Starting phenix.real_space_refine on Tue Nov 19 09:23:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynm_39427/11_2024/8ynm_39427.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynm_39427/11_2024/8ynm_39427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynm_39427/11_2024/8ynm_39427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynm_39427/11_2024/8ynm_39427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynm_39427/11_2024/8ynm_39427.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynm_39427/11_2024/8ynm_39427.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4446 atoms to isotropic. 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 90 5.16 5 C 9955 2.51 5 N 2687 2.21 5 O 2931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15663 Number of models: 1 Model: "" Number of chains: 11 Chain: "O" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1306 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 3, 'TRANS': 157} Chain breaks: 1 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "H" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1403 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain breaks: 1 Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "F" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "N" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1380 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Time building chain proxies: 9.64, per 1000 atoms: 0.62 Number of scatterers: 15663 At special positions: 0 Unit cell: (110.88, 107.52, 152.04, 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 90 16.00 O 2931 8.00 N 2687 7.00 C 9955 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: 4.00 Conformation dependent library (CDL) restraints added in 1.8 seconds 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3714 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'O' and resid 1 through 13 removed outlier: 3.616A pdb=" N ILE O 6 " --> pdb=" O SER O 2 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 11 " --> pdb=" O HIS O 7 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA O 12 " --> pdb=" O GLN O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 25 Processing helix chain 'O' and resid 36 through 48 removed outlier: 3.508A pdb=" N ASP O 42 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 63 removed outlier: 3.901A pdb=" N LEU O 58 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 73 Processing helix chain 'O' and resid 91 through 104 removed outlier: 3.772A pdb=" N VAL O 95 " --> pdb=" O SER O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 116 removed outlier: 3.646A pdb=" N VAL O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER O 110 " --> pdb=" O LYS O 106 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 126 Processing helix chain 'O' and resid 130 through 141 removed outlier: 3.504A pdb=" N LEU O 141 " --> pdb=" O GLU O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 159 Processing helix chain 'O' and resid 161 through 175 removed outlier: 3.902A pdb=" N LYS O 165 " --> pdb=" O ARG O 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL O 175 " --> pdb=" O TYR O 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.688A pdb=" N GLN A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.576A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.537A pdb=" N ILE A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.563A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 99 through 111 Processing helix chain 'A' and resid 113 through 123 Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.572A pdb=" N LYS A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.826A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.667A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.943A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.616A pdb=" N LYS B 132 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.873A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.528A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.912A pdb=" N LEU C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 157 through 166 removed outlier: 3.788A pdb=" N GLN C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'H' and resid 3 through 11 removed outlier: 3.611A pdb=" N HIS H 7 " --> pdb=" O ALA H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 47 Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 64 through 71 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 117 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.572A pdb=" N ILE H 125 " --> pdb=" O GLY H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.502A pdb=" N LEU H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 159 removed outlier: 3.681A pdb=" N ILE H 159 " --> pdb=" O CYS H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 175 removed outlier: 3.793A pdb=" N LYS H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 removed outlier: 3.555A pdb=" N ILE I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 62 removed outlier: 3.574A pdb=" N VAL I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 91 through 102 removed outlier: 3.639A pdb=" N VAL I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 175 removed outlier: 4.035A pdb=" N LYS I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 removed outlier: 3.582A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 25 Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 51 through 62 Processing helix chain 'J' and resid 64 through 71 removed outlier: 3.750A pdb=" N LEU J 68 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 removed outlier: 3.513A pdb=" N VAL J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 104 removed outlier: 3.572A pdb=" N VAL J 95 " --> pdb=" O SER J 91 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 removed outlier: 3.559A pdb=" N SER J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 120 No H-bonds generated for 'chain 'J' and resid 118 through 120' Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.640A pdb=" N LYS J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 removed outlier: 3.728A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU K 13 " --> pdb=" O VAL K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 51 through 62 removed outlier: 3.663A pdb=" N VAL K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 71 removed outlier: 3.633A pdb=" N LEU K 68 " --> pdb=" O ARG K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 91 through 104 removed outlier: 3.627A pdb=" N VAL K 95 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 116 removed outlier: 4.137A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.889A pdb=" N ILE K 125 " --> pdb=" O GLY K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 162 through 175 removed outlier: 3.585A pdb=" N VAL K 175 " --> pdb=" O TYR K 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.668A pdb=" N ILE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.930A pdb=" N GLU G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 47 Processing helix chain 'G' and resid 51 through 63 Processing helix chain 'G' and resid 64 through 71 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 91 through 102 Processing helix chain 'G' and resid 105 through 116 removed outlier: 3.632A pdb=" N SER G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 161 through 175 removed outlier: 3.908A pdb=" N LYS G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.945A pdb=" N ILE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 26 Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 64 through 71 removed outlier: 3.711A pdb=" N LEU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 105 through 121 removed outlier: 5.132A pdb=" N ASP F 118 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 removed outlier: 3.605A pdb=" N LEU F 141 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.566A pdb=" N ILE F 159 " --> pdb=" O CYS F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 175 removed outlier: 3.877A pdb=" N LYS F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 removed outlier: 4.322A pdb=" N ILE N 6 " --> pdb=" O SER N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 25 removed outlier: 3.540A pdb=" N LYS N 18 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 48 Processing helix chain 'N' and resid 51 through 63 removed outlier: 3.577A pdb=" N ALA N 56 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU N 57 " --> pdb=" O GLY N 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU N 58 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 59 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 71 removed outlier: 3.719A pdb=" N LYS N 69 " --> pdb=" O PHE N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 86 removed outlier: 3.575A pdb=" N VAL N 79 " --> pdb=" O ASP N 75 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 84 " --> pdb=" O GLU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 103 removed outlier: 3.620A pdb=" N VAL N 95 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 116 removed outlier: 3.574A pdb=" N VAL N 109 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER N 110 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 141 Processing helix chain 'N' and resid 149 through 159 Processing helix chain 'N' and resid 162 through 175 870 hydrogen bonds defined for protein. 2598 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: 4.09 Time building geometry restraints manager: 4.57 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: 5233 1.34 - 1.46: 1909 1.46 - 1.57: 8521 1.57 - 1.69: 0 1.69 - 1.81: 158 Bond restraints: 15821 Sorted by residual: bond pdb=" CA VAL F 33 " pdb=" CB VAL F 33 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 7.16e-01 bond pdb=" CA ILE F 159 " pdb=" C ILE F 159 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.12e-02 7.97e+03 5.21e-01 bond pdb=" C ILE C 151 " pdb=" O ILE C 151 " ideal model delta sigma weight residual 1.235 1.225 0.009 1.45e-02 4.76e+03 4.19e-01 bond pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 1.526 1.533 -0.007 1.03e-02 9.43e+03 4.06e-01 bond pdb=" CA LEU C 152 " pdb=" CB LEU C 152 " ideal model delta sigma weight residual 1.523 1.514 0.009 1.35e-02 5.49e+03 4.06e-01 ... (remaining 15816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 20811 1.16 - 2.33: 309 2.33 - 3.49: 60 3.49 - 4.66: 12 4.66 - 5.82: 3 Bond angle restraints: 21195 Sorted by residual: angle pdb=" N ILE O 159 " pdb=" CA ILE O 159 " pdb=" C ILE O 159 " ideal model delta sigma weight residual 112.29 109.56 2.73 9.40e-01 1.13e+00 8.42e+00 angle pdb=" C ARG B 149 " pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 121.97 126.36 -4.39 1.80e+00 3.09e-01 5.94e+00 angle pdb=" C ARG A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.40e+00 angle pdb=" C ARG C 149 " pdb=" N VAL C 150 " pdb=" CA VAL C 150 " ideal model delta sigma weight residual 121.97 126.01 -4.04 1.80e+00 3.09e-01 5.05e+00 angle pdb=" C LEU O 72 " pdb=" N LYS O 73 " pdb=" CA LYS O 73 " ideal model delta sigma weight residual 121.54 125.75 -4.21 1.91e+00 2.74e-01 4.87e+00 ... (remaining 21190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8996 17.95 - 35.91: 922 35.91 - 53.86: 99 53.86 - 71.81: 25 71.81 - 89.76: 9 Dihedral angle restraints: 10051 sinusoidal: 4390 harmonic: 5661 Sorted by residual: dihedral pdb=" CG ARG A 82 " pdb=" CD ARG A 82 " pdb=" NE ARG A 82 " pdb=" CZ ARG A 82 " ideal model delta sinusoidal sigma weight residual -90.00 -133.61 43.61 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA ARG O 122 " pdb=" CB ARG O 122 " pdb=" CG ARG O 122 " pdb=" CD ARG O 122 " ideal model delta sinusoidal sigma weight residual -180.00 -120.72 -59.28 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET G 97 " pdb=" CG MET G 97 " pdb=" SD MET G 97 " pdb=" CE MET G 97 " ideal model delta sinusoidal sigma weight residual 180.00 121.49 58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 10048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1587 0.027 - 0.053: 603 0.053 - 0.080: 225 0.080 - 0.107: 56 0.107 - 0.134: 13 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CB VAL A 150 " pdb=" CA VAL A 150 " pdb=" CG1 VAL A 150 " pdb=" CG2 VAL A 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CB VAL H 62 " pdb=" CA VAL H 62 " pdb=" CG1 VAL H 62 " pdb=" CG2 VAL H 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CB VAL C 150 " pdb=" CA VAL C 150 " pdb=" CG1 VAL C 150 " pdb=" CG2 VAL C 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 2481 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 145 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.45e+00 pdb=" N PRO H 146 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO H 34 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 145 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO F 146 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 146 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 146 " 0.016 5.00e-02 4.00e+02 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3204 2.78 - 3.31: 15157 3.31 - 3.84: 23835 3.84 - 4.37: 26868 4.37 - 4.90: 46495 Nonbonded interactions: 115559 Sorted by model distance: nonbonded pdb=" OH TYR C 29 " pdb=" O GLN C 97 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 29 " pdb=" O GLN A 97 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU C 50 " pdb=" NH1 ARG K 122 " model vdw 2.252 3.120 nonbonded pdb=" OE2 GLU B 89 " pdb=" NH1 ARG B 95 " model vdw 2.265 3.120 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.266 3.040 ... (remaining 115554 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'F' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 12 \ 1 or resid 128 through 175)) selection = (chain 'G' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 12 \ 1 or resid 128 through 175)) selection = (chain 'H' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 12 \ 1 or resid 128 through 175)) selection = (chain 'I' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 17 \ 5)) selection = (chain 'J' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 12 \ 1 or resid 128 through 175)) selection = (chain 'K' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 12 \ 1 or resid 128 through 175)) selection = (chain 'N' and (resid 2 through 28 or resid 37 through 74 or resid 89 through 12 \ 1 or resid 128 through 175)) selection = (chain 'O' and (resid 2 through 28 or resid 37 through 121 or resid 128 through \ 175)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.330 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.002 0.030 15821 Z= 0.145 Angle : 0.395 5.824 21195 Z= 0.216 Chirality : 0.034 0.134 2484 Planarity : 0.003 0.030 2682 Dihedral : 13.834 89.764 6337 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1881 helix: 1.88 (0.15), residues: 1372 sheet: None (None), residues: 0 loop : -0.91 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 82 PHE 0.007 0.001 PHE A 120 TYR 0.009 0.001 TYR K 171 ARG 0.003 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5936 (ttt-90) cc_final: 0.5404 (mtm-85) REVERT: O 102 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8196 (mm-30) REVERT: O 142 ASN cc_start: 0.8793 (t0) cc_final: 0.8553 (t0) REVERT: O 148 GLN cc_start: 0.7389 (tt0) cc_final: 0.7095 (tm-30) REVERT: A 12 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7861 (tt0) REVERT: A 43 MET cc_start: 0.8427 (mmm) cc_final: 0.8197 (mmp) REVERT: B 80 ASN cc_start: 0.9134 (t0) cc_final: 0.8640 (p0) REVERT: B 101 TYR cc_start: 0.7716 (t80) cc_final: 0.7513 (t80) REVERT: B 104 MET cc_start: 0.8919 (tmm) cc_final: 0.8694 (tmm) REVERT: B 111 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 101 TYR cc_start: 0.8038 (t80) cc_final: 0.7626 (t80) REVERT: C 124 LEU cc_start: 0.8709 (mt) cc_final: 0.8450 (tp) REVERT: C 125 GLN cc_start: 0.8707 (mt0) cc_final: 0.7909 (tp40) REVERT: H 16 ASP cc_start: 0.8622 (p0) cc_final: 0.7881 (m-30) REVERT: H 39 ASP cc_start: 0.9306 (m-30) cc_final: 0.9093 (m-30) REVERT: H 130 SER cc_start: 0.8664 (t) cc_final: 0.8321 (p) REVERT: I 1 MET cc_start: 0.7960 (ttm) cc_final: 0.7611 (tpt) REVERT: I 17 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8639 (mt-10) REVERT: I 39 ASP cc_start: 0.7742 (t0) cc_final: 0.7461 (t0) REVERT: I 142 ASN cc_start: 0.9195 (t0) cc_final: 0.8959 (t0) REVERT: I 153 GLU cc_start: 0.8662 (tt0) cc_final: 0.8333 (tm-30) REVERT: J 57 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8471 (tt0) REVERT: J 102 GLU cc_start: 0.8656 (tp30) cc_final: 0.8389 (tp30) REVERT: K 106 LYS cc_start: 0.8955 (mttt) cc_final: 0.8741 (mmmt) REVERT: G 19 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8443 (mp0) REVERT: G 43 ILE cc_start: 0.9314 (mm) cc_final: 0.9079 (mt) REVERT: G 99 GLU cc_start: 0.9018 (tt0) cc_final: 0.8443 (tm-30) REVERT: G 102 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7773 (pt0) REVERT: F 44 LEU cc_start: 0.9203 (tp) cc_final: 0.8938 (tp) REVERT: N 119 TYR cc_start: 0.8153 (m-80) cc_final: 0.7759 (m-10) REVERT: N 158 ASN cc_start: 0.8251 (m-40) cc_final: 0.7864 (m110) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.3284 time to fit residues: 177.4668 Evaluate side-chains 223 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15821 Z= 0.240 Angle : 0.544 7.474 21195 Z= 0.282 Chirality : 0.037 0.171 2484 Planarity : 0.004 0.064 2682 Dihedral : 3.559 13.641 2089 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.06 % Allowed : 9.28 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.20), residues: 1881 helix: 1.71 (0.14), residues: 1413 sheet: None (None), residues: 0 loop : -0.90 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.011 0.001 PHE C 120 TYR 0.013 0.001 TYR N 93 ARG 0.007 0.000 ARG O 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 1.864 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: O 38 ARG cc_start: 0.5729 (ttt-90) cc_final: 0.5290 (mtm-85) REVERT: O 102 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8294 (mm-30) REVERT: O 142 ASN cc_start: 0.8848 (t0) cc_final: 0.8608 (t0) REVERT: O 148 GLN cc_start: 0.7422 (tt0) cc_final: 0.7178 (tm-30) REVERT: A 12 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7932 (tt0) REVERT: A 43 MET cc_start: 0.8444 (mmm) cc_final: 0.8198 (mmp) REVERT: B 80 ASN cc_start: 0.9068 (t0) cc_final: 0.8575 (p0) REVERT: B 86 MET cc_start: 0.8481 (mmm) cc_final: 0.8256 (tpp) REVERT: B 104 MET cc_start: 0.8928 (tmm) cc_final: 0.8665 (tmm) REVERT: B 111 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 125 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8674 (mm-40) REVERT: B 137 MET cc_start: 0.8209 (mtt) cc_final: 0.7942 (mtp) REVERT: B 166 GLN cc_start: 0.8774 (mp10) cc_final: 0.8545 (mp10) REVERT: B 168 ASN cc_start: 0.7784 (t0) cc_final: 0.7401 (t0) REVERT: C 29 TYR cc_start: 0.8980 (m-10) cc_final: 0.8757 (m-10) REVERT: C 43 MET cc_start: 0.8605 (mmm) cc_final: 0.8397 (mtp) REVERT: C 125 GLN cc_start: 0.8696 (mt0) cc_final: 0.8198 (tp40) REVERT: C 146 MET cc_start: 0.8679 (mtm) cc_final: 0.8374 (mtm) REVERT: H 14 ASP cc_start: 0.8546 (m-30) cc_final: 0.8087 (m-30) REVERT: H 16 ASP cc_start: 0.8517 (p0) cc_final: 0.7918 (m-30) REVERT: H 39 ASP cc_start: 0.9310 (m-30) cc_final: 0.9100 (m-30) REVERT: I 1 MET cc_start: 0.8028 (ttm) cc_final: 0.7770 (tpt) REVERT: I 17 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8581 (mp0) REVERT: I 39 ASP cc_start: 0.7704 (t0) cc_final: 0.7501 (t0) REVERT: I 54 ASP cc_start: 0.8663 (t0) cc_final: 0.8422 (t0) REVERT: I 84 LEU cc_start: 0.8922 (mt) cc_final: 0.8704 (pp) REVERT: I 153 GLU cc_start: 0.8528 (tt0) cc_final: 0.8124 (tm-30) REVERT: J 102 GLU cc_start: 0.8628 (tp30) cc_final: 0.8413 (tp30) REVERT: K 10 GLU cc_start: 0.8983 (tt0) cc_final: 0.8618 (tm-30) REVERT: K 116 MET cc_start: 0.8525 (mtm) cc_final: 0.8123 (mtt) REVERT: G 102 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7806 (pt0) REVERT: F 44 LEU cc_start: 0.9019 (tp) cc_final: 0.8709 (tp) REVERT: N 119 TYR cc_start: 0.7994 (m-80) cc_final: 0.7634 (m-10) REVERT: N 158 ASN cc_start: 0.8220 (m-40) cc_final: 0.7877 (m110) outliers start: 19 outliers final: 11 residues processed: 253 average time/residue: 0.2848 time to fit residues: 106.9963 Evaluate side-chains 221 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 158 ASN Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 82 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15821 Z= 0.227 Angle : 0.512 6.798 21195 Z= 0.267 Chirality : 0.036 0.173 2484 Planarity : 0.003 0.044 2682 Dihedral : 3.568 14.229 2089 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 12.14 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1881 helix: 1.77 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -0.88 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.019 0.001 PHE C 181 TYR 0.017 0.001 TYR C 101 ARG 0.007 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5669 (ttt-90) cc_final: 0.5216 (mtm-85) REVERT: O 102 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8370 (mm-30) REVERT: O 142 ASN cc_start: 0.8861 (t0) cc_final: 0.8605 (t0) REVERT: O 148 GLN cc_start: 0.7433 (tt0) cc_final: 0.7210 (tm-30) REVERT: A 12 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7930 (tt0) REVERT: A 43 MET cc_start: 0.8449 (mmm) cc_final: 0.8215 (mmp) REVERT: B 80 ASN cc_start: 0.9085 (t0) cc_final: 0.8593 (p0) REVERT: B 104 MET cc_start: 0.8947 (tmm) cc_final: 0.8690 (tmm) REVERT: B 137 MET cc_start: 0.8135 (mtt) cc_final: 0.7843 (mtm) REVERT: B 166 GLN cc_start: 0.8817 (mp10) cc_final: 0.8533 (mp10) REVERT: B 168 ASN cc_start: 0.7800 (t0) cc_final: 0.7340 (t0) REVERT: C 124 LEU cc_start: 0.8508 (tp) cc_final: 0.8201 (tp) REVERT: C 125 GLN cc_start: 0.8668 (mt0) cc_final: 0.8226 (tp40) REVERT: C 137 MET cc_start: 0.7792 (mtp) cc_final: 0.7500 (ttm) REVERT: C 146 MET cc_start: 0.8684 (mtm) cc_final: 0.8282 (mtm) REVERT: H 14 ASP cc_start: 0.8536 (m-30) cc_final: 0.8124 (m-30) REVERT: H 16 ASP cc_start: 0.8590 (p0) cc_final: 0.8044 (m-30) REVERT: H 39 ASP cc_start: 0.9307 (m-30) cc_final: 0.9075 (m-30) REVERT: I 1 MET cc_start: 0.8037 (ttm) cc_final: 0.7798 (tpt) REVERT: I 17 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8596 (mt-10) REVERT: I 39 ASP cc_start: 0.7678 (t0) cc_final: 0.7467 (t0) REVERT: I 54 ASP cc_start: 0.8732 (t0) cc_final: 0.8528 (t0) REVERT: I 153 GLU cc_start: 0.8500 (tt0) cc_final: 0.8087 (tm-30) REVERT: J 102 GLU cc_start: 0.8636 (tp30) cc_final: 0.8431 (tp30) REVERT: J 106 LYS cc_start: 0.9074 (tppt) cc_final: 0.8685 (tppt) REVERT: K 10 GLU cc_start: 0.8961 (tt0) cc_final: 0.8619 (tm-30) REVERT: K 173 GLN cc_start: 0.8991 (tt0) cc_final: 0.8658 (tm-30) REVERT: G 8 GLN cc_start: 0.7566 (mt0) cc_final: 0.7338 (mt0) REVERT: G 102 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7799 (pt0) REVERT: F 44 LEU cc_start: 0.9087 (tp) cc_final: 0.8867 (tp) REVERT: N 119 TYR cc_start: 0.8098 (m-80) cc_final: 0.7825 (m-10) REVERT: N 158 ASN cc_start: 0.8240 (m-40) cc_final: 0.7891 (m110) outliers start: 22 outliers final: 15 residues processed: 234 average time/residue: 0.2667 time to fit residues: 93.8891 Evaluate side-chains 218 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 82 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15821 Z= 0.216 Angle : 0.499 8.756 21195 Z= 0.261 Chirality : 0.036 0.184 2484 Planarity : 0.003 0.041 2682 Dihedral : 3.537 14.329 2089 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.62 % Allowed : 13.48 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1881 helix: 1.81 (0.15), residues: 1404 sheet: None (None), residues: 0 loop : -0.94 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.010 0.001 PHE A 120 TYR 0.011 0.001 TYR K 171 ARG 0.005 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5718 (ttt-90) cc_final: 0.5246 (mtm-85) REVERT: O 102 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8394 (mm-30) REVERT: O 142 ASN cc_start: 0.8869 (t0) cc_final: 0.8609 (t0) REVERT: O 148 GLN cc_start: 0.7442 (tt0) cc_final: 0.7215 (tm-30) REVERT: A 12 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7946 (tt0) REVERT: A 43 MET cc_start: 0.8489 (mmm) cc_final: 0.8236 (mmp) REVERT: B 80 ASN cc_start: 0.9079 (t0) cc_final: 0.8620 (p0) REVERT: B 104 MET cc_start: 0.8931 (tmm) cc_final: 0.8696 (tmm) REVERT: B 137 MET cc_start: 0.8114 (mtt) cc_final: 0.7833 (mtm) REVERT: B 146 MET cc_start: 0.7690 (mmm) cc_final: 0.7379 (mtt) REVERT: B 166 GLN cc_start: 0.8820 (mp10) cc_final: 0.8500 (mp10) REVERT: B 168 ASN cc_start: 0.7710 (t0) cc_final: 0.7260 (t0) REVERT: C 43 MET cc_start: 0.8425 (mtp) cc_final: 0.8188 (mtp) REVERT: C 125 GLN cc_start: 0.8662 (mt0) cc_final: 0.8165 (tp40) REVERT: C 146 MET cc_start: 0.8682 (mtm) cc_final: 0.8290 (mtm) REVERT: H 14 ASP cc_start: 0.8539 (m-30) cc_final: 0.8157 (m-30) REVERT: H 16 ASP cc_start: 0.8525 (p0) cc_final: 0.8131 (m-30) REVERT: H 39 ASP cc_start: 0.9274 (m-30) cc_final: 0.9042 (m-30) REVERT: I 1 MET cc_start: 0.8038 (ttm) cc_final: 0.7798 (tpt) REVERT: I 17 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8572 (mp0) REVERT: I 39 ASP cc_start: 0.7685 (t0) cc_final: 0.7469 (t0) REVERT: I 153 GLU cc_start: 0.8495 (tt0) cc_final: 0.8064 (tm-30) REVERT: I 173 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: J 102 GLU cc_start: 0.8595 (tp30) cc_final: 0.8381 (tp30) REVERT: J 106 LYS cc_start: 0.9060 (tppt) cc_final: 0.8703 (tppt) REVERT: K 10 GLU cc_start: 0.8965 (tt0) cc_final: 0.8604 (tm-30) REVERT: K 173 GLN cc_start: 0.8985 (tt0) cc_final: 0.8652 (tm-30) REVERT: G 57 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8207 (tm-30) REVERT: G 102 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7809 (pt0) REVERT: F 44 LEU cc_start: 0.9104 (tp) cc_final: 0.8889 (tp) REVERT: N 119 TYR cc_start: 0.8123 (m-80) cc_final: 0.7851 (m-10) outliers start: 29 outliers final: 19 residues processed: 231 average time/residue: 0.2731 time to fit residues: 94.8731 Evaluate side-chains 223 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain N residue 168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN C 91 GLN I 86 ASN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15821 Z= 0.282 Angle : 0.545 6.660 21195 Z= 0.282 Chirality : 0.038 0.203 2484 Planarity : 0.003 0.043 2682 Dihedral : 3.668 14.644 2089 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.01 % Allowed : 14.93 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1881 helix: 1.78 (0.15), residues: 1408 sheet: None (None), residues: 0 loop : -1.02 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.015 0.001 PHE O 114 TYR 0.013 0.001 TYR C 106 ARG 0.004 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5737 (ttt-90) cc_final: 0.5178 (mtm-85) REVERT: O 120 MET cc_start: 0.8117 (ppp) cc_final: 0.7576 (ppp) REVERT: O 142 ASN cc_start: 0.8889 (t0) cc_final: 0.8649 (t0) REVERT: A 12 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7946 (tt0) REVERT: A 43 MET cc_start: 0.8538 (mmm) cc_final: 0.8245 (mmp) REVERT: B 80 ASN cc_start: 0.9077 (t0) cc_final: 0.8656 (p0) REVERT: B 104 MET cc_start: 0.8915 (tmm) cc_final: 0.8690 (tmm) REVERT: B 166 GLN cc_start: 0.8817 (mp10) cc_final: 0.8477 (mp10) REVERT: B 168 ASN cc_start: 0.7763 (t0) cc_final: 0.7299 (t0) REVERT: C 43 MET cc_start: 0.8470 (mtp) cc_final: 0.8257 (mtp) REVERT: C 125 GLN cc_start: 0.8660 (mt0) cc_final: 0.8268 (tp40) REVERT: C 146 MET cc_start: 0.8752 (mtm) cc_final: 0.8358 (mtm) REVERT: H 14 ASP cc_start: 0.8546 (m-30) cc_final: 0.8290 (m-30) REVERT: H 16 ASP cc_start: 0.8459 (p0) cc_final: 0.8254 (m-30) REVERT: H 39 ASP cc_start: 0.9274 (m-30) cc_final: 0.9024 (m-30) REVERT: I 1 MET cc_start: 0.8038 (ttm) cc_final: 0.7736 (tpt) REVERT: I 17 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8546 (mp0) REVERT: I 39 ASP cc_start: 0.7707 (t0) cc_final: 0.7485 (t0) REVERT: I 140 LYS cc_start: 0.8665 (tppt) cc_final: 0.8428 (mttt) REVERT: I 153 GLU cc_start: 0.8519 (tt0) cc_final: 0.8077 (tm-30) REVERT: I 173 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8253 (tm-30) REVERT: J 106 LYS cc_start: 0.9059 (tppt) cc_final: 0.8748 (tppt) REVERT: J 132 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8048 (mm) REVERT: K 10 GLU cc_start: 0.9004 (tt0) cc_final: 0.8626 (tm-30) REVERT: K 173 GLN cc_start: 0.9004 (tt0) cc_final: 0.8678 (tm-30) REVERT: G 102 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7827 (pt0) REVERT: F 44 LEU cc_start: 0.9121 (tp) cc_final: 0.8912 (tp) REVERT: F 74 MET cc_start: 0.8001 (tpt) cc_final: 0.7574 (tpt) REVERT: F 116 MET cc_start: 0.7317 (mmp) cc_final: 0.6976 (mmt) outliers start: 36 outliers final: 26 residues processed: 236 average time/residue: 0.2772 time to fit residues: 97.9192 Evaluate side-chains 234 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain N residue 168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN C 91 GLN F 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15821 Z= 0.197 Angle : 0.504 7.454 21195 Z= 0.263 Chirality : 0.036 0.209 2484 Planarity : 0.003 0.039 2682 Dihedral : 3.592 14.025 2089 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 15.88 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1881 helix: 1.84 (0.15), residues: 1411 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.025 0.001 PHE O 114 TYR 0.011 0.001 TYR C 106 ARG 0.005 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5768 (ttt-90) cc_final: 0.5202 (mtm-85) REVERT: O 120 MET cc_start: 0.8083 (ppp) cc_final: 0.7519 (ppp) REVERT: A 12 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7919 (tt0) REVERT: A 43 MET cc_start: 0.8515 (mmm) cc_final: 0.8239 (mmp) REVERT: B 80 ASN cc_start: 0.9038 (t0) cc_final: 0.8682 (p0) REVERT: B 104 MET cc_start: 0.8926 (tmm) cc_final: 0.8711 (tmm) REVERT: B 166 GLN cc_start: 0.8819 (mp10) cc_final: 0.8469 (mp10) REVERT: B 168 ASN cc_start: 0.7717 (t0) cc_final: 0.7252 (t0) REVERT: C 43 MET cc_start: 0.8451 (mtp) cc_final: 0.8250 (mtp) REVERT: C 125 GLN cc_start: 0.8652 (mt0) cc_final: 0.8302 (tp40) REVERT: C 146 MET cc_start: 0.8673 (mtm) cc_final: 0.8257 (mtm) REVERT: H 14 ASP cc_start: 0.8464 (m-30) cc_final: 0.8121 (m-30) REVERT: H 16 ASP cc_start: 0.8469 (p0) cc_final: 0.8268 (m-30) REVERT: H 39 ASP cc_start: 0.9265 (m-30) cc_final: 0.9042 (m-30) REVERT: H 86 ASN cc_start: 0.7580 (m-40) cc_final: 0.7339 (m-40) REVERT: I 1 MET cc_start: 0.8026 (ttm) cc_final: 0.7748 (tpt) REVERT: I 17 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8545 (mp0) REVERT: I 39 ASP cc_start: 0.7685 (t0) cc_final: 0.7460 (t0) REVERT: I 140 LYS cc_start: 0.8679 (tppt) cc_final: 0.8439 (mttt) REVERT: I 153 GLU cc_start: 0.8482 (tt0) cc_final: 0.8009 (tm-30) REVERT: I 173 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8262 (tm-30) REVERT: J 17 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7527 (mt-10) REVERT: J 106 LYS cc_start: 0.9024 (tppt) cc_final: 0.8731 (tppt) REVERT: J 132 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8016 (mm) REVERT: K 10 GLU cc_start: 0.8954 (tt0) cc_final: 0.8615 (tm-30) REVERT: K 173 GLN cc_start: 0.8983 (tt0) cc_final: 0.8651 (tm-30) REVERT: G 102 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7815 (pt0) REVERT: G 116 MET cc_start: 0.8516 (mmm) cc_final: 0.8270 (mmm) REVERT: F 44 LEU cc_start: 0.9104 (tp) cc_final: 0.8886 (tp) REVERT: N 17 GLU cc_start: 0.8346 (tt0) cc_final: 0.7991 (mt-10) outliers start: 38 outliers final: 25 residues processed: 248 average time/residue: 0.2631 time to fit residues: 98.0612 Evaluate side-chains 239 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 169 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 102 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 148 GLN I 82 HIS F 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15821 Z= 0.147 Angle : 0.483 7.146 21195 Z= 0.253 Chirality : 0.035 0.214 2484 Planarity : 0.003 0.060 2682 Dihedral : 3.469 14.516 2089 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.45 % Allowed : 17.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1881 helix: 1.94 (0.15), residues: 1412 sheet: None (None), residues: 0 loop : -1.09 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS F 82 PHE 0.023 0.001 PHE O 114 TYR 0.017 0.001 TYR O 93 ARG 0.008 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5773 (ttt-90) cc_final: 0.5263 (mtm-85) REVERT: O 120 MET cc_start: 0.8126 (ppp) cc_final: 0.7492 (ppp) REVERT: A 12 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7881 (tt0) REVERT: A 43 MET cc_start: 0.8446 (mmm) cc_final: 0.8184 (mmp) REVERT: B 80 ASN cc_start: 0.9028 (t0) cc_final: 0.8764 (p0) REVERT: B 104 MET cc_start: 0.8906 (tmm) cc_final: 0.8683 (tmm) REVERT: B 137 MET cc_start: 0.8079 (mtt) cc_final: 0.7828 (mtm) REVERT: B 166 GLN cc_start: 0.8834 (mp10) cc_final: 0.8479 (mp10) REVERT: C 43 MET cc_start: 0.8394 (mtp) cc_final: 0.8132 (mtm) REVERT: C 125 GLN cc_start: 0.8611 (mt0) cc_final: 0.8282 (tp40) REVERT: C 146 MET cc_start: 0.8623 (mtm) cc_final: 0.8242 (mtm) REVERT: H 39 ASP cc_start: 0.9272 (m-30) cc_final: 0.9037 (m-30) REVERT: I 1 MET cc_start: 0.7960 (ttm) cc_final: 0.7657 (tpt) REVERT: I 17 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8515 (mt-10) REVERT: I 39 ASP cc_start: 0.7631 (t0) cc_final: 0.7323 (t0) REVERT: I 105 ASP cc_start: 0.7984 (t0) cc_final: 0.7778 (t70) REVERT: I 140 LYS cc_start: 0.8674 (tppt) cc_final: 0.8457 (mttt) REVERT: I 153 GLU cc_start: 0.8402 (tt0) cc_final: 0.7912 (tm-30) REVERT: I 173 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: J 106 LYS cc_start: 0.8983 (tppt) cc_final: 0.8711 (tppt) REVERT: J 132 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7948 (mm) REVERT: K 10 GLU cc_start: 0.8926 (tt0) cc_final: 0.8614 (tm-30) REVERT: K 17 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8028 (mt-10) REVERT: K 173 GLN cc_start: 0.8968 (tt0) cc_final: 0.8628 (tm-30) REVERT: G 19 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8500 (mm-30) REVERT: G 102 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7793 (tt0) REVERT: G 116 MET cc_start: 0.8547 (mmm) cc_final: 0.8334 (mmm) REVERT: F 8 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7620 (pp30) REVERT: F 44 LEU cc_start: 0.9101 (tp) cc_final: 0.8882 (tp) REVERT: F 74 MET cc_start: 0.7905 (tpt) cc_final: 0.7615 (tpt) REVERT: F 116 MET cc_start: 0.7378 (mmp) cc_final: 0.6889 (mmt) outliers start: 26 outliers final: 15 residues processed: 239 average time/residue: 0.2853 time to fit residues: 101.5539 Evaluate side-chains 223 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 169 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN I 8 GLN F 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15821 Z= 0.225 Angle : 0.534 8.448 21195 Z= 0.274 Chirality : 0.037 0.218 2484 Planarity : 0.003 0.053 2682 Dihedral : 3.524 13.898 2089 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.29 % Allowed : 17.95 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.21), residues: 1881 helix: 1.92 (0.15), residues: 1412 sheet: None (None), residues: 0 loop : -1.04 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.016 0.001 PHE O 114 TYR 0.023 0.001 TYR N 93 ARG 0.008 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5801 (ttt-90) cc_final: 0.5274 (mtm-85) REVERT: O 120 MET cc_start: 0.8103 (ppp) cc_final: 0.7470 (ppp) REVERT: A 12 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7910 (tt0) REVERT: A 43 MET cc_start: 0.8506 (mmm) cc_final: 0.8220 (mmp) REVERT: B 80 ASN cc_start: 0.9044 (t0) cc_final: 0.8773 (p0) REVERT: B 104 MET cc_start: 0.8895 (tmm) cc_final: 0.8666 (tmm) REVERT: B 137 MET cc_start: 0.7984 (mtt) cc_final: 0.7727 (mtp) REVERT: B 166 GLN cc_start: 0.8841 (mp10) cc_final: 0.8495 (mp10) REVERT: B 168 ASN cc_start: 0.7705 (t0) cc_final: 0.7220 (t0) REVERT: C 125 GLN cc_start: 0.8645 (mt0) cc_final: 0.8283 (tp40) REVERT: C 146 MET cc_start: 0.8726 (mtm) cc_final: 0.8326 (mtm) REVERT: H 39 ASP cc_start: 0.9258 (m-30) cc_final: 0.9017 (m-30) REVERT: I 1 MET cc_start: 0.7977 (ttm) cc_final: 0.7664 (tpt) REVERT: I 17 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8535 (mt-10) REVERT: I 39 ASP cc_start: 0.7748 (t0) cc_final: 0.7504 (t0) REVERT: I 140 LYS cc_start: 0.8677 (tppt) cc_final: 0.8452 (mttt) REVERT: I 153 GLU cc_start: 0.8489 (tt0) cc_final: 0.7999 (tm-30) REVERT: I 173 GLN cc_start: 0.8783 (tt0) cc_final: 0.8270 (tm-30) REVERT: J 17 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7302 (mt-10) REVERT: J 106 LYS cc_start: 0.9009 (tppt) cc_final: 0.8742 (tppt) REVERT: J 132 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8002 (mm) REVERT: K 10 GLU cc_start: 0.8950 (tt0) cc_final: 0.8621 (tm-30) REVERT: K 20 MET cc_start: 0.9168 (tpp) cc_final: 0.8802 (tpp) REVERT: K 173 GLN cc_start: 0.8976 (tt0) cc_final: 0.8641 (tm-30) REVERT: G 19 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8523 (mm-30) REVERT: G 97 MET cc_start: 0.8238 (tpp) cc_final: 0.7986 (mpp) REVERT: G 99 GLU cc_start: 0.9050 (tt0) cc_final: 0.8478 (tm-30) REVERT: G 102 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7742 (tt0) REVERT: G 120 MET cc_start: 0.8356 (mpp) cc_final: 0.8111 (ptp) REVERT: F 44 LEU cc_start: 0.9096 (tp) cc_final: 0.8895 (tp) REVERT: F 74 MET cc_start: 0.7921 (tpt) cc_final: 0.7680 (tpt) REVERT: F 116 MET cc_start: 0.7344 (mmp) cc_final: 0.7003 (mmt) outliers start: 23 outliers final: 17 residues processed: 225 average time/residue: 0.2767 time to fit residues: 93.8668 Evaluate side-chains 222 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 169 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15821 Z= 0.197 Angle : 0.520 8.151 21195 Z= 0.270 Chirality : 0.036 0.226 2484 Planarity : 0.003 0.050 2682 Dihedral : 3.524 13.478 2089 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.23 % Allowed : 18.06 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.21), residues: 1881 helix: 1.91 (0.15), residues: 1414 sheet: None (None), residues: 0 loop : -1.05 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.016 0.001 PHE O 114 TYR 0.024 0.001 TYR N 93 ARG 0.011 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5798 (ttt-90) cc_final: 0.5251 (mtm-85) REVERT: O 120 MET cc_start: 0.8084 (ppp) cc_final: 0.7435 (ppp) REVERT: A 12 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7897 (tt0) REVERT: A 43 MET cc_start: 0.8503 (mmm) cc_final: 0.8215 (mmp) REVERT: B 80 ASN cc_start: 0.9052 (t0) cc_final: 0.8805 (p0) REVERT: B 104 MET cc_start: 0.8891 (tmm) cc_final: 0.8665 (tmm) REVERT: B 137 MET cc_start: 0.7959 (mtt) cc_final: 0.7711 (mtp) REVERT: B 166 GLN cc_start: 0.8834 (mp10) cc_final: 0.8485 (mp10) REVERT: B 168 ASN cc_start: 0.7699 (t0) cc_final: 0.7208 (t0) REVERT: C 125 GLN cc_start: 0.8639 (mt0) cc_final: 0.8275 (tp40) REVERT: C 146 MET cc_start: 0.8694 (mtm) cc_final: 0.8278 (mtm) REVERT: H 39 ASP cc_start: 0.9263 (m-30) cc_final: 0.9023 (m-30) REVERT: I 1 MET cc_start: 0.7981 (ttm) cc_final: 0.7674 (tpt) REVERT: I 17 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8491 (mt-10) REVERT: I 39 ASP cc_start: 0.7762 (t0) cc_final: 0.7534 (t0) REVERT: I 140 LYS cc_start: 0.8659 (tppt) cc_final: 0.8414 (mttt) REVERT: I 153 GLU cc_start: 0.8424 (tt0) cc_final: 0.7919 (tm-30) REVERT: I 173 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: J 17 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7279 (mt-10) REVERT: J 106 LYS cc_start: 0.9002 (tppt) cc_final: 0.8730 (tppt) REVERT: J 132 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8016 (mm) REVERT: K 10 GLU cc_start: 0.8942 (tt0) cc_final: 0.8636 (tm-30) REVERT: K 17 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7902 (mt-10) REVERT: K 20 MET cc_start: 0.9161 (tpp) cc_final: 0.8797 (tpp) REVERT: K 173 GLN cc_start: 0.8974 (tt0) cc_final: 0.8642 (tm-30) REVERT: G 39 ASP cc_start: 0.8729 (t0) cc_final: 0.8386 (t0) REVERT: G 99 GLU cc_start: 0.9046 (tt0) cc_final: 0.8481 (tm-30) REVERT: G 102 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7704 (tt0) REVERT: G 120 MET cc_start: 0.8329 (mpp) cc_final: 0.8069 (ptp) REVERT: F 44 LEU cc_start: 0.9091 (tp) cc_final: 0.8887 (tp) REVERT: F 116 MET cc_start: 0.7324 (mmp) cc_final: 0.7018 (mmt) outliers start: 22 outliers final: 20 residues processed: 223 average time/residue: 0.2734 time to fit residues: 93.2130 Evaluate side-chains 226 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 169 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 0.0270 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 158 optimal weight: 0.0050 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN F 8 GLN N 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15821 Z= 0.142 Angle : 0.507 7.953 21195 Z= 0.266 Chirality : 0.035 0.229 2484 Planarity : 0.003 0.049 2682 Dihedral : 3.406 15.558 2089 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1881 helix: 1.93 (0.15), residues: 1417 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 7 PHE 0.018 0.001 PHE O 114 TYR 0.023 0.001 TYR N 93 ARG 0.009 0.000 ARG F 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 38 ARG cc_start: 0.5847 (ttt-90) cc_final: 0.5335 (mtm-85) REVERT: O 120 MET cc_start: 0.8112 (ppp) cc_final: 0.7450 (ppp) REVERT: A 12 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7855 (tt0) REVERT: A 43 MET cc_start: 0.8435 (mmm) cc_final: 0.8155 (mmp) REVERT: A 104 MET cc_start: 0.8863 (tmm) cc_final: 0.8598 (ppp) REVERT: B 35 GLN cc_start: 0.7795 (tp40) cc_final: 0.7594 (tp40) REVERT: B 108 ILE cc_start: 0.7744 (mt) cc_final: 0.7541 (mm) REVERT: B 166 GLN cc_start: 0.8825 (mp10) cc_final: 0.8479 (mp10) REVERT: C 125 GLN cc_start: 0.8672 (mt0) cc_final: 0.8290 (tp40) REVERT: C 146 MET cc_start: 0.8593 (mtm) cc_final: 0.8178 (mtm) REVERT: H 39 ASP cc_start: 0.9259 (m-30) cc_final: 0.9027 (m-30) REVERT: I 1 MET cc_start: 0.7943 (ttm) cc_final: 0.7686 (tpt) REVERT: I 17 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8492 (mp0) REVERT: I 39 ASP cc_start: 0.7735 (t0) cc_final: 0.7499 (t0) REVERT: I 140 LYS cc_start: 0.8644 (tppt) cc_final: 0.8401 (mttt) REVERT: I 153 GLU cc_start: 0.8406 (tt0) cc_final: 0.7847 (tm-30) REVERT: I 173 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: J 17 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7239 (mt-10) REVERT: J 106 LYS cc_start: 0.8959 (tppt) cc_final: 0.8710 (tppt) REVERT: J 132 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7962 (mm) REVERT: K 10 GLU cc_start: 0.8909 (tt0) cc_final: 0.8628 (tm-30) REVERT: K 17 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7935 (mt-10) REVERT: K 20 MET cc_start: 0.9172 (tpp) cc_final: 0.8825 (tpp) REVERT: K 173 GLN cc_start: 0.8920 (tt0) cc_final: 0.8608 (tm-30) REVERT: G 19 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8486 (mm-30) REVERT: G 39 ASP cc_start: 0.8716 (t0) cc_final: 0.8356 (t0) REVERT: G 102 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7632 (tt0) REVERT: G 120 MET cc_start: 0.8330 (mpp) cc_final: 0.8102 (ptp) REVERT: F 44 LEU cc_start: 0.9059 (tp) cc_final: 0.8852 (tp) REVERT: F 116 MET cc_start: 0.7300 (mmp) cc_final: 0.7013 (mmt) outliers start: 17 outliers final: 11 residues processed: 232 average time/residue: 0.2779 time to fit residues: 96.9939 Evaluate side-chains 219 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN B 91 GLN F 8 GLN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075054 restraints weight = 36617.857| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.89 r_work: 0.2976 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15821 Z= 0.163 Angle : 0.523 8.344 21195 Z= 0.275 Chirality : 0.036 0.232 2484 Planarity : 0.003 0.048 2682 Dihedral : 3.412 16.777 2089 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.78 % Allowed : 18.57 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.21), residues: 1881 helix: 1.95 (0.15), residues: 1418 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.017 0.001 PHE O 114 TYR 0.051 0.001 TYR G 93 ARG 0.010 0.000 ARG F 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.55 seconds wall clock time: 63 minutes 14.69 seconds (3794.69 seconds total)