Starting phenix.real_space_refine on Sat May 24 20:16:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ukm_42355/05_2025/8ukm_42355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ukm_42355/05_2025/8ukm_42355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ukm_42355/05_2025/8ukm_42355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ukm_42355/05_2025/8ukm_42355.map" model { file = "/net/cci-nas-00/data/ceres_data/8ukm_42355/05_2025/8ukm_42355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ukm_42355/05_2025/8ukm_42355.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 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 17004 2.51 5 N 4464 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26184 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Restraints were copied for chains: D, F, H, J, L, N, P, R, T, V, X, C, E, G, I, K, M, O, Q, S, U, W Time building chain proxies: 6.70, per 1000 atoms: 0.26 Number of scatterers: 26184 At special positions: 0 Unit cell: (144.1, 141.9, 137.5, 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 4668 8.00 N 4464 7.00 C 17004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 3.2 seconds 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 48 sheets defined 43.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'B' and resid 13 through 33 Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 73 through 93 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.682A pdb=" N PHE C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'D' and resid 13 through 33 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 73 through 93 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 66 through 82 Processing helix chain 'E' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 167 through 183 Processing helix chain 'F' and resid 13 through 33 Processing helix chain 'F' and resid 35 through 39 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 73 through 93 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 66 through 82 Processing helix chain 'G' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 107 " --> pdb=" O PRO G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'H' and resid 13 through 33 Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 47 through 50 Processing helix chain 'H' and resid 73 through 93 Processing helix chain 'H' and resid 95 through 97 No H-bonds generated for 'chain 'H' and resid 95 through 97' Processing helix chain 'I' and resid 29 through 44 Processing helix chain 'I' and resid 66 through 82 Processing helix chain 'I' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU I 107 " --> pdb=" O PRO I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 143 Processing helix chain 'I' and resid 167 through 183 Processing helix chain 'J' and resid 13 through 33 Processing helix chain 'J' and resid 35 through 39 Processing helix chain 'J' and resid 47 through 50 Processing helix chain 'J' and resid 73 through 93 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'K' and resid 29 through 44 Processing helix chain 'K' and resid 66 through 82 Processing helix chain 'K' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 107 " --> pdb=" O PRO K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 167 through 183 Processing helix chain 'L' and resid 13 through 33 Processing helix chain 'L' and resid 35 through 39 Processing helix chain 'L' and resid 47 through 50 Processing helix chain 'L' and resid 73 through 93 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'M' and resid 29 through 44 Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'M' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU M 107 " --> pdb=" O PRO M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 143 Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'N' and resid 13 through 33 Processing helix chain 'N' and resid 35 through 39 Processing helix chain 'N' and resid 47 through 50 Processing helix chain 'N' and resid 73 through 93 Processing helix chain 'N' and resid 95 through 97 No H-bonds generated for 'chain 'N' and resid 95 through 97' Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 66 through 82 Processing helix chain 'O' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE O 104 " --> pdb=" O ALA O 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU O 107 " --> pdb=" O PRO O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 143 Processing helix chain 'O' and resid 167 through 183 Processing helix chain 'P' and resid 13 through 33 Processing helix chain 'P' and resid 35 through 39 Processing helix chain 'P' and resid 47 through 50 Processing helix chain 'P' and resid 73 through 93 Processing helix chain 'P' and resid 95 through 97 No H-bonds generated for 'chain 'P' and resid 95 through 97' Processing helix chain 'Q' and resid 29 through 44 Processing helix chain 'Q' and resid 66 through 82 Processing helix chain 'Q' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE Q 104 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 143 Processing helix chain 'Q' and resid 167 through 183 Processing helix chain 'R' and resid 13 through 33 Processing helix chain 'R' and resid 35 through 39 Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 73 through 93 Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'S' and resid 29 through 44 Processing helix chain 'S' and resid 66 through 82 Processing helix chain 'S' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU S 107 " --> pdb=" O PRO S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 143 Processing helix chain 'S' and resid 167 through 183 Processing helix chain 'T' and resid 13 through 33 Processing helix chain 'T' and resid 35 through 39 Processing helix chain 'T' and resid 47 through 50 Processing helix chain 'T' and resid 73 through 93 Processing helix chain 'T' and resid 95 through 97 No H-bonds generated for 'chain 'T' and resid 95 through 97' Processing helix chain 'U' and resid 29 through 44 Processing helix chain 'U' and resid 66 through 82 Processing helix chain 'U' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU U 107 " --> pdb=" O PRO U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 143 Processing helix chain 'U' and resid 167 through 183 Processing helix chain 'V' and resid 13 through 33 Processing helix chain 'V' and resid 35 through 39 Processing helix chain 'V' and resid 47 through 50 Processing helix chain 'V' and resid 73 through 93 Processing helix chain 'V' and resid 95 through 97 No H-bonds generated for 'chain 'V' and resid 95 through 97' Processing helix chain 'W' and resid 29 through 44 Processing helix chain 'W' and resid 66 through 82 Processing helix chain 'W' and resid 100 through 107 removed outlier: 3.682A pdb=" N PHE W 104 " --> pdb=" O ALA W 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU W 107 " --> pdb=" O PRO W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 143 Processing helix chain 'W' and resid 167 through 183 Processing helix chain 'X' and resid 13 through 33 Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 47 through 50 Processing helix chain 'X' and resid 73 through 93 Processing helix chain 'X' and resid 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing sheet with id=1, first strand: chain 'A' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU A 48 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 50 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 90 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU A 147 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 165 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 149 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 160 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 126 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 162 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 124 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 121 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE A 191 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 123 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 189 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 125 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU B 4 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 44 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 6 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 46 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 8 " --> pdb=" O TYR B 46 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=5, first strand: chain 'C' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU C 48 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR C 64 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 50 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 90 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU C 147 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 165 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 149 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 160 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 126 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE C 162 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 124 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 121 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE C 191 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 123 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE C 189 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU C 125 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU D 4 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 44 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 6 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR D 46 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 8 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=9, first strand: chain 'E' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU E 48 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 64 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 50 " --> pdb=" O MET E 62 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 90 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU E 147 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL E 165 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG E 149 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 160 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 126 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE E 162 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL E 124 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU E 121 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE E 191 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE E 123 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE E 189 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU E 125 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU F 4 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR F 44 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL F 6 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR F 46 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 8 " --> pdb=" O TYR F 46 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=13, first strand: chain 'G' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU G 48 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G 64 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 50 " --> pdb=" O MET G 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 90 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU G 147 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG G 149 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 160 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL G 126 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE G 162 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL G 124 " --> pdb=" O PHE G 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU G 121 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE G 191 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE G 123 " --> pdb=" O ILE G 189 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE G 189 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 125 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU H 4 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 44 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL H 6 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR H 46 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 8 " --> pdb=" O TYR H 46 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=17, first strand: chain 'I' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU I 48 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR I 64 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 50 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 90 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU I 147 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL I 165 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG I 149 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA I 160 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL I 126 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE I 162 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL I 124 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU I 121 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE I 191 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE I 123 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE I 189 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU I 125 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU J 4 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR J 44 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL J 6 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR J 46 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL J 8 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=21, first strand: chain 'K' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU K 48 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR K 64 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS K 50 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 90 " --> pdb=" O GLU K 26 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'K' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU K 147 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL K 165 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG K 149 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA K 160 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL K 126 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE K 162 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 124 " --> pdb=" O PHE K 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU K 121 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE K 191 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE K 123 " --> pdb=" O ILE K 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE K 189 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU K 125 " --> pdb=" O LEU K 187 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU L 4 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR L 44 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL L 6 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR L 46 " --> pdb=" O VAL L 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL L 8 " --> pdb=" O TYR L 46 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=25, first strand: chain 'M' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU M 48 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR M 64 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 50 " --> pdb=" O MET M 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP M 90 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'M' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU M 147 " --> pdb=" O VAL M 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL M 165 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA M 160 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL M 126 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE M 162 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL M 124 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 121 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE M 191 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE M 123 " --> pdb=" O ILE M 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE M 189 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU M 125 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU N 4 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR N 44 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL N 6 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR N 46 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL N 8 " --> pdb=" O TYR N 46 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'N' and resid 52 through 53 Processing sheet with id=29, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU O 48 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS O 50 " --> pdb=" O MET O 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 90 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'O' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU O 147 " --> pdb=" O VAL O 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL O 165 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG O 149 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA O 160 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL O 126 " --> pdb=" O ALA O 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE O 162 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 124 " --> pdb=" O PHE O 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU O 121 " --> pdb=" O ILE O 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE O 191 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE O 123 " --> pdb=" O ILE O 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE O 189 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU O 125 " --> pdb=" O LEU O 187 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 42 through 46 removed outlier: 5.526A pdb=" N LEU P 4 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR P 44 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL P 6 " --> pdb=" O THR P 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR P 46 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL P 8 " --> pdb=" O TYR P 46 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'P' and resid 52 through 53 Processing sheet with id=33, first strand: chain 'Q' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU Q 48 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR Q 64 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Q 50 " --> pdb=" O MET Q 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 90 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'Q' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU Q 147 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL Q 165 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG Q 149 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA Q 160 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE Q 162 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL Q 124 " --> pdb=" O PHE Q 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU Q 121 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE Q 191 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE Q 123 " --> pdb=" O ILE Q 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE Q 189 " --> pdb=" O PHE Q 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU R 4 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR R 44 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL R 6 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR R 46 " --> pdb=" O VAL R 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL R 8 " --> pdb=" O TYR R 46 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'R' and resid 52 through 53 Processing sheet with id=37, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU S 48 " --> pdb=" O THR S 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR S 64 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS S 50 " --> pdb=" O MET S 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 90 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU S 147 " --> pdb=" O VAL S 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG S 149 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA S 160 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL S 126 " --> pdb=" O ALA S 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE S 162 " --> pdb=" O VAL S 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL S 124 " --> pdb=" O PHE S 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU S 121 " --> pdb=" O ILE S 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE S 191 " --> pdb=" O LEU S 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE S 123 " --> pdb=" O ILE S 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE S 189 " --> pdb=" O PHE S 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU S 125 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU T 4 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR T 44 " --> pdb=" O LEU T 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL T 6 " --> pdb=" O THR T 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR T 46 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL T 8 " --> pdb=" O TYR T 46 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'T' and resid 52 through 53 Processing sheet with id=41, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU U 48 " --> pdb=" O THR U 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR U 64 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS U 50 " --> pdb=" O MET U 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP U 90 " --> pdb=" O GLU U 26 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU U 147 " --> pdb=" O VAL U 165 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL U 165 " --> pdb=" O LEU U 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG U 149 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA U 160 " --> pdb=" O VAL U 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL U 126 " --> pdb=" O ALA U 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE U 162 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL U 124 " --> pdb=" O PHE U 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU U 121 " --> pdb=" O ILE U 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE U 191 " --> pdb=" O LEU U 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE U 123 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE U 189 " --> pdb=" O PHE U 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU U 125 " --> pdb=" O LEU U 187 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'V' and resid 42 through 46 removed outlier: 5.524A pdb=" N LEU V 4 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR V 44 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL V 6 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR V 46 " --> pdb=" O VAL V 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL V 8 " --> pdb=" O TYR V 46 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 52 through 53 Processing sheet with id=45, first strand: chain 'W' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU W 48 " --> pdb=" O THR W 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR W 64 " --> pdb=" O LEU W 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS W 50 " --> pdb=" O MET W 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP W 90 " --> pdb=" O GLU W 26 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'W' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU W 147 " --> pdb=" O VAL W 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL W 165 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG W 149 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA W 160 " --> pdb=" O VAL W 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL W 126 " --> pdb=" O ALA W 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE W 162 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL W 124 " --> pdb=" O PHE W 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU W 121 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE W 191 " --> pdb=" O LEU W 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE W 123 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE W 189 " --> pdb=" O PHE W 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU W 125 " --> pdb=" O LEU W 187 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'X' and resid 42 through 46 removed outlier: 5.526A pdb=" N LEU X 4 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR X 44 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL X 6 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR X 46 " --> pdb=" O VAL X 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL X 8 " --> pdb=" O TYR X 46 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'X' and resid 52 through 53 1512 hydrogen bonds defined for protein. 4284 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: 8.52 Time building geometry restraints manager: 7.25 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: 8669 1.34 - 1.46: 4132 1.46 - 1.58: 13755 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 26640 Sorted by residual: bond pdb=" N VAL V 62 " pdb=" CA VAL V 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.27e+00 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.15e+00 bond pdb=" N VAL N 62 " pdb=" CA VAL N 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" N VAL F 62 " pdb=" CA VAL F 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.05e+00 bond pdb=" N VAL X 62 " pdb=" CA VAL X 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.04e+00 ... (remaining 26635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 34265 1.40 - 2.80: 1670 2.80 - 4.19: 329 4.19 - 5.59: 120 5.59 - 6.99: 36 Bond angle restraints: 36420 Sorted by residual: angle pdb=" N GLY M 201 " pdb=" CA GLY M 201 " pdb=" C GLY M 201 " ideal model delta sigma weight residual 115.08 110.47 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N GLY K 201 " pdb=" CA GLY K 201 " pdb=" C GLY K 201 " ideal model delta sigma weight residual 115.08 110.47 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N GLY Q 201 " pdb=" CA GLY Q 201 " pdb=" C GLY Q 201 " ideal model delta sigma weight residual 115.08 110.49 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" N GLY I 201 " pdb=" CA GLY I 201 " pdb=" C GLY I 201 " ideal model delta sigma weight residual 115.08 110.49 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" N GLY C 201 " pdb=" CA GLY C 201 " pdb=" C GLY C 201 " ideal model delta sigma weight residual 115.08 110.50 4.58 1.19e+00 7.06e-01 1.48e+01 ... (remaining 36415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15080 17.47 - 34.93: 1276 34.93 - 52.40: 168 52.40 - 69.87: 36 69.87 - 87.34: 12 Dihedral angle restraints: 16572 sinusoidal: 6348 harmonic: 10224 Sorted by residual: dihedral pdb=" CA LEU O 152 " pdb=" C LEU O 152 " pdb=" N SER O 153 " pdb=" CA SER O 153 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LEU G 152 " pdb=" C LEU G 152 " pdb=" N SER G 153 " pdb=" CA SER G 153 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU C 152 " pdb=" C LEU C 152 " pdb=" N SER C 153 " pdb=" CA SER C 153 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 16569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3100 0.042 - 0.083: 932 0.083 - 0.125: 448 0.125 - 0.166: 72 0.166 - 0.208: 20 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CA ILE P 64 " pdb=" N ILE P 64 " pdb=" C ILE P 64 " pdb=" CB ILE P 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE J 64 " pdb=" N ILE J 64 " pdb=" C ILE J 64 " pdb=" CB ILE J 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 4569 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 19 " 0.179 9.50e-02 1.11e+02 8.05e-02 4.18e+00 pdb=" NE ARG G 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG G 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 19 " 0.179 9.50e-02 1.11e+02 8.04e-02 4.17e+00 pdb=" NE ARG A 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 19 " 0.179 9.50e-02 1.11e+02 8.05e-02 4.17e+00 pdb=" NE ARG Q 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG Q 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 19 " 0.009 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3740 2.76 - 3.29: 27993 3.29 - 3.83: 44337 3.83 - 4.36: 48519 4.36 - 4.90: 82777 Nonbonded interactions: 207366 Sorted by model distance: nonbonded pdb=" O GLU J 97 " pdb=" NH1 ARG J 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU R 97 " pdb=" NH1 ARG R 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU F 97 " pdb=" NH1 ARG F 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU T 97 " pdb=" NH1 ARG T 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU H 97 " pdb=" NH1 ARG H 100 " model vdw 2.220 3.120 ... (remaining 207361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.24 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 46.340 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 0.039 26640 Z= 0.194 Angle : 0.752 6.988 36420 Z= 0.394 Chirality : 0.050 0.208 4572 Planarity : 0.007 0.081 4680 Dihedral : 13.153 87.335 9924 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3480 helix: 1.21 (0.13), residues: 1308 sheet: -1.51 (0.15), residues: 876 loop : 0.44 (0.21), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS U 196 PHE 0.013 0.002 PHE K 162 TYR 0.009 0.002 TYR I 30 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.13240 ( 1512) hydrogen bonds : angle 5.93724 ( 4284) covalent geometry : bond 0.00396 (26640) covalent geometry : angle 0.75177 (36420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.8819 (m-10) cc_final: 0.8590 (m-10) REVERT: B 17 LYS cc_start: 0.9096 (pttm) cc_final: 0.8799 (pttm) REVERT: B 90 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 75 LYS cc_start: 0.9336 (pttm) cc_final: 0.9115 (ptmm) REVERT: C 150 MET cc_start: 0.8584 (tmm) cc_final: 0.8324 (tmm) REVERT: D 90 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 75 LYS cc_start: 0.9303 (pttm) cc_final: 0.9040 (ptmm) REVERT: H 90 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8276 (tm-30) REVERT: I 150 MET cc_start: 0.8576 (tmm) cc_final: 0.8283 (tmm) REVERT: J 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8265 (tm-30) REVERT: L 7 TYR cc_start: 0.8913 (m-10) cc_final: 0.8710 (m-10) REVERT: L 90 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8404 (tm-30) REVERT: M 75 LYS cc_start: 0.9363 (pttm) cc_final: 0.9133 (ptmm) REVERT: M 150 MET cc_start: 0.8491 (tmm) cc_final: 0.8217 (tmm) REVERT: N 90 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8399 (tm-30) REVERT: O 75 LYS cc_start: 0.9366 (pttm) cc_final: 0.9141 (ptmm) REVERT: P 90 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8379 (tm-30) REVERT: Q 75 LYS cc_start: 0.9265 (pttm) cc_final: 0.9041 (ptmm) REVERT: Q 150 MET cc_start: 0.8464 (tmm) cc_final: 0.8005 (tmm) REVERT: R 7 TYR cc_start: 0.9016 (m-10) cc_final: 0.8766 (m-10) REVERT: R 90 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8178 (tm-30) REVERT: T 12 TYR cc_start: 0.8788 (m-10) cc_final: 0.8534 (m-10) REVERT: T 17 LYS cc_start: 0.9073 (pttm) cc_final: 0.8776 (pttm) REVERT: T 90 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8361 (tm-30) REVERT: U 75 LYS cc_start: 0.9305 (pttm) cc_final: 0.9072 (ptmm) REVERT: U 150 MET cc_start: 0.8473 (tmm) cc_final: 0.8254 (tmm) REVERT: V 90 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8382 (tm-30) REVERT: W 75 LYS cc_start: 0.9403 (pttm) cc_final: 0.9149 (ptmm) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3842 time to fit residues: 306.5155 Evaluate side-chains 416 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 10.0000 chunk 254 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 ASN N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 ASN T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 ASN V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 ASN X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059972 restraints weight = 116054.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061589 restraints weight = 83359.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062829 restraints weight = 65071.121| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 26640 Z= 0.190 Angle : 0.670 7.631 36420 Z= 0.340 Chirality : 0.047 0.183 4572 Planarity : 0.007 0.043 4680 Dihedral : 4.795 24.445 3780 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.78 % Allowed : 8.26 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3480 helix: 1.22 (0.13), residues: 1260 sheet: -1.43 (0.15), residues: 864 loop : 0.07 (0.19), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 98 PHE 0.015 0.002 PHE E 162 TYR 0.008 0.001 TYR F 46 ARG 0.007 0.001 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1512) hydrogen bonds : angle 4.93048 ( 4284) covalent geometry : bond 0.00424 (26640) covalent geometry : angle 0.66988 (36420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 498 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8986 (tmmt) cc_final: 0.8623 (mmtt) REVERT: A 150 MET cc_start: 0.8851 (tmm) cc_final: 0.7875 (tmm) REVERT: B 17 LYS cc_start: 0.9109 (pttm) cc_final: 0.8872 (pttm) REVERT: B 90 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 97 GLU cc_start: 0.8827 (mp0) cc_final: 0.8610 (mp0) REVERT: C 42 LYS cc_start: 0.9078 (tmmt) cc_final: 0.8629 (mmmm) REVERT: C 75 LYS cc_start: 0.9390 (pttm) cc_final: 0.9170 (ptmm) REVERT: C 128 THR cc_start: 0.9234 (t) cc_final: 0.8995 (t) REVERT: D 53 LEU cc_start: 0.9014 (tp) cc_final: 0.8765 (tp) REVERT: D 90 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 97 GLU cc_start: 0.8940 (mp0) cc_final: 0.8689 (mp0) REVERT: E 75 LYS cc_start: 0.9269 (pttm) cc_final: 0.9041 (ptmm) REVERT: E 150 MET cc_start: 0.9057 (tmm) cc_final: 0.8330 (tmm) REVERT: F 53 LEU cc_start: 0.8872 (tp) cc_final: 0.8496 (tp) REVERT: F 97 GLU cc_start: 0.8896 (mp0) cc_final: 0.8669 (mp0) REVERT: H 53 LEU cc_start: 0.8863 (tp) cc_final: 0.8575 (tp) REVERT: H 90 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8374 (tm-30) REVERT: I 42 LYS cc_start: 0.8996 (tmmt) cc_final: 0.8641 (mmmm) REVERT: J 53 LEU cc_start: 0.8860 (tp) cc_final: 0.8567 (tp) REVERT: J 90 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8398 (tm-30) REVERT: K 75 LYS cc_start: 0.9303 (pttm) cc_final: 0.9048 (pttt) REVERT: L 7 TYR cc_start: 0.8882 (m-10) cc_final: 0.8656 (m-10) REVERT: L 53 LEU cc_start: 0.8863 (tp) cc_final: 0.8606 (tp) REVERT: M 75 LYS cc_start: 0.9322 (pttm) cc_final: 0.9108 (ptmm) REVERT: N 53 LEU cc_start: 0.8926 (tp) cc_final: 0.8721 (tp) REVERT: N 68 LEU cc_start: 0.8544 (tp) cc_final: 0.8325 (tp) REVERT: N 90 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8513 (tm-30) REVERT: P 38 ASN cc_start: 0.6595 (OUTLIER) cc_final: 0.6212 (m110) REVERT: P 53 LEU cc_start: 0.8888 (tp) cc_final: 0.8498 (tp) REVERT: P 90 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8500 (tm-30) REVERT: Q 75 LYS cc_start: 0.9287 (pttm) cc_final: 0.9080 (ptmm) REVERT: R 7 TYR cc_start: 0.9022 (m-10) cc_final: 0.8811 (m-10) REVERT: R 17 LYS cc_start: 0.9076 (pttm) cc_final: 0.8846 (pttm) REVERT: R 53 LEU cc_start: 0.8935 (tp) cc_final: 0.8593 (tp) REVERT: R 90 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8474 (tm-30) REVERT: S 150 MET cc_start: 0.8897 (tmm) cc_final: 0.8301 (tmm) REVERT: T 17 LYS cc_start: 0.9185 (pttm) cc_final: 0.8940 (pttm) REVERT: T 38 ASN cc_start: 0.6460 (OUTLIER) cc_final: 0.6222 (t0) REVERT: T 90 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8470 (tm-30) REVERT: U 75 LYS cc_start: 0.9336 (pttm) cc_final: 0.9113 (ptmm) REVERT: V 53 LEU cc_start: 0.8979 (tp) cc_final: 0.8751 (tp) REVERT: V 90 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8601 (tm-30) REVERT: W 75 LYS cc_start: 0.9393 (pttm) cc_final: 0.9150 (ptmm) REVERT: X 53 LEU cc_start: 0.8945 (tp) cc_final: 0.8656 (tp) outliers start: 21 outliers final: 0 residues processed: 515 average time/residue: 0.3921 time to fit residues: 311.0754 Evaluate side-chains 403 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 323 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 153 optimal weight: 0.0970 chunk 331 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.075465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.060131 restraints weight = 115086.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061766 restraints weight = 82674.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.062922 restraints weight = 64408.087| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26640 Z= 0.143 Angle : 0.640 7.025 36420 Z= 0.317 Chirality : 0.048 0.187 4572 Planarity : 0.006 0.040 4680 Dihedral : 4.701 23.807 3780 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3480 helix: 1.32 (0.13), residues: 1248 sheet: -1.33 (0.15), residues: 864 loop : 0.17 (0.19), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 196 PHE 0.014 0.002 PHE Q 162 TYR 0.011 0.002 TYR P 12 ARG 0.005 0.000 ARG P 40 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1512) hydrogen bonds : angle 4.73932 ( 4284) covalent geometry : bond 0.00324 (26640) covalent geometry : angle 0.63951 (36420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 504 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8970 (tmmt) cc_final: 0.8656 (mmtt) REVERT: B 12 TYR cc_start: 0.8750 (m-10) cc_final: 0.8547 (m-10) REVERT: B 17 LYS cc_start: 0.9113 (pttm) cc_final: 0.8841 (pttm) REVERT: B 53 LEU cc_start: 0.8931 (tp) cc_final: 0.8454 (tp) REVERT: B 90 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8477 (tm-30) REVERT: B 97 GLU cc_start: 0.8725 (mp0) cc_final: 0.8433 (mp0) REVERT: C 42 LYS cc_start: 0.8988 (tmmt) cc_final: 0.8617 (mmmm) REVERT: C 75 LYS cc_start: 0.9377 (pttm) cc_final: 0.9163 (ptmm) REVERT: D 90 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8507 (tm-30) REVERT: D 97 GLU cc_start: 0.8862 (mp0) cc_final: 0.8602 (mp0) REVERT: E 75 LYS cc_start: 0.9287 (pttm) cc_final: 0.9001 (ptmm) REVERT: F 97 GLU cc_start: 0.8842 (mp0) cc_final: 0.8605 (mp0) REVERT: G 42 LYS cc_start: 0.9077 (tmmt) cc_final: 0.8630 (mmmm) REVERT: H 90 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8345 (tm-30) REVERT: I 42 LYS cc_start: 0.8970 (tmmt) cc_final: 0.8666 (mmmm) REVERT: I 75 LYS cc_start: 0.9488 (ptmm) cc_final: 0.9099 (pttt) REVERT: J 90 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8355 (tm-30) REVERT: K 42 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8636 (mmmm) REVERT: K 188 ASP cc_start: 0.8251 (t70) cc_final: 0.8031 (t0) REVERT: L 7 TYR cc_start: 0.8864 (m-10) cc_final: 0.8628 (m-10) REVERT: L 12 TYR cc_start: 0.8755 (m-10) cc_final: 0.8463 (m-10) REVERT: M 75 LYS cc_start: 0.9323 (pttm) cc_final: 0.9106 (ptmm) REVERT: N 90 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8503 (tm-30) REVERT: O 42 LYS cc_start: 0.8996 (tmmt) cc_final: 0.8696 (mmmm) REVERT: P 90 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8542 (tm-30) REVERT: Q 42 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8411 (mmmm) REVERT: Q 75 LYS cc_start: 0.9298 (pttm) cc_final: 0.9026 (pttp) REVERT: Q 150 MET cc_start: 0.9010 (tmm) cc_final: 0.8029 (tmm) REVERT: R 7 TYR cc_start: 0.9018 (m-10) cc_final: 0.8800 (m-10) REVERT: R 90 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8337 (tm-30) REVERT: S 75 LYS cc_start: 0.9445 (pttp) cc_final: 0.9143 (pttp) REVERT: T 12 TYR cc_start: 0.8744 (m-10) cc_final: 0.8488 (m-10) REVERT: T 53 LEU cc_start: 0.8893 (tp) cc_final: 0.8535 (tp) REVERT: T 90 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8320 (tm-30) REVERT: U 75 LYS cc_start: 0.9341 (pttm) cc_final: 0.9119 (ptmm) REVERT: V 90 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8515 (tm-30) REVERT: W 42 LYS cc_start: 0.9025 (tmmt) cc_final: 0.8660 (mmtt) REVERT: W 75 LYS cc_start: 0.9389 (pttm) cc_final: 0.9140 (ptmm) outliers start: 2 outliers final: 0 residues processed: 506 average time/residue: 0.3746 time to fit residues: 297.2480 Evaluate side-chains 409 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 122 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN X 76 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059715 restraints weight = 117031.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061368 restraints weight = 83542.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062603 restraints weight = 64716.415| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26640 Z= 0.155 Angle : 0.632 9.312 36420 Z= 0.314 Chirality : 0.048 0.184 4572 Planarity : 0.006 0.042 4680 Dihedral : 4.643 24.147 3780 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3480 helix: 1.48 (0.13), residues: 1320 sheet: -1.36 (0.15), residues: 864 loop : 0.37 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS A 196 PHE 0.013 0.002 PHE Q 162 TYR 0.012 0.001 TYR B 46 ARG 0.006 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 1512) hydrogen bonds : angle 4.68393 ( 4284) covalent geometry : bond 0.00353 (26640) covalent geometry : angle 0.63229 (36420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8855 (tmm) cc_final: 0.7831 (tmm) REVERT: B 17 LYS cc_start: 0.9134 (pttm) cc_final: 0.8870 (pttm) REVERT: B 90 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 97 GLU cc_start: 0.8794 (mp0) cc_final: 0.8521 (mp0) REVERT: C 75 LYS cc_start: 0.9393 (pttm) cc_final: 0.9189 (ptmm) REVERT: D 90 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 97 GLU cc_start: 0.8881 (mp0) cc_final: 0.8617 (mp0) REVERT: E 75 LYS cc_start: 0.9323 (pttm) cc_final: 0.9020 (ptmm) REVERT: E 150 MET cc_start: 0.9043 (tmm) cc_final: 0.8253 (tmm) REVERT: H 90 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8428 (tm-30) REVERT: I 75 LYS cc_start: 0.9479 (ptmm) cc_final: 0.9084 (pttt) REVERT: J 90 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8313 (tm-30) REVERT: K 188 ASP cc_start: 0.8231 (t70) cc_final: 0.8029 (t0) REVERT: L 7 TYR cc_start: 0.8860 (m-10) cc_final: 0.8638 (m-10) REVERT: M 75 LYS cc_start: 0.9322 (pttm) cc_final: 0.9082 (ptmm) REVERT: M 150 MET cc_start: 0.8968 (tmm) cc_final: 0.7974 (tmm) REVERT: N 90 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8416 (tm-30) REVERT: O 42 LYS cc_start: 0.9016 (tmmt) cc_final: 0.8706 (mmtt) REVERT: P 7 TYR cc_start: 0.8878 (m-80) cc_final: 0.8675 (m-10) REVERT: P 90 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8633 (tm-30) REVERT: Q 150 MET cc_start: 0.9033 (tmm) cc_final: 0.8085 (tmm) REVERT: R 7 TYR cc_start: 0.9021 (m-10) cc_final: 0.8787 (m-10) REVERT: R 90 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8345 (tm-30) REVERT: S 42 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8567 (mmmt) REVERT: S 75 LYS cc_start: 0.9453 (pttp) cc_final: 0.9181 (pttt) REVERT: T 90 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8414 (tm-30) REVERT: U 75 LYS cc_start: 0.9361 (pttm) cc_final: 0.9084 (ptmm) REVERT: V 90 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8480 (tm-30) REVERT: W 75 LYS cc_start: 0.9390 (pttm) cc_final: 0.9069 (ptmm) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3735 time to fit residues: 291.4746 Evaluate side-chains 419 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 196 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060700 restraints weight = 114474.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062329 restraints weight = 81569.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063614 restraints weight = 63282.122| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26640 Z= 0.127 Angle : 0.642 6.885 36420 Z= 0.313 Chirality : 0.049 0.190 4572 Planarity : 0.006 0.043 4680 Dihedral : 4.546 23.027 3780 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3480 helix: 1.50 (0.13), residues: 1320 sheet: -1.43 (0.15), residues: 888 loop : 0.50 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS C 196 PHE 0.013 0.002 PHE E 162 TYR 0.012 0.001 TYR L 12 ARG 0.002 0.000 ARG T 40 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1512) hydrogen bonds : angle 4.59132 ( 4284) covalent geometry : bond 0.00296 (26640) covalent geometry : angle 0.64163 (36420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8893 (tmm) cc_final: 0.7857 (tmm) REVERT: B 17 LYS cc_start: 0.9144 (pttm) cc_final: 0.8880 (pttm) REVERT: B 90 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8451 (tm-30) REVERT: B 97 GLU cc_start: 0.8805 (mp0) cc_final: 0.8514 (mp0) REVERT: C 75 LYS cc_start: 0.9397 (pttm) cc_final: 0.9171 (ptmm) REVERT: D 90 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8477 (tm-30) REVERT: D 97 GLU cc_start: 0.8914 (mp0) cc_final: 0.8644 (mp0) REVERT: E 75 LYS cc_start: 0.9328 (pttm) cc_final: 0.9003 (ptmm) REVERT: E 150 MET cc_start: 0.9056 (tmm) cc_final: 0.8189 (tmm) REVERT: F 97 GLU cc_start: 0.8968 (mp0) cc_final: 0.8610 (mp0) REVERT: G 75 LYS cc_start: 0.9463 (ptmm) cc_final: 0.8996 (pttt) REVERT: H 90 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8408 (tm-30) REVERT: I 75 LYS cc_start: 0.9480 (ptmm) cc_final: 0.9094 (pttt) REVERT: J 68 LEU cc_start: 0.8410 (tp) cc_final: 0.8071 (tt) REVERT: J 90 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8253 (tm-30) REVERT: K 75 LYS cc_start: 0.9338 (pttt) cc_final: 0.9026 (ptmm) REVERT: L 7 TYR cc_start: 0.8825 (m-10) cc_final: 0.8610 (m-10) REVERT: M 75 LYS cc_start: 0.9337 (pttm) cc_final: 0.9012 (ptmm) REVERT: N 90 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8399 (tm-30) REVERT: P 90 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8621 (tm-30) REVERT: Q 42 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8729 (mmtt) REVERT: Q 75 LYS cc_start: 0.9291 (pttt) cc_final: 0.9018 (ptmm) REVERT: Q 150 MET cc_start: 0.8228 (tmm) cc_final: 0.7838 (tmm) REVERT: R 7 TYR cc_start: 0.8970 (m-10) cc_final: 0.8707 (m-10) REVERT: R 90 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8325 (tm-30) REVERT: S 75 LYS cc_start: 0.9452 (pttp) cc_final: 0.9188 (pttt) REVERT: T 12 TYR cc_start: 0.8665 (m-10) cc_final: 0.8465 (m-10) REVERT: T 90 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8459 (tm-30) REVERT: U 75 LYS cc_start: 0.9377 (pttm) cc_final: 0.9097 (ptmm) REVERT: V 90 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8491 (tm-30) REVERT: W 75 LYS cc_start: 0.9393 (pttm) cc_final: 0.9061 (ptmm) outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.3816 time to fit residues: 320.9331 Evaluate side-chains 430 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 6 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 40.0000 chunk 287 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN D 76 GLN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.074218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059100 restraints weight = 117234.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060725 restraints weight = 83821.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061974 restraints weight = 65117.767| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 26640 Z= 0.167 Angle : 0.659 8.493 36420 Z= 0.324 Chirality : 0.049 0.184 4572 Planarity : 0.006 0.041 4680 Dihedral : 4.611 24.160 3780 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3480 helix: 1.56 (0.13), residues: 1320 sheet: -1.44 (0.15), residues: 864 loop : 0.49 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 196 PHE 0.012 0.002 PHE I 162 TYR 0.011 0.002 TYR H 46 ARG 0.003 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 1512) hydrogen bonds : angle 4.64682 ( 4284) covalent geometry : bond 0.00380 (26640) covalent geometry : angle 0.65887 (36420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9140 (pttm) cc_final: 0.8897 (pttm) REVERT: B 90 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 97 GLU cc_start: 0.8805 (mp0) cc_final: 0.8533 (mp0) REVERT: C 75 LYS cc_start: 0.9426 (pttm) cc_final: 0.9191 (ptmm) REVERT: D 90 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8444 (tm-30) REVERT: D 97 GLU cc_start: 0.8925 (mp0) cc_final: 0.8667 (mp0) REVERT: E 75 LYS cc_start: 0.9345 (pttm) cc_final: 0.9046 (ptmm) REVERT: F 68 LEU cc_start: 0.8617 (tt) cc_final: 0.8417 (tt) REVERT: H 90 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8397 (tm-30) REVERT: I 75 LYS cc_start: 0.9521 (ptmm) cc_final: 0.9188 (pttt) REVERT: J 90 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8238 (tm-30) REVERT: L 7 TYR cc_start: 0.8860 (m-10) cc_final: 0.8640 (m-10) REVERT: L 90 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8550 (tm-30) REVERT: M 75 LYS cc_start: 0.9329 (pttm) cc_final: 0.9023 (ptmm) REVERT: N 70 GLU cc_start: 0.8796 (mp0) cc_final: 0.8584 (mp0) REVERT: N 90 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8426 (tm-30) REVERT: O 188 ASP cc_start: 0.8669 (t0) cc_final: 0.8468 (t0) REVERT: P 90 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8642 (tm-30) REVERT: Q 75 LYS cc_start: 0.9347 (pttt) cc_final: 0.9079 (ptmm) REVERT: R 7 TYR cc_start: 0.8981 (m-10) cc_final: 0.8719 (m-10) REVERT: R 90 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8368 (tm-30) REVERT: S 42 LYS cc_start: 0.8980 (tmmt) cc_final: 0.8701 (mmtt) REVERT: S 75 LYS cc_start: 0.9465 (pttp) cc_final: 0.9222 (pttt) REVERT: S 150 MET cc_start: 0.8394 (tmm) cc_final: 0.8173 (tmm) REVERT: T 12 TYR cc_start: 0.8715 (m-10) cc_final: 0.8459 (m-10) REVERT: T 90 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8382 (tm-30) REVERT: U 75 LYS cc_start: 0.9394 (pttm) cc_final: 0.9089 (ptmm) REVERT: U 188 ASP cc_start: 0.8389 (t70) cc_final: 0.8186 (t0) REVERT: V 90 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8513 (tm-30) REVERT: W 75 LYS cc_start: 0.9411 (pttm) cc_final: 0.9076 (ptmm) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.3565 time to fit residues: 280.9342 Evaluate side-chains 421 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 280 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 HIS H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 HIS J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 HIS N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 HIS P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 HIS R 76 GLN ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 HIS X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059378 restraints weight = 116690.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060997 restraints weight = 83144.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062251 restraints weight = 64526.817| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26640 Z= 0.143 Angle : 0.657 7.191 36420 Z= 0.321 Chirality : 0.049 0.191 4572 Planarity : 0.006 0.043 4680 Dihedral : 4.545 23.039 3780 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3480 helix: 1.53 (0.13), residues: 1320 sheet: -1.51 (0.15), residues: 888 loop : 0.57 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 196 PHE 0.014 0.002 PHE L 111 TYR 0.013 0.001 TYR J 12 ARG 0.002 0.000 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1512) hydrogen bonds : angle 4.57776 ( 4284) covalent geometry : bond 0.00331 (26640) covalent geometry : angle 0.65657 (36420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9133 (pttm) cc_final: 0.8889 (pttm) REVERT: B 90 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 97 GLU cc_start: 0.8827 (mp0) cc_final: 0.8524 (mp0) REVERT: C 75 LYS cc_start: 0.9433 (pttm) cc_final: 0.9197 (ptmm) REVERT: D 90 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8423 (tm-30) REVERT: D 97 GLU cc_start: 0.8926 (mp0) cc_final: 0.8661 (mp0) REVERT: E 75 LYS cc_start: 0.9347 (pttm) cc_final: 0.9034 (ptmm) REVERT: F 68 LEU cc_start: 0.8634 (tt) cc_final: 0.8427 (tt) REVERT: H 90 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8436 (tm-30) REVERT: I 75 LYS cc_start: 0.9518 (ptmm) cc_final: 0.9136 (pttt) REVERT: J 90 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8248 (tm-30) REVERT: K 42 LYS cc_start: 0.8845 (pptt) cc_final: 0.8467 (pptt) REVERT: K 188 ASP cc_start: 0.8658 (t0) cc_final: 0.8295 (p0) REVERT: L 7 TYR cc_start: 0.8874 (m-10) cc_final: 0.8631 (m-10) REVERT: L 90 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8554 (tm-30) REVERT: M 75 LYS cc_start: 0.9338 (pttm) cc_final: 0.9028 (ptmm) REVERT: N 70 GLU cc_start: 0.8820 (mp0) cc_final: 0.8576 (mp0) REVERT: N 90 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8380 (tm-30) REVERT: O 42 LYS cc_start: 0.8855 (pptt) cc_final: 0.8441 (pptt) REVERT: O 188 ASP cc_start: 0.8583 (t0) cc_final: 0.8356 (t0) REVERT: P 90 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8601 (tm-30) REVERT: Q 75 LYS cc_start: 0.9345 (pttt) cc_final: 0.9105 (ptmm) REVERT: R 7 TYR cc_start: 0.8987 (m-10) cc_final: 0.8692 (m-10) REVERT: R 90 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8337 (tm-30) REVERT: S 75 LYS cc_start: 0.9464 (pttp) cc_final: 0.9239 (pttt) REVERT: S 150 MET cc_start: 0.8360 (tmm) cc_final: 0.8040 (tmm) REVERT: T 12 TYR cc_start: 0.8704 (m-10) cc_final: 0.8461 (m-10) REVERT: T 68 LEU cc_start: 0.8680 (tt) cc_final: 0.8478 (tt) REVERT: T 90 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8454 (tm-30) REVERT: U 75 LYS cc_start: 0.9364 (pttm) cc_final: 0.9080 (ptmm) REVERT: V 90 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8559 (tm-30) REVERT: W 42 LYS cc_start: 0.8956 (pptt) cc_final: 0.8468 (pptt) REVERT: W 75 LYS cc_start: 0.9420 (pttm) cc_final: 0.9077 (ptmm) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.3645 time to fit residues: 288.6784 Evaluate side-chains 431 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 253 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 277 optimal weight: 0.0060 chunk 204 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 333 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 HIS V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.076230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061026 restraints weight = 114754.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062700 restraints weight = 81533.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.063952 restraints weight = 63024.278| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26640 Z= 0.119 Angle : 0.693 8.316 36420 Z= 0.330 Chirality : 0.050 0.198 4572 Planarity : 0.006 0.045 4680 Dihedral : 4.435 22.266 3780 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3480 helix: 1.49 (0.13), residues: 1320 sheet: -1.42 (0.15), residues: 888 loop : 0.64 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS E 196 PHE 0.013 0.002 PHE M 162 TYR 0.014 0.001 TYR J 12 ARG 0.006 0.000 ARG O 66 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 1512) hydrogen bonds : angle 4.52173 ( 4284) covalent geometry : bond 0.00280 (26640) covalent geometry : angle 0.69277 (36420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9103 (pttm) cc_final: 0.8876 (pttm) REVERT: B 90 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 97 GLU cc_start: 0.8803 (mp0) cc_final: 0.8492 (mp0) REVERT: C 75 LYS cc_start: 0.9421 (pttm) cc_final: 0.9198 (ptmm) REVERT: D 90 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 97 GLU cc_start: 0.8853 (mp0) cc_final: 0.8602 (mp0) REVERT: E 75 LYS cc_start: 0.9350 (pttm) cc_final: 0.9028 (ptmm) REVERT: F 97 GLU cc_start: 0.8960 (mp0) cc_final: 0.8581 (mp0) REVERT: H 90 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8354 (tm-30) REVERT: I 75 LYS cc_start: 0.9476 (ptmm) cc_final: 0.9096 (pttt) REVERT: J 68 LEU cc_start: 0.8495 (tp) cc_final: 0.8279 (tp) REVERT: J 90 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8343 (tm-30) REVERT: K 75 LYS cc_start: 0.9314 (pttm) cc_final: 0.8888 (pttt) REVERT: K 188 ASP cc_start: 0.8655 (t0) cc_final: 0.8321 (p0) REVERT: L 7 TYR cc_start: 0.8823 (m-10) cc_final: 0.8596 (m-10) REVERT: L 90 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8458 (tm-30) REVERT: M 75 LYS cc_start: 0.9332 (pttm) cc_final: 0.9013 (ptmm) REVERT: N 90 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8357 (tm-30) REVERT: O 188 ASP cc_start: 0.8485 (t0) cc_final: 0.8230 (t0) REVERT: P 90 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8593 (tm-30) REVERT: Q 75 LYS cc_start: 0.9368 (pttt) cc_final: 0.9139 (pttt) REVERT: R 7 TYR cc_start: 0.8961 (m-10) cc_final: 0.8705 (m-10) REVERT: R 90 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8390 (tm-30) REVERT: S 75 LYS cc_start: 0.9461 (pttp) cc_final: 0.9259 (pttt) REVERT: S 150 MET cc_start: 0.8325 (tmm) cc_final: 0.7952 (tmm) REVERT: T 12 TYR cc_start: 0.8685 (m-10) cc_final: 0.8463 (m-10) REVERT: T 90 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8351 (tm-30) REVERT: U 75 LYS cc_start: 0.9360 (pttm) cc_final: 0.9091 (ptmm) REVERT: U 188 ASP cc_start: 0.8094 (t70) cc_final: 0.7738 (p0) REVERT: V 90 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8518 (tm-30) REVERT: W 75 LYS cc_start: 0.9415 (pttm) cc_final: 0.9089 (ptmm) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.3697 time to fit residues: 320.6092 Evaluate side-chains 442 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 16 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 335 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 129 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 147 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059077 restraints weight = 117189.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060678 restraints weight = 83774.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.061904 restraints weight = 65109.609| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26640 Z= 0.164 Angle : 0.699 7.646 36420 Z= 0.341 Chirality : 0.050 0.192 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.575 24.310 3780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3480 helix: 1.44 (0.13), residues: 1332 sheet: -1.53 (0.15), residues: 888 loop : 0.46 (0.20), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS W 196 PHE 0.014 0.002 PHE E 162 TYR 0.010 0.002 TYR D 12 ARG 0.006 0.001 ARG W 66 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 1512) hydrogen bonds : angle 4.59522 ( 4284) covalent geometry : bond 0.00378 (26640) covalent geometry : angle 0.69873 (36420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9147 (pttm) cc_final: 0.8901 (pttm) REVERT: B 90 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 97 GLU cc_start: 0.8811 (mp0) cc_final: 0.8502 (mp0) REVERT: C 75 LYS cc_start: 0.9411 (pttm) cc_final: 0.9146 (ptmm) REVERT: C 123 PHE cc_start: 0.7723 (t80) cc_final: 0.7500 (t80) REVERT: D 90 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8413 (tm-30) REVERT: D 97 GLU cc_start: 0.8852 (mp0) cc_final: 0.8612 (mp0) REVERT: E 75 LYS cc_start: 0.9348 (pttm) cc_final: 0.9019 (ptmm) REVERT: F 97 GLU cc_start: 0.8956 (mp0) cc_final: 0.8584 (mp0) REVERT: H 90 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8351 (tm-30) REVERT: I 75 LYS cc_start: 0.9501 (ptmm) cc_final: 0.9127 (pttt) REVERT: J 90 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8356 (tm-30) REVERT: K 75 LYS cc_start: 0.9329 (pttm) cc_final: 0.9120 (pttt) REVERT: K 188 ASP cc_start: 0.8690 (t0) cc_final: 0.8295 (p0) REVERT: L 7 TYR cc_start: 0.8865 (m-10) cc_final: 0.8633 (m-10) REVERT: L 90 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8438 (tm-30) REVERT: M 75 LYS cc_start: 0.9319 (pttm) cc_final: 0.9020 (ptmm) REVERT: N 90 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8360 (tm-30) REVERT: O 188 ASP cc_start: 0.8582 (t0) cc_final: 0.8271 (t0) REVERT: P 68 LEU cc_start: 0.8409 (tp) cc_final: 0.8192 (tp) REVERT: P 90 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8562 (tm-30) REVERT: Q 75 LYS cc_start: 0.9375 (pttt) cc_final: 0.9117 (ptmm) REVERT: R 7 TYR cc_start: 0.9010 (m-10) cc_final: 0.8771 (m-10) REVERT: R 90 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8341 (tm-30) REVERT: S 75 LYS cc_start: 0.9464 (pttp) cc_final: 0.9227 (pttt) REVERT: T 12 TYR cc_start: 0.8709 (m-10) cc_final: 0.8420 (m-10) REVERT: T 90 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8444 (tm-30) REVERT: U 75 LYS cc_start: 0.9378 (pttm) cc_final: 0.9098 (ptmm) REVERT: U 188 ASP cc_start: 0.8160 (t70) cc_final: 0.7815 (p0) REVERT: V 90 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8561 (tm-30) REVERT: W 75 LYS cc_start: 0.9423 (pttm) cc_final: 0.9085 (ptmm) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3679 time to fit residues: 297.0726 Evaluate side-chains 432 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 112 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 322 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059349 restraints weight = 116721.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060988 restraints weight = 83049.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062209 restraints weight = 64290.120| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26640 Z= 0.139 Angle : 0.707 7.417 36420 Z= 0.344 Chirality : 0.050 0.196 4572 Planarity : 0.006 0.045 4680 Dihedral : 4.516 25.618 3780 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3480 helix: 1.46 (0.13), residues: 1332 sheet: -1.58 (0.15), residues: 888 loop : 0.48 (0.20), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 196 PHE 0.014 0.002 PHE S 162 TYR 0.011 0.001 TYR T 12 ARG 0.007 0.000 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1512) hydrogen bonds : angle 4.58140 ( 4284) covalent geometry : bond 0.00327 (26640) covalent geometry : angle 0.70672 (36420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8714 (t0) cc_final: 0.8468 (t0) REVERT: B 17 LYS cc_start: 0.9131 (pttm) cc_final: 0.8898 (pttm) REVERT: B 90 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 97 GLU cc_start: 0.8811 (mp0) cc_final: 0.8499 (mp0) REVERT: C 75 LYS cc_start: 0.9393 (pttm) cc_final: 0.9164 (ptmm) REVERT: C 89 ILE cc_start: 0.9198 (mp) cc_final: 0.8517 (mp) REVERT: C 123 PHE cc_start: 0.7730 (t80) cc_final: 0.7347 (t80) REVERT: C 150 MET cc_start: 0.8512 (tmm) cc_final: 0.8235 (tmm) REVERT: D 90 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8424 (tm-30) REVERT: D 97 GLU cc_start: 0.8868 (mp0) cc_final: 0.8616 (mp0) REVERT: E 75 LYS cc_start: 0.9351 (pttm) cc_final: 0.9015 (ptmm) REVERT: F 68 LEU cc_start: 0.8597 (tt) cc_final: 0.8382 (tt) REVERT: F 97 GLU cc_start: 0.8930 (mp0) cc_final: 0.8547 (mp0) REVERT: H 90 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8344 (tm-30) REVERT: I 75 LYS cc_start: 0.9504 (ptmm) cc_final: 0.9128 (pttt) REVERT: J 68 LEU cc_start: 0.8508 (tp) cc_final: 0.8300 (tp) REVERT: J 90 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8314 (tm-30) REVERT: K 75 LYS cc_start: 0.9358 (pttm) cc_final: 0.9086 (pttt) REVERT: K 150 MET cc_start: 0.8374 (tmm) cc_final: 0.8134 (tmm) REVERT: L 90 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8483 (tm-30) REVERT: M 75 LYS cc_start: 0.9312 (pttm) cc_final: 0.9009 (ptmm) REVERT: N 90 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8346 (tm-30) REVERT: O 188 ASP cc_start: 0.8623 (t0) cc_final: 0.8292 (t0) REVERT: P 68 LEU cc_start: 0.8405 (tp) cc_final: 0.8191 (tp) REVERT: P 90 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8555 (tm-30) REVERT: Q 75 LYS cc_start: 0.9354 (pttt) cc_final: 0.9115 (ptmm) REVERT: R 7 TYR cc_start: 0.8951 (m-10) cc_final: 0.8726 (m-10) REVERT: R 90 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8372 (tm-30) REVERT: S 75 LYS cc_start: 0.9469 (pttp) cc_final: 0.9238 (pttt) REVERT: S 150 MET cc_start: 0.8851 (tmm) cc_final: 0.8332 (tmm) REVERT: T 12 TYR cc_start: 0.8687 (m-10) cc_final: 0.8442 (m-10) REVERT: T 90 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8414 (tm-30) REVERT: U 75 LYS cc_start: 0.9382 (pttm) cc_final: 0.9094 (ptmm) REVERT: V 90 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8522 (tm-30) REVERT: W 75 LYS cc_start: 0.9426 (pttm) cc_final: 0.9089 (ptmm) REVERT: X 3 MET cc_start: 0.5063 (tpp) cc_final: 0.4759 (tpp) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.3692 time to fit residues: 302.1968 Evaluate side-chains 431 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 146 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 148 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 292 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060283 restraints weight = 116019.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061948 restraints weight = 82081.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.063193 restraints weight = 63341.555| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26640 Z= 0.123 Angle : 0.718 8.586 36420 Z= 0.344 Chirality : 0.050 0.201 4572 Planarity : 0.006 0.047 4680 Dihedral : 4.474 25.691 3780 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3480 helix: 1.51 (0.13), residues: 1332 sheet: -1.53 (0.16), residues: 888 loop : 0.52 (0.20), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 196 PHE 0.012 0.002 PHE S 162 TYR 0.012 0.002 TYR V 12 ARG 0.007 0.000 ARG U 194 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 1512) hydrogen bonds : angle 4.58052 ( 4284) covalent geometry : bond 0.00294 (26640) covalent geometry : angle 0.71775 (36420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7423.45 seconds wall clock time: 131 minutes 7.11 seconds (7867.11 seconds total)