk 283 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 247 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.157497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124761 restraints weight = 27850.616| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.13 r_work: 0.3291 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1491 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= 0.098 Angle : 0.473 5.239 36792 Z= 0.238 Chirality : 0.043 0.131 4404 Planarity : 0.005 0.031 4788 Dihedral : 3.978 40.293 3840 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.23 % Allowed : 23.46 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 3444 helix: 1.16 (0.14), residues: 1404 sheet: 0.81 (0.18), residues: 972 loop : -0.94 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 58 TYR 0.011 0.002 TYR I 161 PHE 0.010 0.001 PHE I 162 TRP 0.007 0.001 TRP J 67 HIS 0.003 0.000 HIS P 102 Details of bonding type rmsd covalent geometry : bond 0.00226 (27036) covalent geometry : angle 0.47256 (36792) hydrogen bonds : bond 0.03812 ( 1452) hydrogen bonds : angle 4.28739 ( 4140) *********************** 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 381 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 295 time to evaluate : 1.108 Fit side-chains REVERT: A 47 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 185 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7919 (mptt) REVERT: B 69 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.5846 (mp0) REVERT: C 38 ASP cc_start: 0.8160 (t0) cc_final: 0.7914 (t0) REVERT: C 127 LYS cc_start: 0.8397 (mttm) cc_final: 0.8170 (mttt) REVERT: C 150 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8422 (tpp) REVERT: C 156 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.6022 (pt) REVERT: D 35 ARG cc_start: 0.8300 (ttp80) cc_final: 0.8046 (ttp80) REVERT: D 69 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: D 87 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6952 (mp0) REVERT: E 93 PHE cc_start: 0.8718 (t80) cc_final: 0.8364 (t80) REVERT: E 185 LYS cc_start: 0.8358 (mttm) cc_final: 0.7964 (mmtp) REVERT: F 69 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.5873 (mp0) REVERT: G 47 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: G 74 MET cc_start: 0.7907 (mmm) cc_final: 0.7546 (mmm) REVERT: G 184 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: G 185 LYS cc_start: 0.8524 (mttm) cc_final: 0.8052 (mmtm) REVERT: H 58 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7866 (mtp180) REVERT: H 87 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6824 (mp0) REVERT: I 28 LYS cc_start: 0.8501 (mttp) cc_final: 0.8266 (mttt) REVERT: I 185 LYS cc_start: 0.8428 (mttm) cc_final: 0.7927 (mptt) REVERT: J 87 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6710 (mp0) REVERT: K 28 LYS cc_start: 0.8589 (mttp) cc_final: 0.8362 (mttp) REVERT: K 52 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: K 150 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7580 (tpt) REVERT: K 185 LYS cc_start: 0.8521 (mttm) cc_final: 0.8184 (mmtm) REVERT: L 87 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6737 (mp0) REVERT: M 47 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: N 18 ARG cc_start: 0.7557 (mtt90) cc_final: 0.6768 (mtt-85) REVERT: N 86 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7764 (mt-10) REVERT: O 150 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8329 (tpt) REVERT: O 184 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: O 185 LYS cc_start: 0.8582 (mttm) cc_final: 0.8225 (mmtp) REVERT: P 18 ARG cc_start: 0.7473 (mtt90) cc_final: 0.7260 (mtt90) REVERT: Q 28 LYS cc_start: 0.8467 (mttp) cc_final: 0.8247 (mttp) REVERT: Q 52 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7908 (pt0) REVERT: Q 58 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7361 (ttmt) REVERT: R 48 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7487 (mm-30) REVERT: R 58 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7231 (tpp-160) REVERT: R 87 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6869 (mp0) REVERT: S 47 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: S 52 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: S 150 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8298 (tpp) REVERT: S 185 LYS cc_start: 0.8366 (mttm) cc_final: 0.7794 (mptt) REVERT: T 87 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6633 (mp0) REVERT: U 184 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: U 185 LYS cc_start: 0.8436 (mttm) cc_final: 0.8054 (mmtp) REVERT: V 28 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: V 69 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.5879 (mp0) REVERT: W 90 ASP cc_start: 0.8661 (t0) cc_final: 0.8384 (t0) REVERT: W 184 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7050 (pp20) REVERT: X 18 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7303 (mtt90) REVERT: X 87 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6941 (mp0) outliers start: 86 outliers final: 7 residues processed: 354 average time/residue: 0.9801 time to fit residues: 386.4540 Evaluate side-chains 305 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU 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 C residue 156 ILE Chi-restraints excluded: chain D residue 69 GLU 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 I residue 29 SER Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 52 GLU 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 U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 330 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.153855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120802 restraints weight = 27980.285| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.14 r_work: 0.3236 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1360 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= 0.171 Angle : 0.587 6.427 36792 Z= 0.284 Chirality : 0.045 0.128 4404 Planarity : 0.005 0.033 4788 Dihedral : 4.268 46.609 3840 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.82 % Allowed : 24.55 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3444 helix: 1.00 (0.14), residues: 1404 sheet: 0.65 (0.18), residues: 1008 loop : -0.78 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 58 TYR 0.014 0.002 TYR I 161 PHE 0.014 0.002 PHE I 162 TRP 0.012 0.002 TRP B 67 HIS 0.004 0.001 HIS U 91 Details of bonding type rmsd covalent geometry : bond 0.00432 (27036) covalent geometry : angle 0.58747 (36792) hydrogen bonds : bond 0.04983 ( 1452) hydrogen bonds : angle 4.39178 ( 4140) *********************** 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 345 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 270 time to evaluate : 1.192 Fit side-chains REVERT: A 47 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: A 184 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: B 69 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: C 38 ASP cc_start: 0.8207 (t0) cc_final: 0.7962 (t0) REVERT: C 127 LYS cc_start: 0.8564 (mttm) cc_final: 0.8351 (mttp) REVERT: C 150 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8521 (tpp) REVERT: D 69 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: D 87 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7006 (mp0) REVERT: D 93 TYR cc_start: 0.8581 (t80) cc_final: 0.8258 (t80) REVERT: E 93 PHE cc_start: 0.8763 (t80) cc_final: 0.8490 (t80) REVERT: E 185 LYS cc_start: 0.8438 (mttm) cc_final: 0.8036 (mmtp) REVERT: F 69 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: G 47 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: G 185 LYS cc_start: 0.8515 (mttm) cc_final: 0.8097 (mmtp) REVERT: H 58 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7892 (mtp180) REVERT: I 185 LYS cc_start: 0.8511 (mttm) cc_final: 0.7951 (mptt) REVERT: J 87 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6649 (mp0) REVERT: K 28 LYS cc_start: 0.8570 (mttp) cc_final: 0.8306 (mttp) REVERT: K 47 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: K 185 LYS cc_start: 0.8513 (mttm) cc_final: 0.8170 (mmtm) REVERT: L 87 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6698 (mp0) REVERT: M 47 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: M 66 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: N 18 ARG cc_start: 0.7462 (mtt90) cc_final: 0.6755 (mtt-85) REVERT: O 150 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8267 (tpt) REVERT: O 184 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: O 185 LYS cc_start: 0.8589 (mttm) cc_final: 0.8215 (mmtp) REVERT: P 18 ARG cc_start: 0.7432 (mtt90) cc_final: 0.7207 (mtt90) REVERT: Q 28 LYS cc_start: 0.8428 (mttp) cc_final: 0.8220 (mttp) REVERT: Q 47 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: Q 52 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: R 48 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7533 (mm-30) REVERT: R 58 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7221 (tpp-160) REVERT: R 87 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6902 (mp0) REVERT: S 47 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: S 185 LYS cc_start: 0.8353 (mttm) cc_final: 0.7764 (mptt) REVERT: T 87 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6610 (mp0) REVERT: U 169 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: U 184 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: U 185 LYS cc_start: 0.8600 (mttm) cc_final: 0.8112 (mmtp) REVERT: V 28 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: V 69 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.5924 (mp0) REVERT: W 47 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: W 185 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8208 (mmtp) REVERT: X 18 ARG cc_start: 0.7558 (mtt90) cc_final: 0.7274 (mtt90) REVERT: X 87 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6796 (mp0) outliers start: 75 outliers final: 12 residues processed: 322 average time/residue: 0.9940 time to fit residues: 355.7258 Evaluate side-chains 299 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU 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 F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 58 ARG 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 150 MET Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain U residue 169 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 185 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 253 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.154900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121796 restraints weight = 27777.384| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.15 r_work: 0.3256 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27036 Z= 0.131 Angle : 0.529 5.352 36792 Z= 0.259 Chirality : 0.044 0.126 4404 Planarity : 0.005 0.033 4788 Dihedral : 4.170 49.364 3840 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.63 % Allowed : 25.34 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.14), residues: 3444 helix: 1.11 (0.14), residues: 1404 sheet: 0.72 (0.17), residues: 972 loop : -1.03 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 58 TYR 0.012 0.002 TYR I 161 PHE 0.012 0.002 PHE G 162 TRP 0.011 0.002 TRP B 67 HIS 0.003 0.001 HIS U 91 Details of bonding type rmsd covalent geometry : bond 0.00321 (27036) covalent geometry : angle 0.52869 (36792) hydrogen bonds : bond 0.04305 ( 1452) hydrogen bonds : angle 4.27245 ( 4140) *********************** 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 350 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 1.322 Fit side-chains REVERT: A 47 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: B 69 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.5846 (mp0) REVERT: C 38 ASP cc_start: 0.8139 (t0) cc_final: 0.7899 (t0) REVERT: C 150 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8502 (tpp) REVERT: D 69 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: D 87 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6992 (mp0) REVERT: E 93 PHE cc_start: 0.8735 (t80) cc_final: 0.8398 (t80) REVERT: E 184 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7291 (pp20) REVERT: E 185 LYS cc_start: 0.8440 (mttm) cc_final: 0.8065 (mmtp) REVERT: F 69 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.5786 (mp0) REVERT: G 47 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: G 184 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: G 185 LYS cc_start: 0.8458 (mttm) cc_final: 0.8019 (mmtp) REVERT: H 58 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7868 (mtp180) REVERT: I 185 LYS cc_start: 0.8492 (mttm) cc_final: 0.7924 (mptt) REVERT: J 69 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: J 87 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6580 (mp0) REVERT: K 28 LYS cc_start: 0.8544 (mttp) cc_final: 0.8295 (mttp) REVERT: K 52 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: K 184 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7364 (pp20) REVERT: K 185 LYS cc_start: 0.8470 (mttm) cc_final: 0.8112 (mmtm) REVERT: L 69 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: L 87 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6643 (mp0) REVERT: M 47 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: N 18 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6685 (mtt-85) REVERT: N 86 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7560 (mt-10) REVERT: O 150 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8304 (tpt) REVERT: O 184 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: O 185 LYS cc_start: 0.8538 (mttm) cc_final: 0.8148 (mmtp) REVERT: P 18 ARG cc_start: 0.7392 (mtt90) cc_final: 0.7169 (mtt90) REVERT: Q 28 LYS cc_start: 0.8417 (mttp) cc_final: 0.8204 (mttp) REVERT: Q 47 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: Q 52 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7914 (pt0) REVERT: Q 58 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7424 (ttmt) REVERT: R 48 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7460 (mm-30) REVERT: R 58 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7186 (tpp-160) REVERT: R 87 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6877 (mp0) REVERT: S 47 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: S 52 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: S 185 LYS cc_start: 0.8301 (mttm) cc_final: 0.7673 (mptt) REVERT: T 87 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6571 (mp0) REVERT: U 169 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: U 185 LYS cc_start: 0.8454 (mttm) cc_final: 0.7943 (mmtp) REVERT: V 28 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: V 69 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: W 47 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: W 184 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: W 185 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8184 (mmtp) REVERT: X 18 ARG cc_start: 0.7513 (mtt90) cc_final: 0.7223 (mtt90) REVERT: X 87 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6763 (mp0) outliers start: 70 outliers final: 12 residues processed: 330 average time/residue: 0.9799 time to fit residues: 358.9277 Evaluate side-chains 309 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL 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 141 ASP Chi-restraints excluded: chain E residue 184 GLU 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 I residue 25 LEU Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET 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 O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 150 MET 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 U residue 169 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain W residue 185 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 1 optimal weight: 4.9990 chunk 194 optimal weight: 0.1980 chunk 311 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 217 optimal weight: 0.9980 chunk 289 optimal weight: 0.0170 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 0.0060 chunk 176 optimal weight: 0.9980 overall best weight: 0.4434 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.158371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125614 restraints weight = 27819.917| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.14 r_work: 0.3304 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27036 Z= 0.091 Angle : 0.460 5.272 36792 Z= 0.231 Chirality : 0.042 0.147 4404 Planarity : 0.004 0.033 4788 Dihedral : 3.877 48.578 3840 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.82 % Allowed : 25.19 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 3444 helix: 1.43 (0.14), residues: 1404 sheet: 1.10 (0.18), residues: 912 loop : -1.17 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 58 TYR 0.009 0.001 TYR T 93 PHE 0.009 0.001 PHE M 162 TRP 0.007 0.001 TRP B 67 HIS 0.002 0.000 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00208 (27036) covalent geometry : angle 0.45974 (36792) hydrogen bonds : bond 0.03370 ( 1452) hydrogen bonds : angle 4.08770 ( 4140) *********************** 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 370 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 1.049 Fit side-chains REVERT: A 47 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: B 58 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7769 (mtp180) REVERT: B 69 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: C 38 ASP cc_start: 0.8147 (t0) cc_final: 0.7894 (t0) REVERT: C 127 LYS cc_start: 0.8398 (mttm) cc_final: 0.8164 (mttt) REVERT: D 69 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: D 87 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6934 (mp0) REVERT: E 49 LEU cc_start: 0.8658 (mt) cc_final: 0.8455 (mt) REVERT: E 93 PHE cc_start: 0.8750 (t80) cc_final: 0.8459 (t80) REVERT: E 184 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7289 (pp20) REVERT: E 185 LYS cc_start: 0.8352 (mttm) cc_final: 0.7976 (mmtp) REVERT: F 69 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: G 47 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: G 74 MET cc_start: 0.7862 (mmm) cc_final: 0.7529 (mmm) REVERT: G 184 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: G 185 LYS cc_start: 0.8403 (mttm) cc_final: 0.7968 (mmtp) REVERT: H 58 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7887 (mtp180) REVERT: H 87 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6689 (mp0) REVERT: I 52 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: I 90 ASP cc_start: 0.8587 (t0) cc_final: 0.8294 (t0) REVERT: I 185 LYS cc_start: 0.8474 (mttm) cc_final: 0.7884 (mptt) REVERT: J 87 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6540 (mp0) REVERT: K 28 LYS cc_start: 0.8543 (mttp) cc_final: 0.8332 (mttp) REVERT: K 47 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: K 52 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: K 184 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7255 (pp20) REVERT: K 185 LYS cc_start: 0.8477 (mttm) cc_final: 0.8118 (mmtm) REVERT: L 28 GLU cc_start: 0.8378 (tt0) cc_final: 0.8167 (tt0) REVERT: L 69 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: L 87 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6763 (mp0) REVERT: M 47 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: M 68 GLU cc_start: 0.7046 (mp0) cc_final: 0.6704 (mp0) REVERT: N 18 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6732 (mtt-85) REVERT: O 150 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8294 (tpt) REVERT: O 185 LYS cc_start: 0.8513 (mttm) cc_final: 0.8134 (mmtp) REVERT: P 18 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7205 (mtt90) REVERT: Q 28 LYS cc_start: 0.8423 (mttp) cc_final: 0.8208 (mttp) REVERT: Q 47 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: Q 49 LEU cc_start: 0.8672 (mt) cc_final: 0.8440 (mt) REVERT: Q 52 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: Q 151 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7844 (mmt180) REVERT: R 58 ARG cc_start: 0.7884 (mtp-110) cc_final: 0.7190 (tpp-160) REVERT: R 87 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6911 (mp0) REVERT: S 47 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: S 52 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: S 159 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6878 (mtpt) REVERT: S 185 LYS cc_start: 0.8305 (mttm) cc_final: 0.7956 (mmmm) REVERT: T 58 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7217 (mmt-90) REVERT: T 87 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6562 (mp0) REVERT: U 184 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: U 185 LYS cc_start: 0.8470 (mttm) cc_final: 0.7993 (mmtp) REVERT: V 28 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: V 69 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: W 47 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: W 90 ASP cc_start: 0.8648 (t0) cc_final: 0.8360 (t0) REVERT: X 18 ARG cc_start: 0.7532 (mtt90) cc_final: 0.7216 (mtt90) REVERT: X 87 GLU cc_start: 0.7598 (mm-30) cc_final: 0.6865 (mp0) outliers start: 75 outliers final: 6 residues processed: 353 average time/residue: 0.9375 time to fit residues: 368.6406 Evaluate side-chains 307 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 69 GLU 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 47 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 GLU 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 M residue 47 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 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 159 LYS Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 171 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 326 optimal weight: 0.3980 chunk 166 optimal weight: 8.9990 chunk 37 optimal weight: 0.0370 chunk 244 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 288 optimal weight: 0.0040 chunk 90 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 overall best weight: 1.4872 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.156990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124178 restraints weight = 27713.713| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.14 r_work: 0.3282 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 27036 Z= 0.109 Angle : 0.495 5.218 36792 Z= 0.244 Chirality : 0.043 0.123 4404 Planarity : 0.005 0.033 4788 Dihedral : 3.898 50.225 3840 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 25.79 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3444 helix: 1.42 (0.14), residues: 1404 sheet: 0.78 (0.18), residues: 972 loop : -0.97 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 58 TYR 0.012 0.001 TYR H 93 PHE 0.011 0.001 PHE G 162 TRP 0.010 0.002 TRP B 67 HIS 0.002 0.001 HIS U 91 Details of bonding type rmsd covalent geometry : bond 0.00262 (27036) covalent geometry : angle 0.49527 (36792) hydrogen bonds : bond 0.03784 ( 1452) hydrogen bonds : angle 4.09111 ( 4140) *********************** 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 332 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 1.078 Fit side-chains REVERT: A 47 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: B 69 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.5831 (mp0) REVERT: C 38 ASP cc_start: 0.8224 (t0) cc_final: 0.7974 (t0) REVERT: C 127 LYS cc_start: 0.8453 (mttm) cc_final: 0.8204 (mttt) REVERT: C 156 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6044 (pt) REVERT: D 69 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: D 87 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6945 (mp0) REVERT: E 93 PHE cc_start: 0.8753 (t80) cc_final: 0.8421 (t80) REVERT: E 184 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: E 185 LYS cc_start: 0.8396 (mttm) cc_final: 0.8023 (mmtp) REVERT: F 69 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.5860 (mp0) REVERT: G 47 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: G 185 LYS cc_start: 0.8415 (mttm) cc_final: 0.8002 (mmtp) REVERT: H 58 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7865 (mtp180) REVERT: H 87 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6686 (mp0) REVERT: I 52 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: I 90 ASP cc_start: 0.8552 (t0) cc_final: 0.8267 (t0) REVERT: I 185 LYS cc_start: 0.8481 (mttm) cc_final: 0.8075 (mttp) REVERT: J 87 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6572 (mp0) REVERT: K 28 LYS cc_start: 0.8507 (mttp) cc_final: 0.8274 (mttp) REVERT: K 47 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: K 52 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: K 184 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: K 185 LYS cc_start: 0.8488 (mttm) cc_final: 0.8133 (mmtm) REVERT: L 28 GLU cc_start: 0.8390 (tt0) cc_final: 0.8179 (tt0) REVERT: L 69 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: L 87 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6770 (mp0) REVERT: M 47 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: M 68 GLU cc_start: 0.7062 (mp0) cc_final: 0.6713 (mp0) REVERT: N 18 ARG cc_start: 0.7354 (mtt90) cc_final: 0.6721 (mtt-85) REVERT: O 150 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8304 (tpt) REVERT: O 185 LYS cc_start: 0.8537 (mttm) cc_final: 0.8161 (mmtp) REVERT: P 18 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7188 (mtt90) REVERT: Q 28 LYS cc_start: 0.8462 (mttp) cc_final: 0.8241 (mttp) REVERT: Q 47 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: Q 49 LEU cc_start: 0.8680 (mt) cc_final: 0.8454 (mt) REVERT: Q 52 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: Q 151 ARG cc_start: 0.8083 (mmt180) cc_final: 0.7873 (mmt180) REVERT: Q 185 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7671 (mttm) REVERT: R 58 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7172 (tpp-160) REVERT: R 87 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6853 (mp0) REVERT: S 47 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: S 52 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: S 150 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8311 (tpt) REVERT: S 159 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6909 (mtpt) REVERT: S 185 LYS cc_start: 0.8317 (mttm) cc_final: 0.7916 (mmmm) REVERT: T 87 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6564 (mp0) REVERT: U 184 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7340 (pp20) REVERT: U 185 LYS cc_start: 0.8514 (mttm) cc_final: 0.8034 (mmtp) REVERT: V 28 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: V 69 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6004 (mp0) REVERT: W 47 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: W 90 ASP cc_start: 0.8679 (t0) cc_final: 0.8369 (t0) REVERT: W 184 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: W 185 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8088 (mmtp) REVERT: X 18 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7212 (mtt90) REVERT: X 87 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6905 (mp0) outliers start: 56 outliers final: 4 residues processed: 316 average time/residue: 0.9077 time to fit residues: 319.0506 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 156 ILE 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 47 GLU Chi-restraints excluded: chain I residue 52 GLU 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 M residue 47 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 185 LYS 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 159 LYS Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 184 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 12 optimal weight: 0.0270 chunk 183 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.159043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126372 restraints weight = 27879.851| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.15 r_work: 0.3310 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27036 Z= 0.091 Angle : 0.459 5.259 36792 Z= 0.229 Chirality : 0.042 0.129 4404 Planarity : 0.004 0.034 4788 Dihedral : 3.747 50.923 3840 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.73 % Allowed : 26.35 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.15), residues: 3444 helix: 1.57 (0.14), residues: 1404 sheet: 0.79 (0.17), residues: 1020 loop : -0.97 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 35 TYR 0.009 0.001 TYR I 161 PHE 0.010 0.001 PHE G 162 TRP 0.008 0.001 TRP P 67 HIS 0.002 0.000 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00215 (27036) covalent geometry : angle 0.45891 (36792) hydrogen bonds : bond 0.03289 ( 1452) hydrogen bonds : angle 3.99708 ( 4140) *********************** 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 334 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.070 Fit side-chains REVERT: A 47 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: B 58 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7807 (mtp180) REVERT: B 69 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6028 (mp0) REVERT: C 38 ASP cc_start: 0.8222 (t0) cc_final: 0.7958 (t0) REVERT: C 156 ILE cc_start: 0.6243 (OUTLIER) cc_final: 0.5968 (pt) REVERT: D 69 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: D 87 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6969 (mp0) REVERT: E 90 ASP cc_start: 0.8632 (t0) cc_final: 0.8394 (t0) REVERT: E 93 PHE cc_start: 0.8768 (t80) cc_final: 0.8498 (t80) REVERT: E 184 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: E 185 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8051 (mmtp) REVERT: F 69 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.5847 (mp0) REVERT: G 47 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: G 74 MET cc_start: 0.7884 (mmm) cc_final: 0.7407 (mmm) REVERT: G 184 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: G 185 LYS cc_start: 0.8427 (mttm) cc_final: 0.8016 (mmtp) REVERT: H 87 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6679 (mp0) REVERT: I 52 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: I 90 ASP cc_start: 0.8587 (t0) cc_final: 0.8252 (t0) REVERT: I 185 LYS cc_start: 0.8483 (mttm) cc_final: 0.8161 (mmtp) REVERT: J 87 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6560 (mp0) REVERT: K 28 LYS cc_start: 0.8558 (mttp) cc_final: 0.8320 (mttp) REVERT: K 47 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: K 52 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: K 184 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: K 185 LYS cc_start: 0.8492 (mttm) cc_final: 0.8143 (mmtm) REVERT: L 28 GLU cc_start: 0.8367 (tt0) cc_final: 0.8142 (tt0) REVERT: L 69 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: L 87 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6847 (mp0) REVERT: M 47 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: M 68 GLU cc_start: 0.7010 (mp0) cc_final: 0.6681 (mp0) REVERT: N 18 ARG cc_start: 0.7448 (mtt90) cc_final: 0.6756 (mtt-85) REVERT: O 150 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8301 (tpt) REVERT: O 184 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: O 185 LYS cc_start: 0.8520 (mttm) cc_final: 0.8131 (mmtp) REVERT: P 18 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7195 (mtt90) REVERT: Q 28 LYS cc_start: 0.8489 (mttp) cc_final: 0.8273 (mttp) REVERT: Q 47 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: Q 49 LEU cc_start: 0.8655 (mt) cc_final: 0.8447 (mt) REVERT: Q 52 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: R 58 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7183 (tpp-160) REVERT: R 87 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6925 (mp0) REVERT: S 47 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: S 52 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: S 79 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5830 (mt-10) REVERT: S 185 LYS cc_start: 0.8287 (mttm) cc_final: 0.7950 (mmmm) REVERT: T 58 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7195 (mmt-90) REVERT: T 87 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6592 (mp0) REVERT: U 184 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: U 185 LYS cc_start: 0.8488 (mttm) cc_final: 0.8239 (mmtm) REVERT: V 28 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: V 69 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: W 47 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: W 90 ASP cc_start: 0.8720 (t0) cc_final: 0.8407 (t0) REVERT: W 184 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7080 (pp20) REVERT: W 185 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8104 (mmtp) REVERT: X 18 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7255 (mtt90) REVERT: X 87 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6925 (mp0) outliers start: 46 outliers final: 6 residues processed: 320 average time/residue: 0.9476 time to fit residues: 338.0724 Evaluate side-chains 308 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 185 LYS 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 I residue 52 GLU 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 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 171 VAL 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 166 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 330 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.153633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120712 restraints weight = 27939.793| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.13 r_work: 0.3238 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 27036 Z= 0.204 Angle : 0.630 7.138 36792 Z= 0.303 Chirality : 0.047 0.144 4404 Planarity : 0.005 0.038 4788 Dihedral : 4.245 54.143 3840 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.76 % Allowed : 26.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3444 helix: 1.09 (0.14), residues: 1404 sheet: 0.76 (0.17), residues: 972 loop : -1.06 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 58 TYR 0.016 0.002 TYR H 93 PHE 0.015 0.002 PHE W 162 TRP 0.014 0.003 TRP B 67 HIS 0.004 0.001 HIS G 196 Details of bonding type rmsd covalent geometry : bond 0.00524 (27036) covalent geometry : angle 0.63046 (36792) hydrogen bonds : bond 0.05224 ( 1452) hydrogen bonds : angle 4.34883 ( 4140) *********************** 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 327 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: A 79 GLU cc_start: 0.5615 (mt-10) cc_final: 0.5406 (mt-10) REVERT: B 28 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8279 (tp30) REVERT: B 69 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.5897 (mp0) REVERT: C 38 ASP cc_start: 0.8247 (t0) cc_final: 0.7970 (t0) REVERT: D 69 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: D 87 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7039 (mp0) REVERT: D 93 TYR cc_start: 0.8569 (t80) cc_final: 0.8264 (t80) REVERT: E 93 PHE cc_start: 0.8761 (t80) cc_final: 0.8459 (t80) REVERT: E 185 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8019 (mmtp) REVERT: F 69 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: G 47 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: G 185 LYS cc_start: 0.8508 (mttm) cc_final: 0.8049 (mmtp) REVERT: I 185 LYS cc_start: 0.8473 (mttm) cc_final: 0.8103 (mttp) REVERT: J 87 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6611 (mp0) REVERT: K 28 LYS cc_start: 0.8533 (mttp) cc_final: 0.8285 (mttp) REVERT: K 47 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: K 184 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7390 (pp20) REVERT: K 185 LYS cc_start: 0.8493 (mttm) cc_final: 0.8119 (mmtm) REVERT: L 28 GLU cc_start: 0.8465 (tt0) cc_final: 0.8219 (tt0) REVERT: L 69 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: L 87 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6662 (mp0) REVERT: M 47 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: M 68 GLU cc_start: 0.7117 (mp0) cc_final: 0.6749 (mp0) REVERT: N 18 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6657 (mtt-85) REVERT: O 87 ASN cc_start: 0.8083 (m-40) cc_final: 0.6942 (m-40) REVERT: O 150 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: O 184 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7759 (pt0) REVERT: O 185 LYS cc_start: 0.8542 (mttm) cc_final: 0.8160 (mmtp) REVERT: P 18 ARG cc_start: 0.7365 (mtt90) cc_final: 0.7061 (mtt90) REVERT: Q 28 LYS cc_start: 0.8477 (mttp) cc_final: 0.8271 (mttp) REVERT: Q 47 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: Q 151 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7843 (mmt180) REVERT: R 58 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7164 (tpp-160) REVERT: R 87 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6887 (mp0) REVERT: S 47 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: S 185 LYS cc_start: 0.8343 (mttm) cc_final: 0.8024 (mmtm) REVERT: T 87 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6646 (mp0) REVERT: U 47 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: U 184 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: U 185 LYS cc_start: 0.8562 (mttm) cc_final: 0.8044 (mmtp) REVERT: V 28 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: V 69 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.5975 (mp0) REVERT: W 47 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: W 184 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: W 185 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8196 (mmtp) REVERT: X 18 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7218 (mtt90) REVERT: X 87 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6781 (mp0) outliers start: 47 outliers final: 6 residues processed: 313 average time/residue: 0.9877 time to fit residues: 343.7606 Evaluate side-chains 303 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL 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 D residue 69 GLU Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain K residue 47 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 O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain X residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 3 optimal weight: 0.5980 chunk 239 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.156661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123795 restraints weight = 27766.948| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.14 r_work: 0.3280 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 27036 Z= 0.106 Angle : 0.500 5.230 36792 Z= 0.248 Chirality : 0.043 0.126 4404 Planarity : 0.005 0.035 4788 Dihedral : 4.033 55.669 3840 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.16 % Allowed : 27.29 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.15), residues: 3444 helix: 1.37 (0.14), residues: 1404 sheet: 0.72 (0.17), residues: 972 loop : -1.04 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 58 TYR 0.011 0.001 TYR H 93 PHE 0.011 0.001 PHE G 162 TRP 0.009 0.002 TRP B 67 HIS 0.002 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00253 (27036) covalent geometry : angle 0.50016 (36792) hydrogen bonds : bond 0.03799 ( 1452) hydrogen bonds : angle 4.14617 ( 4140) ********************** 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 310 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: B 69 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: C 38 ASP cc_start: 0.8153 (t0) cc_final: 0.7898 (t0) REVERT: D 69 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: D 87 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6963 (mp0) REVERT: E 93 PHE cc_start: 0.8718 (t80) cc_final: 0.8412 (t80) REVERT: E 185 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7922 (mmtp) REVERT: F 69 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: G 47 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: G 74 MET cc_start: 0.7855 (mmm) cc_final: 0.7543 (mmm) REVERT: G 185 LYS cc_start: 0.8465 (mttm) cc_final: 0.8007 (mmtp) REVERT: I 90 ASP cc_start: 0.8557 (t0) cc_final: 0.8298 (t0) REVERT: I 185 LYS cc_start: 0.8450 (mttm) cc_final: 0.8039 (mttp) REVERT: J 87 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6590 (mp0) REVERT: K 28 LYS cc_start: 0.8533 (mttp) cc_final: 0.8299 (mttp) REVERT: K 47 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: K 184 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: K 185 LYS cc_start: 0.8484 (mttm) cc_final: 0.8123 (mmtm) REVERT: L 28 GLU cc_start: 0.8403 (tt0) cc_final: 0.8156 (tt0) REVERT: L 69 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: L 87 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6649 (mp0) REVERT: M 47 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: M 68 GLU cc_start: 0.7014 (mp0) cc_final: 0.6640 (mp0) REVERT: N 18 ARG cc_start: 0.7316 (mtt90) cc_final: 0.6670 (mtt-85) REVERT: O 150 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8325 (tpt) REVERT: O 185 LYS cc_start: 0.8508 (mttm) cc_final: 0.8112 (mmtp) REVERT: P 18 ARG cc_start: 0.7346 (mtt90) cc_final: 0.7067 (mtt90) REVERT: Q 28 LYS cc_start: 0.8411 (mttp) cc_final: 0.8184 (mttp) REVERT: Q 47 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: Q 49 LEU cc_start: 0.8670 (mt) cc_final: 0.8420 (mt) REVERT: Q 151 ARG cc_start: 0.8067 (mmt180) cc_final: 0.7833 (mmt180) REVERT: R 58 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7140 (tpp-160) REVERT: R 87 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6875 (mp0) REVERT: S 47 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: S 185 LYS cc_start: 0.8307 (mttm) cc_final: 0.7950 (mmtm) REVERT: T 87 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6610 (mp0) REVERT: U 47 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: U 184 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7369 (pp20) REVERT: U 185 LYS cc_start: 0.8502 (mttm) cc_final: 0.8207 (mmtm) REVERT: V 28 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: V 69 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.5995 (mp0) REVERT: W 47 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: W 90 ASP cc_start: 0.8507 (t0) cc_final: 0.8293 (t0) REVERT: W 184 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7147 (pp20) REVERT: W 185 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8118 (mmtp) REVERT: X 18 ARG cc_start: 0.7532 (mtt90) cc_final: 0.7188 (mtt90) REVERT: X 87 GLU cc_start: 0.7644 (mm-30) cc_final: 0.6788 (mp0) outliers start: 31 outliers final: 4 residues processed: 299 average time/residue: 0.9894 time to fit residues: 328.6405 Evaluate side-chains 300 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain K residue 47 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 O residue 150 MET Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain X residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 139 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 278 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 227 optimal weight: 0.4980 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 315 optimal weight: 0.4980 overall best weight: 1.1700 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.157971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125424 restraints weight = 27815.981| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.12 r_work: 0.3295 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 27036 Z= 0.102 Angle : 0.485 5.275 36792 Z= 0.240 Chirality : 0.043 0.125 4404 Planarity : 0.004 0.036 4788 Dihedral : 3.904 55.908 3840 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 27.33 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3444 helix: 1.47 (0.14), residues: 1404 sheet: 0.75 (0.18), residues: 972 loop : -1.01 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 58 TYR 0.011 0.001 TYR I 161 PHE 0.010 0.001 PHE W 162 TRP 0.009 0.002 TRP B 67 HIS 0.002 0.001 HIS U 91 Details of bonding type rmsd covalent geometry : bond 0.00243 (27036) covalent geometry : angle 0.48484 (36792) hydrogen bonds : bond 0.03593 ( 1452) hydrogen bonds : angle 4.06372 ( 4140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9305.05 seconds wall clock time: 158 minutes 25.91 seconds (9505.91 seconds total)