Starting phenix.real_space_refine on Mon Aug 25 06:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ukm_42355/08_2025/8ukm_42355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ukm_42355/08_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_42355/08_2025/8ukm_42355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ukm_42355/08_2025/8ukm_42355.map" model { file = "/net/cci-nas-00/data/ceres_data/8ukm_42355/08_2025/8ukm_42355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ukm_42355/08_2025/8ukm_42355.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 2.35, per 1000 atoms: 0.09 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: 2.14 Conformation dependent library (CDL) restraints added in 963.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.82 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: 4.47 Time building geometry restraints manager: 2.83 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.640 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.760 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- 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 : 21.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (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 ARG 0.008 0.001 ARG C 19 TYR 0.009 0.002 TYR I 30 PHE 0.013 0.002 PHE K 162 HIS 0.006 0.002 HIS U 196 Details of bonding type rmsd covalent geometry : bond 0.00396 (26640) covalent geometry : angle 0.75177 (36420) hydrogen bonds : bond 0.13240 ( 1512) hydrogen bonds : angle 5.93724 ( 4284) *********************** 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 : 0.836 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: 0.1549 time to fit residues: 125.1722 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 : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.0370 overall best weight: 1.1062 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.078372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062705 restraints weight = 113491.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.064444 restraints weight = 80634.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065738 restraints weight = 62345.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066767 restraints weight = 51139.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067583 restraints weight = 43536.854| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 26640 Z= 0.128 Angle : 0.661 6.699 36420 Z= 0.327 Chirality : 0.048 0.191 4572 Planarity : 0.007 0.047 4680 Dihedral : 4.622 22.079 3780 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.14), residues: 3480 helix: 1.25 (0.13), residues: 1260 sheet: -1.24 (0.15), residues: 864 loop : 0.23 (0.19), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.010 0.001 TYR J 12 PHE 0.015 0.002 PHE X 22 HIS 0.003 0.001 HIS M 98 Details of bonding type rmsd covalent geometry : bond 0.00293 (26640) covalent geometry : angle 0.66090 (36420) hydrogen bonds : bond 0.03922 ( 1512) hydrogen bonds : angle 4.96724 ( 4284) *********************** 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 545 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 541 time to evaluate : 1.108 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: symmetry clash REVERT: A 42 LYS cc_start: 0.8947 (tmmt) cc_final: 0.8608 (mmtt) REVERT: B 17 LYS cc_start: 0.9116 (pttm) cc_final: 0.8889 (pttm) REVERT: B 90 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8445 (tm-30) REVERT: B 97 GLU cc_start: 0.8808 (mp0) cc_final: 0.8568 (mp0) REVERT: C 42 LYS cc_start: 0.9059 (tmmt) cc_final: 0.8679 (mmmm) REVERT: C 75 LYS cc_start: 0.9354 (pttm) cc_final: 0.9130 (ptmm) REVERT: D 90 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 97 GLU cc_start: 0.8907 (mp0) cc_final: 0.8646 (mp0) REVERT: E 75 LYS cc_start: 0.9258 (pttm) cc_final: 0.9013 (ptmm) REVERT: E 150 MET cc_start: 0.9016 (tmm) cc_final: 0.8245 (tmm) REVERT: F 53 LEU cc_start: 0.8859 (tp) cc_final: 0.8413 (tp) REVERT: F 97 GLU cc_start: 0.8879 (mp0) cc_final: 0.8623 (mp0) REVERT: G 75 LYS cc_start: 0.9357 (pttm) cc_final: 0.9087 (pttp) REVERT: H 53 LEU cc_start: 0.8883 (tp) cc_final: 0.8557 (tp) REVERT: H 90 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8370 (tm-30) REVERT: I 42 LYS cc_start: 0.8961 (tmmt) cc_final: 0.8568 (mmmm) REVERT: I 75 LYS cc_start: 0.9409 (ptmm) cc_final: 0.8909 (pttt) REVERT: J 90 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8312 (tm-30) REVERT: K 75 LYS cc_start: 0.9271 (pttm) cc_final: 0.8924 (pttp) REVERT: L 7 TYR cc_start: 0.8907 (m-10) cc_final: 0.8665 (m-10) REVERT: L 53 LEU cc_start: 0.8912 (tp) cc_final: 0.8679 (tp) REVERT: M 75 LYS cc_start: 0.9338 (pttm) cc_final: 0.9118 (ptmm) REVERT: N 90 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8414 (tm-30) REVERT: O 75 LYS cc_start: 0.9373 (pttm) cc_final: 0.9165 (ptmm) REVERT: P 53 LEU cc_start: 0.8895 (tp) cc_final: 0.8539 (tp) REVERT: P 68 LEU cc_start: 0.8308 (tp) cc_final: 0.8090 (tp) REVERT: P 90 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8480 (tm-30) REVERT: Q 75 LYS cc_start: 0.9278 (pttm) cc_final: 0.9046 (ptmm) REVERT: R 7 TYR cc_start: 0.9052 (m-10) cc_final: 0.8823 (m-10) REVERT: R 90 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8333 (tm-30) REVERT: S 75 LYS cc_start: 0.9317 (pttm) cc_final: 0.8977 (pttp) REVERT: S 150 MET cc_start: 0.8926 (tmm) cc_final: 0.8308 (tmm) REVERT: T 17 LYS cc_start: 0.9166 (pttm) cc_final: 0.8938 (pttm) REVERT: T 90 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8358 (tm-30) REVERT: U 38 ASP cc_start: 0.9124 (m-30) cc_final: 0.8479 (m-30) REVERT: U 75 LYS cc_start: 0.9331 (pttm) cc_final: 0.9100 (ptmm) REVERT: V 53 LEU cc_start: 0.8967 (tp) cc_final: 0.8530 (tp) REVERT: V 90 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8557 (tm-30) REVERT: V 97 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9025 (mp0) REVERT: W 75 LYS cc_start: 0.9369 (pttm) cc_final: 0.9106 (ptmm) REVERT: X 53 LEU cc_start: 0.8876 (tp) cc_final: 0.8630 (tp) outliers start: 4 outliers final: 1 residues processed: 542 average time/residue: 0.1853 time to fit residues: 157.2807 Evaluate side-chains 412 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 155 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 157 optimal weight: 50.0000 chunk 120 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.073868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058577 restraints weight = 117050.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.060150 restraints weight = 84210.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061338 restraints weight = 65912.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062240 restraints weight = 54694.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.062960 restraints weight = 47246.388| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26640 Z= 0.223 Angle : 0.684 8.742 36420 Z= 0.344 Chirality : 0.048 0.288 4572 Planarity : 0.007 0.053 4680 Dihedral : 4.892 25.555 3780 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.04 % Allowed : 9.07 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3480 helix: 1.15 (0.13), residues: 1248 sheet: -1.40 (0.15), residues: 888 loop : 0.21 (0.19), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 40 TYR 0.011 0.002 TYR J 12 PHE 0.016 0.002 PHE Q 162 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00494 (26640) covalent geometry : angle 0.68409 (36420) hydrogen bonds : bond 0.04026 ( 1512) hydrogen bonds : angle 4.86782 ( 4284) *********************** 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 482 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8981 (tmmt) cc_final: 0.8636 (mmmm) REVERT: A 188 ASP cc_start: 0.8612 (t0) cc_final: 0.8370 (t0) REVERT: B 17 LYS cc_start: 0.9109 (pttm) cc_final: 0.8850 (pttm) REVERT: B 53 LEU cc_start: 0.8969 (tp) cc_final: 0.8591 (tp) REVERT: B 90 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 97 GLU cc_start: 0.8750 (mp0) cc_final: 0.8486 (mp0) REVERT: C 42 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8699 (mmmm) REVERT: C 75 LYS cc_start: 0.9403 (pttm) cc_final: 0.9180 (ptmm) REVERT: C 188 ASP cc_start: 0.8384 (t0) cc_final: 0.8134 (t0) REVERT: D 90 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 97 GLU cc_start: 0.8881 (mp0) cc_final: 0.8620 (mp0) REVERT: E 75 LYS cc_start: 0.9304 (pttm) cc_final: 0.9004 (ptmm) REVERT: E 188 ASP cc_start: 0.8524 (t0) cc_final: 0.8311 (t0) REVERT: G 42 LYS cc_start: 0.9086 (tmmt) cc_final: 0.8658 (mmmm) REVERT: H 90 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8365 (tm-30) REVERT: I 42 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8657 (mmmm) REVERT: J 53 LEU cc_start: 0.8860 (tp) cc_final: 0.8579 (tp) REVERT: J 90 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8357 (tm-30) REVERT: K 42 LYS cc_start: 0.8957 (tmmt) cc_final: 0.8693 (mmmm) REVERT: K 75 LYS cc_start: 0.9321 (pttm) cc_final: 0.9075 (pttt) REVERT: L 7 TYR cc_start: 0.8938 (m-10) cc_final: 0.8725 (m-10) REVERT: M 42 LYS cc_start: 0.9042 (tmmt) cc_final: 0.8659 (mmmm) REVERT: M 75 LYS cc_start: 0.9308 (pttm) cc_final: 0.9070 (ptmm) REVERT: M 150 MET cc_start: 0.9050 (tmm) cc_final: 0.8200 (tmm) REVERT: N 90 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8482 (tm-30) REVERT: O 42 LYS cc_start: 0.9000 (tmmt) cc_final: 0.8718 (mmmm) REVERT: O 75 LYS cc_start: 0.9392 (pttm) cc_final: 0.9188 (ptmm) REVERT: P 90 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8495 (tm-30) REVERT: Q 75 LYS cc_start: 0.9333 (pttm) cc_final: 0.9093 (ptmm) REVERT: Q 150 MET cc_start: 0.9036 (tmm) cc_final: 0.8082 (tmm) REVERT: R 7 TYR cc_start: 0.9061 (m-10) cc_final: 0.8791 (m-10) REVERT: R 90 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8337 (tm-30) REVERT: S 42 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8261 (mmmm) REVERT: S 75 LYS cc_start: 0.9389 (pttm) cc_final: 0.9153 (pttt) REVERT: S 150 MET cc_start: 0.8599 (tmm) cc_final: 0.8170 (tmm) REVERT: T 17 LYS cc_start: 0.9165 (pttm) cc_final: 0.8915 (pttm) REVERT: T 50 ASP cc_start: 0.8534 (t0) cc_final: 0.8316 (t0) REVERT: T 53 LEU cc_start: 0.8964 (tp) cc_final: 0.8678 (tp) REVERT: T 90 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8318 (tm-30) REVERT: U 75 LYS cc_start: 0.9365 (pttm) cc_final: 0.9102 (ptmm) REVERT: V 90 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8506 (tm-30) REVERT: W 42 LYS cc_start: 0.9047 (tmmt) cc_final: 0.8724 (mmtt) REVERT: W 75 LYS cc_start: 0.9375 (pttm) cc_final: 0.9095 (ptmm) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.1653 time to fit residues: 124.6644 Evaluate side-chains 403 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ** 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 = 0.3442 r_free = 0.3442 target = 0.075383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060196 restraints weight = 115644.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061860 restraints weight = 82443.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063062 restraints weight = 63889.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064112 restraints weight = 52316.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064812 restraints weight = 44794.077| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26640 Z= 0.135 Angle : 0.646 6.766 36420 Z= 0.316 Chirality : 0.048 0.188 4572 Planarity : 0.006 0.043 4680 Dihedral : 4.669 23.423 3780 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.14), residues: 3480 helix: 1.44 (0.13), residues: 1320 sheet: -1.31 (0.16), residues: 864 loop : 0.36 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.011 0.001 TYR B 46 PHE 0.014 0.002 PHE E 162 HIS 0.009 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00312 (26640) covalent geometry : angle 0.64583 (36420) hydrogen bonds : bond 0.03551 ( 1512) hydrogen bonds : angle 4.67215 ( 4284) *********************** 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 500 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8573 (t0) cc_final: 0.8325 (t0) REVERT: B 17 LYS cc_start: 0.9144 (pttm) cc_final: 0.8859 (pttm) REVERT: B 90 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 97 GLU cc_start: 0.8794 (mp0) cc_final: 0.8530 (mp0) REVERT: C 75 LYS cc_start: 0.9392 (pttm) cc_final: 0.9158 (ptmm) REVERT: C 188 ASP cc_start: 0.8348 (t0) cc_final: 0.8118 (t0) REVERT: D 90 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8445 (tm-30) REVERT: D 97 GLU cc_start: 0.8865 (mp0) cc_final: 0.8599 (mp0) REVERT: E 75 LYS cc_start: 0.9328 (pttm) cc_final: 0.9011 (ptmm) REVERT: E 150 MET cc_start: 0.8995 (tmm) cc_final: 0.8245 (tmm) REVERT: E 188 ASP cc_start: 0.8526 (t0) cc_final: 0.8317 (t0) REVERT: F 97 GLU cc_start: 0.8987 (mp0) cc_final: 0.8656 (mp0) REVERT: G 75 LYS cc_start: 0.9334 (pttt) cc_final: 0.9097 (pttp) REVERT: H 68 LEU cc_start: 0.8408 (tp) cc_final: 0.8156 (tt) REVERT: H 90 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8388 (tm-30) REVERT: I 75 LYS cc_start: 0.9486 (ptmm) cc_final: 0.9102 (pttt) REVERT: J 90 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8281 (tm-30) REVERT: K 75 LYS cc_start: 0.9355 (pttm) cc_final: 0.9086 (pttt) REVERT: L 7 TYR cc_start: 0.8869 (m-10) cc_final: 0.8643 (m-10) REVERT: N 90 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8384 (tm-30) REVERT: O 75 LYS cc_start: 0.9415 (pttm) cc_final: 0.9194 (pttt) REVERT: P 90 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8581 (tm-30) REVERT: R 7 TYR cc_start: 0.9036 (m-10) cc_final: 0.8810 (m-10) REVERT: R 90 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8325 (tm-30) REVERT: S 75 LYS cc_start: 0.9366 (pttm) cc_final: 0.9074 (pttt) REVERT: S 150 MET cc_start: 0.8615 (tmm) cc_final: 0.8105 (tmm) REVERT: T 17 LYS cc_start: 0.9163 (pttm) cc_final: 0.8940 (pttm) REVERT: T 50 ASP cc_start: 0.8597 (t0) cc_final: 0.8360 (t0) REVERT: T 90 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8380 (tm-30) REVERT: U 75 LYS cc_start: 0.9357 (pttm) cc_final: 0.9059 (ptmm) REVERT: U 188 ASP cc_start: 0.8256 (t70) cc_final: 0.8034 (t0) REVERT: V 50 ASP cc_start: 0.8502 (t0) cc_final: 0.8301 (t0) REVERT: V 90 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8446 (tm-30) REVERT: W 75 LYS cc_start: 0.9389 (pttm) cc_final: 0.9054 (ptmm) REVERT: W 188 ASP cc_start: 0.8523 (t0) cc_final: 0.8301 (t0) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1546 time to fit residues: 122.1191 Evaluate side-chains 420 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 306 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 34 optimal weight: 0.0980 chunk 287 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.075528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060488 restraints weight = 114370.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062110 restraints weight = 81409.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063386 restraints weight = 63285.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064368 restraints weight = 51817.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065114 restraints weight = 44249.297| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26640 Z= 0.134 Angle : 0.633 7.654 36420 Z= 0.312 Chirality : 0.048 0.189 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.569 23.649 3780 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.14), residues: 3480 helix: 1.42 (0.13), residues: 1320 sheet: -1.44 (0.15), residues: 888 loop : 0.54 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.012 0.001 TYR L 46 PHE 0.013 0.002 PHE E 162 HIS 0.007 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00313 (26640) covalent geometry : angle 0.63298 (36420) hydrogen bonds : bond 0.03395 ( 1512) hydrogen bonds : angle 4.60704 ( 4284) *********************** 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 522 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.026 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: A 188 ASP cc_start: 0.8601 (t0) cc_final: 0.8383 (t0) REVERT: B 17 LYS cc_start: 0.9146 (pttm) cc_final: 0.8903 (pttm) REVERT: B 90 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8424 (tm-30) REVERT: B 97 GLU cc_start: 0.8749 (mp0) cc_final: 0.8470 (mp0) REVERT: C 75 LYS cc_start: 0.9399 (pttm) cc_final: 0.9154 (ptmm) REVERT: D 90 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8440 (tm-30) REVERT: D 97 GLU cc_start: 0.8855 (mp0) cc_final: 0.8588 (mp0) REVERT: E 75 LYS cc_start: 0.9341 (pttm) cc_final: 0.9008 (ptmm) REVERT: E 150 MET cc_start: 0.9067 (tmm) cc_final: 0.8230 (tmm) REVERT: E 188 ASP cc_start: 0.8505 (t0) cc_final: 0.8285 (t0) REVERT: H 90 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8351 (tm-30) REVERT: I 75 LYS cc_start: 0.9480 (ptmm) cc_final: 0.9094 (pttt) REVERT: I 188 ASP cc_start: 0.8198 (t70) cc_final: 0.7970 (t0) REVERT: J 70 GLU cc_start: 0.8437 (mp0) cc_final: 0.8219 (mp0) REVERT: J 90 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8220 (tm-30) REVERT: K 75 LYS cc_start: 0.9369 (pttm) cc_final: 0.9059 (pttt) REVERT: L 7 TYR cc_start: 0.8842 (m-10) cc_final: 0.8549 (m-10) REVERT: M 75 LYS cc_start: 0.9273 (pttm) cc_final: 0.9024 (ptmm) REVERT: M 150 MET cc_start: 0.8985 (tmm) cc_final: 0.7934 (tmm) REVERT: N 90 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8339 (tm-30) REVERT: O 75 LYS cc_start: 0.9411 (pttm) cc_final: 0.9179 (pttt) REVERT: O 188 ASP cc_start: 0.8273 (t70) cc_final: 0.8067 (t0) REVERT: P 68 LEU cc_start: 0.8251 (tp) cc_final: 0.8049 (tp) REVERT: P 90 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8553 (tm-30) REVERT: Q 75 LYS cc_start: 0.9294 (pttt) cc_final: 0.9014 (ptmm) REVERT: R 7 TYR cc_start: 0.9037 (m-10) cc_final: 0.8739 (m-10) REVERT: R 70 GLU cc_start: 0.8703 (mp0) cc_final: 0.8496 (mp0) REVERT: R 90 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8272 (tm-30) REVERT: S 42 LYS cc_start: 0.8947 (tmmt) cc_final: 0.8616 (mmtt) REVERT: S 75 LYS cc_start: 0.9361 (pttm) cc_final: 0.9061 (pttt) REVERT: S 150 MET cc_start: 0.8673 (tmm) cc_final: 0.8089 (tmm) REVERT: T 50 ASP cc_start: 0.8630 (t0) cc_final: 0.8359 (t0) REVERT: T 90 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8402 (tm-30) REVERT: U 75 LYS cc_start: 0.9368 (pttm) cc_final: 0.9062 (ptmm) REVERT: V 90 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8443 (tm-30) REVERT: W 75 LYS cc_start: 0.9400 (pttm) cc_final: 0.9053 (ptmm) REVERT: W 188 ASP cc_start: 0.8544 (t0) cc_final: 0.8266 (t0) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.1700 time to fit residues: 138.7827 Evaluate side-chains 426 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 332 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 334 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 76 GLN ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 HIS H 76 GLN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 HIS J 76 GLN ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 HIS N 76 GLN ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 HIS 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057243 restraints weight = 118996.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058780 restraints weight = 85593.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059960 restraints weight = 67011.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060867 restraints weight = 55435.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061431 restraints weight = 47744.650| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26640 Z= 0.247 Angle : 0.722 10.219 36420 Z= 0.361 Chirality : 0.050 0.186 4572 Planarity : 0.007 0.050 4680 Dihedral : 4.923 26.298 3780 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3480 helix: 1.33 (0.13), residues: 1296 sheet: -1.56 (0.15), residues: 864 loop : 0.58 (0.20), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 19 TYR 0.012 0.002 TYR N 46 PHE 0.013 0.003 PHE O 162 HIS 0.006 0.002 HIS O 196 Details of bonding type rmsd covalent geometry : bond 0.00541 (26640) covalent geometry : angle 0.72214 (36420) hydrogen bonds : bond 0.03850 ( 1512) hydrogen bonds : angle 4.81535 ( 4284) *********************** 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 480 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.843 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: A 188 ASP cc_start: 0.8691 (t0) cc_final: 0.8348 (t0) REVERT: B 17 LYS cc_start: 0.9146 (pttm) cc_final: 0.8892 (pttm) REVERT: B 50 ASP cc_start: 0.8601 (t0) cc_final: 0.8400 (t0) REVERT: B 90 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8431 (tm-30) REVERT: B 97 GLU cc_start: 0.8806 (mp0) cc_final: 0.8566 (mp0) REVERT: C 75 LYS cc_start: 0.9437 (pttm) cc_final: 0.9200 (ptmm) REVERT: D 90 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 97 GLU cc_start: 0.8910 (mp0) cc_final: 0.8677 (mp0) REVERT: E 75 LYS cc_start: 0.9363 (pttm) cc_final: 0.9057 (ptmm) REVERT: E 188 ASP cc_start: 0.8547 (t0) cc_final: 0.8299 (t0) REVERT: G 75 LYS cc_start: 0.9368 (pttt) cc_final: 0.9132 (ptmm) REVERT: G 150 MET cc_start: 0.9002 (tmm) cc_final: 0.8642 (tmm) REVERT: H 90 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8338 (tm-30) REVERT: I 75 LYS cc_start: 0.9500 (ptmm) cc_final: 0.9163 (pttt) REVERT: J 90 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8226 (tm-30) REVERT: K 42 LYS cc_start: 0.8910 (pptt) cc_final: 0.8527 (pptt) REVERT: K 75 LYS cc_start: 0.9382 (pttm) cc_final: 0.9122 (pttt) REVERT: L 7 TYR cc_start: 0.8840 (m-10) cc_final: 0.8604 (m-10) REVERT: M 75 LYS cc_start: 0.9309 (pttm) cc_final: 0.9073 (ptmm) REVERT: N 90 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8361 (tm-30) REVERT: O 75 LYS cc_start: 0.9406 (pttm) cc_final: 0.9119 (ptmm) REVERT: O 150 MET cc_start: 0.9077 (tmm) cc_final: 0.8651 (tmm) REVERT: O 188 ASP cc_start: 0.8323 (t70) cc_final: 0.8102 (t0) REVERT: P 90 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8531 (tm-30) REVERT: Q 75 LYS cc_start: 0.9346 (pttt) cc_final: 0.9082 (ptmm) REVERT: R 7 TYR cc_start: 0.8993 (m-10) cc_final: 0.8666 (m-10) REVERT: R 90 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8291 (tm-30) REVERT: S 75 LYS cc_start: 0.9396 (pttm) cc_final: 0.9123 (pttt) REVERT: S 150 MET cc_start: 0.8792 (tmm) cc_final: 0.8110 (tmm) REVERT: T 50 ASP cc_start: 0.8601 (t0) cc_final: 0.8332 (t0) REVERT: T 90 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8360 (tm-30) REVERT: U 75 LYS cc_start: 0.9333 (pttm) cc_final: 0.9015 (ptmm) REVERT: V 90 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8462 (tm-30) REVERT: W 75 LYS cc_start: 0.9433 (pttm) cc_final: 0.9100 (ptmm) REVERT: W 188 ASP cc_start: 0.8638 (t0) cc_final: 0.8294 (t0) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.1621 time to fit residues: 123.9224 Evaluate side-chains 411 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 212 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** 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** K 155 HIS 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 155 HIS R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** U 155 HIS 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059314 restraints weight = 115313.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060891 restraints weight = 83042.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.062086 restraints weight = 64826.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063041 restraints weight = 53568.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063789 restraints weight = 45885.781| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2667 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= 0.146 Angle : 0.677 7.690 36420 Z= 0.331 Chirality : 0.050 0.187 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.709 23.205 3780 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3480 helix: 1.43 (0.13), residues: 1308 sheet: -1.51 (0.15), residues: 864 loop : 0.50 (0.20), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.012 0.002 TYR I 30 PHE 0.015 0.002 PHE G 162 HIS 0.004 0.001 HIS O 196 Details of bonding type rmsd covalent geometry : bond 0.00341 (26640) covalent geometry : angle 0.67682 (36420) hydrogen bonds : bond 0.03430 ( 1512) hydrogen bonds : angle 4.62912 ( 4284) *********************** 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 508 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.873 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: A 188 ASP cc_start: 0.8617 (t0) cc_final: 0.8309 (t0) REVERT: B 17 LYS cc_start: 0.9123 (pttm) cc_final: 0.8878 (pttm) REVERT: B 50 ASP cc_start: 0.8628 (t0) cc_final: 0.8424 (t0) REVERT: B 90 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 97 GLU cc_start: 0.8797 (mp0) cc_final: 0.8515 (mp0) REVERT: C 75 LYS cc_start: 0.9433 (pttm) cc_final: 0.9173 (ptmm) REVERT: C 150 MET cc_start: 0.8521 (tmm) cc_final: 0.8280 (tmm) REVERT: D 90 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8419 (tm-30) REVERT: D 97 GLU cc_start: 0.8834 (mp0) cc_final: 0.8604 (mp0) REVERT: E 75 LYS cc_start: 0.9374 (pttm) cc_final: 0.9039 (ptmm) REVERT: G 75 LYS cc_start: 0.9336 (pttt) cc_final: 0.9031 (pttp) REVERT: H 90 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8307 (tm-30) REVERT: I 52 LYS cc_start: 0.8595 (mptt) cc_final: 0.8314 (mmtt) REVERT: I 75 LYS cc_start: 0.9496 (ptmm) cc_final: 0.9114 (pttt) REVERT: J 68 LEU cc_start: 0.8524 (tp) cc_final: 0.8268 (tt) REVERT: J 90 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8169 (tm-30) REVERT: K 75 LYS cc_start: 0.9385 (pttm) cc_final: 0.9087 (pttt) REVERT: L 7 TYR cc_start: 0.8855 (m-10) cc_final: 0.8614 (m-10) REVERT: M 75 LYS cc_start: 0.9304 (pttm) cc_final: 0.8981 (ptmm) REVERT: N 68 LEU cc_start: 0.8585 (tp) cc_final: 0.8328 (tt) REVERT: N 90 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8304 (tm-30) REVERT: O 42 LYS cc_start: 0.8821 (pptt) cc_final: 0.8424 (pptt) REVERT: O 75 LYS cc_start: 0.9446 (pttm) cc_final: 0.9196 (ptmm) REVERT: O 188 ASP cc_start: 0.8187 (t70) cc_final: 0.7980 (t0) REVERT: P 90 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8566 (tm-30) REVERT: Q 75 LYS cc_start: 0.9348 (pttt) cc_final: 0.9094 (ptmm) REVERT: R 7 TYR cc_start: 0.9003 (m-10) cc_final: 0.8681 (m-10) REVERT: R 90 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8268 (tm-30) REVERT: S 75 LYS cc_start: 0.9374 (pttm) cc_final: 0.9124 (pttt) REVERT: S 150 MET cc_start: 0.8774 (tmm) cc_final: 0.8050 (tmm) REVERT: T 50 ASP cc_start: 0.8614 (t0) cc_final: 0.8393 (t0) REVERT: T 90 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8347 (tm-30) REVERT: U 75 LYS cc_start: 0.9369 (pttm) cc_final: 0.9071 (ptmm) REVERT: V 90 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8472 (tm-30) REVERT: W 42 LYS cc_start: 0.8896 (pptt) cc_final: 0.8332 (pptt) REVERT: W 75 LYS cc_start: 0.9442 (pttm) cc_final: 0.9083 (ptmm) REVERT: W 188 ASP cc_start: 0.8506 (t0) cc_final: 0.8253 (t0) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.1664 time to fit residues: 134.4771 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 299 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 107 optimal weight: 0.0470 chunk 252 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 307 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- 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** ** I 98 HIS ** 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** ** 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** 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 = 0.3432 r_free = 0.3432 target = 0.074814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059962 restraints weight = 114691.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061511 restraints weight = 82447.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062764 restraints weight = 64147.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063712 restraints weight = 52669.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.064476 restraints weight = 45012.137| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26640 Z= 0.125 Angle : 0.688 7.343 36420 Z= 0.331 Chirality : 0.050 0.195 4572 Planarity : 0.006 0.046 4680 Dihedral : 4.581 24.092 3780 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.14), residues: 3480 helix: 1.34 (0.13), residues: 1320 sheet: -1.55 (0.15), residues: 888 loop : 0.55 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 40 TYR 0.012 0.001 TYR D 46 PHE 0.013 0.002 PHE Q 162 HIS 0.006 0.001 HIS S 196 Details of bonding type rmsd covalent geometry : bond 0.00294 (26640) covalent geometry : angle 0.68822 (36420) hydrogen bonds : bond 0.03325 ( 1512) hydrogen bonds : angle 4.55390 ( 4284) *********************** 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 511 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 0.727 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: A 42 LYS cc_start: 0.9044 (tmmt) cc_final: 0.8732 (tttp) REVERT: A 188 ASP cc_start: 0.8488 (t0) cc_final: 0.8281 (t0) REVERT: B 17 LYS cc_start: 0.9100 (pttm) cc_final: 0.8860 (pttm) REVERT: B 50 ASP cc_start: 0.8557 (t0) cc_final: 0.8319 (t0) REVERT: B 90 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8409 (tm-30) REVERT: B 97 GLU cc_start: 0.8793 (mp0) cc_final: 0.8499 (mp0) REVERT: C 75 LYS cc_start: 0.9410 (pttm) cc_final: 0.9142 (ptmm) REVERT: C 150 MET cc_start: 0.8491 (tmm) cc_final: 0.8226 (tmm) REVERT: D 90 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 97 GLU cc_start: 0.8817 (mp0) cc_final: 0.8587 (mp0) REVERT: E 75 LYS cc_start: 0.9375 (pttm) cc_final: 0.9041 (ptmm) REVERT: F 68 LEU cc_start: 0.8696 (tt) cc_final: 0.8487 (tt) REVERT: H 90 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8379 (tm-30) REVERT: I 75 LYS cc_start: 0.9462 (ptmm) cc_final: 0.9080 (pttt) REVERT: J 12 TYR cc_start: 0.8656 (m-10) cc_final: 0.8416 (m-10) REVERT: J 90 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8216 (tm-30) REVERT: K 75 LYS cc_start: 0.9333 (pttm) cc_final: 0.9034 (pttt) REVERT: L 7 TYR cc_start: 0.8849 (m-10) cc_final: 0.8538 (m-10) REVERT: M 75 LYS cc_start: 0.9291 (pttm) cc_final: 0.8960 (ptmm) REVERT: N 90 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8289 (tm-30) REVERT: O 75 LYS cc_start: 0.9414 (pttm) cc_final: 0.9111 (ptmm) REVERT: O 188 ASP cc_start: 0.8103 (t70) cc_final: 0.7878 (t0) REVERT: P 90 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8564 (tm-30) REVERT: R 7 TYR cc_start: 0.9014 (m-10) cc_final: 0.8732 (m-10) REVERT: R 90 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8313 (tm-30) REVERT: S 75 LYS cc_start: 0.9387 (pttm) cc_final: 0.9164 (pttt) REVERT: S 150 MET cc_start: 0.8743 (tmm) cc_final: 0.8036 (tmm) REVERT: T 50 ASP cc_start: 0.8707 (t0) cc_final: 0.8481 (t0) REVERT: T 90 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8376 (tm-30) REVERT: U 75 LYS cc_start: 0.9366 (pttm) cc_final: 0.9071 (ptmm) REVERT: U 188 ASP cc_start: 0.8345 (t70) cc_final: 0.8139 (t0) REVERT: V 90 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8465 (tm-30) REVERT: W 75 LYS cc_start: 0.9443 (pttm) cc_final: 0.9086 (ptmm) REVERT: W 188 ASP cc_start: 0.8560 (t0) cc_final: 0.8267 (t0) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.1558 time to fit residues: 126.7045 Evaluate side-chains 423 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 26 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 247 optimal weight: 0.4980 chunk 161 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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** ** 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** ** K 196 HIS ** 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** ** 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 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 = 0.3418 r_free = 0.3418 target = 0.074020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059296 restraints weight = 116435.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060843 restraints weight = 83657.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.062062 restraints weight = 65091.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063000 restraints weight = 53601.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063714 restraints weight = 45961.555| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2873 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= 0.152 Angle : 0.700 7.687 36420 Z= 0.342 Chirality : 0.050 0.192 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.606 24.377 3780 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3480 helix: 1.39 (0.13), residues: 1332 sheet: -1.59 (0.15), residues: 888 loop : 0.45 (0.20), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 66 TYR 0.010 0.002 TYR X 12 PHE 0.013 0.002 PHE A 162 HIS 0.006 0.001 HIS O 196 Details of bonding type rmsd covalent geometry : bond 0.00353 (26640) covalent geometry : angle 0.69954 (36420) hydrogen bonds : bond 0.03445 ( 1512) hydrogen bonds : angle 4.61046 ( 4284) *********************** 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 510 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 1.074 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: A 188 ASP cc_start: 0.8521 (t0) cc_final: 0.8299 (t0) REVERT: B 17 LYS cc_start: 0.9116 (pttm) cc_final: 0.8868 (pttm) REVERT: B 50 ASP cc_start: 0.8590 (t0) cc_final: 0.8367 (t0) REVERT: B 90 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8323 (tm-30) REVERT: B 97 GLU cc_start: 0.8773 (mp0) cc_final: 0.8494 (mp0) REVERT: C 75 LYS cc_start: 0.9386 (pttm) cc_final: 0.9127 (ptmm) REVERT: C 150 MET cc_start: 0.8535 (tmm) cc_final: 0.8210 (tmm) REVERT: D 90 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8405 (tm-30) REVERT: D 97 GLU cc_start: 0.8803 (mp0) cc_final: 0.8578 (mp0) REVERT: E 42 LYS cc_start: 0.8665 (tptt) cc_final: 0.8457 (tptt) REVERT: E 75 LYS cc_start: 0.9377 (pttm) cc_final: 0.9044 (ptmm) REVERT: F 68 LEU cc_start: 0.8724 (tt) cc_final: 0.8512 (tt) REVERT: G 75 LYS cc_start: 0.9211 (pttp) cc_final: 0.9010 (ptmm) REVERT: H 68 LEU cc_start: 0.8341 (tp) cc_final: 0.8141 (tp) REVERT: H 90 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8224 (tm-30) REVERT: I 52 LYS cc_start: 0.8588 (mptt) cc_final: 0.8309 (mmtt) REVERT: I 75 LYS cc_start: 0.9483 (ptmm) cc_final: 0.9110 (pttt) REVERT: J 12 TYR cc_start: 0.8697 (m-10) cc_final: 0.8416 (m-10) REVERT: J 90 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8226 (tm-30) REVERT: K 75 LYS cc_start: 0.9340 (pttm) cc_final: 0.9050 (pttt) REVERT: K 150 MET cc_start: 0.8443 (tmm) cc_final: 0.8230 (tmm) REVERT: L 7 TYR cc_start: 0.8868 (m-10) cc_final: 0.8610 (m-10) REVERT: M 75 LYS cc_start: 0.9284 (pttm) cc_final: 0.8948 (ptmm) REVERT: N 90 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8298 (tm-30) REVERT: O 75 LYS cc_start: 0.9413 (pttm) cc_final: 0.9118 (ptmm) REVERT: O 188 ASP cc_start: 0.8102 (t70) cc_final: 0.7883 (t70) REVERT: P 90 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8564 (tm-30) REVERT: Q 75 LYS cc_start: 0.9290 (pttt) cc_final: 0.9005 (ptmm) REVERT: R 7 TYR cc_start: 0.8987 (m-10) cc_final: 0.8685 (m-10) REVERT: R 90 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8299 (tm-30) REVERT: S 75 LYS cc_start: 0.9383 (pttm) cc_final: 0.9146 (pttt) REVERT: S 150 MET cc_start: 0.8770 (tmm) cc_final: 0.8065 (tmm) REVERT: T 90 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8395 (tm-30) REVERT: U 75 LYS cc_start: 0.9377 (pttm) cc_final: 0.9092 (ptmm) REVERT: U 150 MET cc_start: 0.8460 (tmm) cc_final: 0.8214 (tmm) REVERT: V 90 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8466 (tm-30) REVERT: W 75 LYS cc_start: 0.9435 (pttm) cc_final: 0.9087 (ptmm) REVERT: W 188 ASP cc_start: 0.8596 (t0) cc_final: 0.8307 (t0) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.1683 time to fit residues: 135.4436 Evaluate side-chains 415 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 191 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 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 ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** 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** 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** 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** ** 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** 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 = 0.3405 r_free = 0.3405 target = 0.073359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058507 restraints weight = 116841.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060067 restraints weight = 83128.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.061304 restraints weight = 64370.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062236 restraints weight = 53031.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.062978 restraints weight = 45455.980| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26640 Z= 0.167 Angle : 0.719 7.954 36420 Z= 0.355 Chirality : 0.051 0.193 4572 Planarity : 0.006 0.043 4680 Dihedral : 4.655 26.420 3780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3480 helix: 1.42 (0.13), residues: 1332 sheet: -1.59 (0.15), residues: 900 loop : 0.49 (0.20), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 194 TYR 0.013 0.002 TYR S 30 PHE 0.013 0.002 PHE S 162 HIS 0.006 0.001 HIS O 196 Details of bonding type rmsd covalent geometry : bond 0.00383 (26640) covalent geometry : angle 0.71887 (36420) hydrogen bonds : bond 0.03595 ( 1512) hydrogen bonds : angle 4.68616 ( 4284) ********************** 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 505 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.9127 (tmmt) cc_final: 0.8742 (tttp) REVERT: A 188 ASP cc_start: 0.8524 (t0) cc_final: 0.8272 (t0) REVERT: B 17 LYS cc_start: 0.9132 (pttm) cc_final: 0.8888 (pttm) REVERT: B 50 ASP cc_start: 0.8646 (t0) cc_final: 0.8356 (t0) REVERT: B 90 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 97 GLU cc_start: 0.8793 (mp0) cc_final: 0.8505 (mp0) REVERT: C 75 LYS cc_start: 0.9387 (pttm) cc_final: 0.9140 (ptmm) REVERT: C 123 PHE cc_start: 0.7851 (t80) cc_final: 0.7434 (t80) REVERT: C 150 MET cc_start: 0.8571 (tmm) cc_final: 0.8174 (tmm) REVERT: D 90 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 97 GLU cc_start: 0.8826 (mp0) cc_final: 0.8595 (mp0) REVERT: E 42 LYS cc_start: 0.8662 (tptt) cc_final: 0.8452 (tptt) REVERT: E 75 LYS cc_start: 0.9370 (pttm) cc_final: 0.9030 (ptmm) REVERT: F 70 GLU cc_start: 0.8457 (mp0) cc_final: 0.8216 (mp0) REVERT: F 97 GLU cc_start: 0.8928 (mp0) cc_final: 0.8557 (mp0) REVERT: H 90 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8207 (tm-30) REVERT: I 52 LYS cc_start: 0.8620 (mptt) cc_final: 0.8372 (mmtt) REVERT: I 75 LYS cc_start: 0.9484 (ptmm) cc_final: 0.9113 (pttt) REVERT: I 188 ASP cc_start: 0.8751 (p0) cc_final: 0.8373 (p0) REVERT: J 12 TYR cc_start: 0.8669 (m-10) cc_final: 0.8435 (m-10) REVERT: J 90 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8228 (tm-30) REVERT: K 75 LYS cc_start: 0.9349 (pttm) cc_final: 0.9051 (pttt) REVERT: K 150 MET cc_start: 0.8498 (tmm) cc_final: 0.8221 (tmm) REVERT: L 7 TYR cc_start: 0.8897 (m-10) cc_final: 0.8640 (m-10) REVERT: M 75 LYS cc_start: 0.9285 (pttm) cc_final: 0.8954 (ptmm) REVERT: N 90 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8309 (tm-30) REVERT: O 75 LYS cc_start: 0.9345 (pttm) cc_final: 0.9043 (ptmm) REVERT: P 68 LEU cc_start: 0.8329 (tp) cc_final: 0.8123 (tp) REVERT: P 90 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8533 (tm-30) REVERT: Q 75 LYS cc_start: 0.9300 (pttt) cc_final: 0.8999 (ptmm) REVERT: R 7 TYR cc_start: 0.8979 (m-10) cc_final: 0.8684 (m-10) REVERT: R 90 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8278 (tm-30) REVERT: S 75 LYS cc_start: 0.9388 (pttm) cc_final: 0.9158 (pttt) REVERT: S 150 MET cc_start: 0.8783 (tmm) cc_final: 0.8092 (tmm) REVERT: T 90 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8377 (tm-30) REVERT: U 75 LYS cc_start: 0.9387 (pttm) cc_final: 0.9100 (ptmm) REVERT: U 150 MET cc_start: 0.8506 (tmm) cc_final: 0.8147 (tmm) REVERT: V 53 LEU cc_start: 0.8781 (tp) cc_final: 0.8572 (tp) REVERT: V 90 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8479 (tm-30) REVERT: W 42 LYS cc_start: 0.8883 (pptt) cc_final: 0.8311 (pptt) REVERT: W 75 LYS cc_start: 0.9437 (pttm) cc_final: 0.9081 (ptmm) REVERT: W 188 ASP cc_start: 0.8578 (t0) cc_final: 0.8271 (t0) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.1640 time to fit residues: 131.1045 Evaluate side-chains 407 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 244 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 121 optimal weight: 0.0050 chunk 195 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- 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** 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** ** K 196 HIS ** 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** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 HIS ** 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 = 0.3399 r_free = 0.3399 target = 0.073232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058824 restraints weight = 118659.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060379 restraints weight = 84638.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061597 restraints weight = 65777.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.062518 restraints weight = 53941.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063248 restraints weight = 46053.532| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26640 Z= 0.148 Angle : 0.707 7.998 36420 Z= 0.347 Chirality : 0.051 0.197 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.630 26.198 3780 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 3480 helix: 1.42 (0.13), residues: 1332 sheet: -1.61 (0.15), residues: 900 loop : 0.51 (0.20), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 194 TYR 0.012 0.002 TYR V 12 PHE 0.013 0.002 PHE S 162 HIS 0.006 0.001 HIS O 196 Details of bonding type rmsd covalent geometry : bond 0.00345 (26640) covalent geometry : angle 0.70727 (36420) hydrogen bonds : bond 0.03524 ( 1512) hydrogen bonds : angle 4.67039 ( 4284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.13 seconds wall clock time: 62 minutes 11.58 seconds (3731.58 seconds total)