Starting phenix.real_space_refine on Mon Jun 16 20:34:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynm_39427/06_2025/8ynm_39427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynm_39427/06_2025/8ynm_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/cci-nas-00/data/ceres_data/8ynm_39427/06_2025/8ynm_39427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynm_39427/06_2025/8ynm_39427.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynm_39427/06_2025/8ynm_39427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynm_39427/06_2025/8ynm_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-5710/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: 10.29, per 1000 atoms: 0.66 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: 3.94 Conformation dependent library (CDL) restraints added in 1.9 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: 1.41 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: 4.01 Time building geometry restraints manager: 4.62 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.870 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.750 ------------------------------------------------------------------------------- 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= 0.101 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 Details of bonding type rmsd hydrogen bonds : bond 0.16335 ( 870) hydrogen bonds : angle 4.67929 ( 2598) covalent geometry : bond 0.00229 (15821) covalent geometry : angle 0.39468 (21195) *********************** 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 : 2.030 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: 0.2900 time to fit residues: 157.2877 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 : 1.854 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078434 restraints weight = 37753.475| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.37 r_work: 0.3052 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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= 0.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 870) hydrogen bonds : angle 4.08217 ( 2598) covalent geometry : bond 0.00376 (15821) covalent geometry : angle 0.54433 (21195) *********************** 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 : 1.964 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: 0.5818 (ttt-90) cc_final: 0.5275 (mtm-85) REVERT: O 102 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8485 (mm-30) REVERT: O 142 ASN cc_start: 0.8853 (t0) cc_final: 0.8608 (t0) REVERT: B 80 ASN cc_start: 0.9108 (t0) cc_final: 0.8801 (p0) REVERT: B 86 MET cc_start: 0.8689 (mmm) cc_final: 0.8426 (tpp) REVERT: B 111 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 125 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8680 (mm-40) REVERT: B 137 MET cc_start: 0.8485 (mtt) cc_final: 0.8202 (mtp) REVERT: B 166 GLN cc_start: 0.8842 (mp10) cc_final: 0.8631 (mp10) REVERT: B 168 ASN cc_start: 0.8052 (t0) cc_final: 0.7767 (t0) REVERT: C 125 GLN cc_start: 0.8601 (mt0) cc_final: 0.8215 (tp40) REVERT: C 146 MET cc_start: 0.9112 (mtm) cc_final: 0.8888 (mtm) REVERT: H 14 ASP cc_start: 0.8701 (m-30) cc_final: 0.8359 (m-30) REVERT: H 16 ASP cc_start: 0.8509 (p0) cc_final: 0.7945 (m-30) REVERT: I 39 ASP cc_start: 0.7815 (t0) cc_final: 0.7610 (t0) REVERT: I 54 ASP cc_start: 0.8670 (t0) cc_final: 0.8446 (t0) REVERT: I 84 LEU cc_start: 0.8880 (mt) cc_final: 0.8676 (pp) REVERT: I 153 GLU cc_start: 0.8913 (tt0) cc_final: 0.8500 (tm-30) REVERT: K 10 GLU cc_start: 0.9069 (tt0) cc_final: 0.8753 (tm-30) REVERT: K 116 MET cc_start: 0.8709 (mtm) cc_final: 0.8339 (mtt) REVERT: G 102 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8168 (pt0) REVERT: F 44 LEU cc_start: 0.9041 (tp) cc_final: 0.8690 (tp) REVERT: N 119 TYR cc_start: 0.8064 (m-80) cc_final: 0.7688 (m-10) REVERT: N 158 ASN cc_start: 0.8336 (m-40) cc_final: 0.8002 (m110) outliers start: 19 outliers final: 11 residues processed: 253 average time/residue: 0.2728 time to fit residues: 102.2585 Evaluate side-chains 217 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 170 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.108525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079983 restraints weight = 37347.049| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.36 r_work: 0.3082 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15821 Z= 0.107 Angle : 0.482 6.907 21195 Z= 0.253 Chirality : 0.035 0.170 2484 Planarity : 0.003 0.044 2682 Dihedral : 3.485 13.428 2089 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.84 % Allowed : 11.63 % Favored : 87.53 % 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: 1.80 (0.15), residues: 1406 sheet: None (None), residues: 0 loop : -0.91 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS F 82 PHE 0.019 0.001 PHE C 181 TYR 0.018 0.001 TYR C 29 ARG 0.008 0.000 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 870) hydrogen bonds : angle 3.78984 ( 2598) covalent geometry : bond 0.00246 (15821) covalent geometry : angle 0.48215 (21195) *********************** 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 238 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 1.975 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: O 38 ARG cc_start: 0.5813 (ttt-90) cc_final: 0.5259 (mtm-85) REVERT: O 102 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8553 (mm-30) REVERT: O 142 ASN cc_start: 0.8840 (t0) cc_final: 0.8608 (t0) REVERT: A 43 MET cc_start: 0.8799 (mmp) cc_final: 0.8555 (mmm) REVERT: B 80 ASN cc_start: 0.9065 (t0) cc_final: 0.8817 (p0) REVERT: B 166 GLN cc_start: 0.8863 (mp10) cc_final: 0.8606 (mp10) REVERT: B 168 ASN cc_start: 0.8005 (t0) cc_final: 0.7685 (t0) REVERT: C 125 GLN cc_start: 0.8572 (mt0) cc_final: 0.8269 (tp40) REVERT: C 146 MET cc_start: 0.9056 (mtm) cc_final: 0.8817 (mtm) REVERT: H 14 ASP cc_start: 0.8659 (m-30) cc_final: 0.8446 (m-30) REVERT: H 16 ASP cc_start: 0.8479 (p0) cc_final: 0.7905 (m-30) REVERT: I 39 ASP cc_start: 0.7751 (t0) cc_final: 0.7522 (t0) REVERT: I 153 GLU cc_start: 0.8817 (tt0) cc_final: 0.8473 (tm-30) REVERT: J 106 LYS cc_start: 0.9149 (tppt) cc_final: 0.8871 (tppt) REVERT: J 120 MET cc_start: 0.8172 (ptp) cc_final: 0.7763 (mpp) REVERT: K 10 GLU cc_start: 0.9018 (tt0) cc_final: 0.8753 (tm-30) REVERT: K 173 GLN cc_start: 0.9004 (tt0) cc_final: 0.8706 (tm-30) REVERT: G 102 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8186 (pt0) REVERT: F 44 LEU cc_start: 0.9083 (tp) cc_final: 0.8821 (tp) REVERT: N 119 TYR cc_start: 0.8196 (m-80) cc_final: 0.7884 (m-10) REVERT: N 158 ASN cc_start: 0.8364 (m-40) cc_final: 0.8031 (m110) outliers start: 15 outliers final: 11 residues processed: 233 average time/residue: 0.2575 time to fit residues: 90.1924 Evaluate side-chains 209 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain A residue 5 ARG 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 F residue 82 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 153 optimal weight: 0.0970 chunk 82 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 184 optimal weight: 0.0770 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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** N 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.105387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075178 restraints weight = 35901.548| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.90 r_work: 0.3005 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2666 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= 0.092 Angle : 0.460 13.384 21195 Z= 0.241 Chirality : 0.035 0.185 2484 Planarity : 0.003 0.039 2682 Dihedral : 3.324 12.421 2089 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.34 % Allowed : 12.98 % Favored : 85.68 % 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 (0.20), residues: 1881 helix: 1.88 (0.15), residues: 1407 sheet: None (None), residues: 0 loop : -0.88 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 82 PHE 0.012 0.001 PHE A 120 TYR 0.021 0.001 TYR B 101 ARG 0.005 0.000 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.02698 ( 870) hydrogen bonds : angle 3.52281 ( 2598) covalent geometry : bond 0.00201 (15821) covalent geometry : angle 0.45997 (21195) *********************** 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 254 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 1.953 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: 0.5848 (ttt-90) cc_final: 0.5294 (mtm-85) REVERT: O 119 TYR cc_start: 0.8863 (m-10) cc_final: 0.8556 (m-10) REVERT: O 142 ASN cc_start: 0.8971 (t0) cc_final: 0.8744 (t0) REVERT: A 43 MET cc_start: 0.8900 (mmp) cc_final: 0.8682 (mmm) REVERT: B 80 ASN cc_start: 0.9183 (t0) cc_final: 0.8784 (p0) REVERT: B 166 GLN cc_start: 0.8846 (mp10) cc_final: 0.8527 (mp10) REVERT: C 125 GLN cc_start: 0.8681 (mt0) cc_final: 0.8286 (tp40) REVERT: C 146 MET cc_start: 0.8755 (mtm) cc_final: 0.8420 (mtm) REVERT: H 14 ASP cc_start: 0.8533 (m-30) cc_final: 0.8153 (m-30) REVERT: H 16 ASP cc_start: 0.8669 (p0) cc_final: 0.8022 (m-30) REVERT: I 25 CYS cc_start: 0.8400 (m) cc_final: 0.8068 (p) REVERT: I 39 ASP cc_start: 0.7805 (t0) cc_final: 0.7482 (t0) REVERT: I 84 LEU cc_start: 0.8909 (mt) cc_final: 0.8683 (pp) REVERT: I 105 ASP cc_start: 0.8047 (t70) cc_final: 0.7794 (t70) REVERT: I 153 GLU cc_start: 0.8882 (tt0) cc_final: 0.8266 (tm-30) REVERT: J 106 LYS cc_start: 0.9092 (tppt) cc_final: 0.8739 (tppt) REVERT: J 120 MET cc_start: 0.7965 (ptp) cc_final: 0.7416 (mpp) REVERT: K 10 GLU cc_start: 0.8953 (tt0) cc_final: 0.8669 (tm-30) REVERT: K 173 GLN cc_start: 0.9184 (tt0) cc_final: 0.8776 (tm-30) REVERT: G 19 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8775 (mm-30) REVERT: G 99 GLU cc_start: 0.9209 (tt0) cc_final: 0.8471 (tm-30) REVERT: G 102 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7705 (tt0) REVERT: F 44 LEU cc_start: 0.9077 (tp) cc_final: 0.8820 (tp) REVERT: N 119 TYR cc_start: 0.7988 (m-80) cc_final: 0.7675 (m-10) outliers start: 24 outliers final: 13 residues processed: 245 average time/residue: 0.2720 time to fit residues: 99.3878 Evaluate side-chains 221 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 1.993 ------------------------------------------------------------------------------- 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 H residue 143 LEU 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 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 82 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 120 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074568 restraints weight = 36634.213| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.92 r_work: 0.2990 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15821 Z= 0.100 Angle : 0.469 9.042 21195 Z= 0.246 Chirality : 0.035 0.197 2484 Planarity : 0.003 0.057 2682 Dihedral : 3.301 13.406 2089 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.34 % Allowed : 14.32 % Favored : 84.34 % 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: 1.85 (0.20), residues: 1881 helix: 1.93 (0.15), residues: 1410 sheet: None (None), residues: 0 loop : -0.95 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS K 82 PHE 0.024 0.001 PHE O 114 TYR 0.020 0.001 TYR N 93 ARG 0.004 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 870) hydrogen bonds : angle 3.49636 ( 2598) covalent geometry : bond 0.00230 (15821) covalent geometry : angle 0.46909 (21195) *********************** 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 243 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 1.919 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: 0.5842 (ttt-90) cc_final: 0.5259 (mtm-85) REVERT: O 102 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8502 (mm-30) REVERT: O 119 TYR cc_start: 0.8838 (m-10) cc_final: 0.8547 (m-10) REVERT: O 120 MET cc_start: 0.8071 (ppp) cc_final: 0.7561 (ppp) REVERT: A 43 MET cc_start: 0.8926 (mmp) cc_final: 0.8684 (mmm) REVERT: B 80 ASN cc_start: 0.9183 (t0) cc_final: 0.8816 (p0) REVERT: B 91 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7883 (mt0) REVERT: B 166 GLN cc_start: 0.8866 (mp10) cc_final: 0.8538 (mp10) REVERT: C 43 MET cc_start: 0.8653 (mtp) cc_final: 0.8397 (mtm) REVERT: C 125 GLN cc_start: 0.8671 (mt0) cc_final: 0.8275 (tp40) REVERT: C 146 MET cc_start: 0.8806 (mtm) cc_final: 0.8459 (mtm) REVERT: H 14 ASP cc_start: 0.8516 (m-30) cc_final: 0.8230 (m-30) REVERT: H 16 ASP cc_start: 0.8626 (p0) cc_final: 0.8108 (m-30) REVERT: I 25 CYS cc_start: 0.8410 (m) cc_final: 0.8068 (p) REVERT: I 39 ASP cc_start: 0.7825 (t0) cc_final: 0.7588 (t0) REVERT: I 105 ASP cc_start: 0.8048 (t70) cc_final: 0.7798 (t70) REVERT: I 153 GLU cc_start: 0.8885 (tt0) cc_final: 0.8236 (tm-30) REVERT: J 106 LYS cc_start: 0.9110 (tppt) cc_final: 0.8765 (tppt) REVERT: J 120 MET cc_start: 0.7921 (ptp) cc_final: 0.7322 (mpp) REVERT: K 10 GLU cc_start: 0.8973 (tt0) cc_final: 0.8672 (tm-30) REVERT: K 173 GLN cc_start: 0.9185 (tt0) cc_final: 0.8778 (tm-30) REVERT: G 99 GLU cc_start: 0.9216 (tt0) cc_final: 0.8476 (tm-30) REVERT: G 102 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7691 (tt0) REVERT: G 116 MET cc_start: 0.8576 (mmm) cc_final: 0.8295 (mmm) REVERT: F 44 LEU cc_start: 0.9092 (tp) cc_final: 0.8839 (tp) REVERT: F 74 MET cc_start: 0.7959 (tpt) cc_final: 0.7442 (tpt) REVERT: F 116 MET cc_start: 0.7194 (mmp) cc_final: 0.6889 (mmt) outliers start: 24 outliers final: 16 residues processed: 230 average time/residue: 0.2800 time to fit residues: 98.4939 Evaluate side-chains 218 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 130 SER 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 97 MET Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU 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 169 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 184 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 0.0050 chunk 181 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074112 restraints weight = 36379.298| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.89 r_work: 0.2983 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15821 Z= 0.105 Angle : 0.480 8.105 21195 Z= 0.252 Chirality : 0.035 0.212 2484 Planarity : 0.003 0.047 2682 Dihedral : 3.310 12.213 2089 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.23 % Allowed : 14.77 % Favored : 84.00 % 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: 1.89 (0.20), residues: 1881 helix: 1.94 (0.15), residues: 1420 sheet: None (None), residues: 0 loop : -0.92 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 82 PHE 0.020 0.001 PHE O 114 TYR 0.022 0.001 TYR B 101 ARG 0.005 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 870) hydrogen bonds : angle 3.47211 ( 2598) covalent geometry : bond 0.00245 (15821) covalent geometry : angle 0.47980 (21195) *********************** 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 238 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 2.290 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: 0.5767 (ttt-90) cc_final: 0.5224 (mtm-85) REVERT: O 102 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8515 (mm-30) REVERT: O 119 TYR cc_start: 0.8803 (m-10) cc_final: 0.8426 (m-10) REVERT: O 120 MET cc_start: 0.8132 (ppp) cc_final: 0.7641 (ppp) REVERT: B 80 ASN cc_start: 0.9193 (t0) cc_final: 0.8985 (p0) REVERT: B 166 GLN cc_start: 0.8875 (mp10) cc_final: 0.8543 (mp10) REVERT: C 43 MET cc_start: 0.8653 (mtp) cc_final: 0.8428 (mtm) REVERT: C 125 GLN cc_start: 0.8660 (mt0) cc_final: 0.8224 (tp40) REVERT: C 146 MET cc_start: 0.8788 (mtm) cc_final: 0.8449 (mtm) REVERT: H 14 ASP cc_start: 0.8471 (m-30) cc_final: 0.8240 (t70) REVERT: H 86 ASN cc_start: 0.7553 (m-40) cc_final: 0.7289 (m-40) REVERT: H 139 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8466 (mt-10) REVERT: I 25 CYS cc_start: 0.8400 (m) cc_final: 0.8049 (p) REVERT: I 39 ASP cc_start: 0.7832 (t0) cc_final: 0.7572 (t0) REVERT: I 105 ASP cc_start: 0.8047 (t70) cc_final: 0.7805 (t70) REVERT: I 153 GLU cc_start: 0.8895 (tt0) cc_final: 0.8234 (tm-30) REVERT: J 106 LYS cc_start: 0.9099 (tppt) cc_final: 0.8778 (tppt) REVERT: J 120 MET cc_start: 0.7950 (ptp) cc_final: 0.7366 (mpp) REVERT: K 10 GLU cc_start: 0.8981 (tt0) cc_final: 0.8676 (tm-30) REVERT: K 173 GLN cc_start: 0.9173 (tt0) cc_final: 0.8764 (tm-30) REVERT: G 19 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8768 (mm-30) REVERT: G 99 GLU cc_start: 0.9222 (tt0) cc_final: 0.8505 (tm-30) REVERT: G 102 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7689 (tt0) REVERT: G 116 MET cc_start: 0.8558 (mmm) cc_final: 0.8258 (mmm) REVERT: F 44 LEU cc_start: 0.9093 (tp) cc_final: 0.8850 (tp) REVERT: F 74 MET cc_start: 0.8135 (tpt) cc_final: 0.7924 (tpt) REVERT: F 116 MET cc_start: 0.7211 (mmp) cc_final: 0.6765 (mmt) REVERT: N 93 TYR cc_start: 0.6730 (t80) cc_final: 0.6245 (t80) outliers start: 22 outliers final: 18 residues processed: 225 average time/residue: 0.3558 time to fit residues: 121.1696 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 : 2.017 ------------------------------------------------------------------------------- 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 130 SER 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 97 MET 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 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 82 HIS 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 146 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 176 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN C 91 GLN N 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075386 restraints weight = 36313.661| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.91 r_work: 0.3012 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15821 Z= 0.091 Angle : 0.462 7.779 21195 Z= 0.245 Chirality : 0.035 0.222 2484 Planarity : 0.003 0.042 2682 Dihedral : 3.285 14.826 2089 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 15.44 % Favored : 83.56 % 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: 1.91 (0.20), residues: 1881 helix: 1.96 (0.15), residues: 1415 sheet: None (None), residues: 0 loop : -0.91 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS F 82 PHE 0.017 0.001 PHE O 114 TYR 0.023 0.001 TYR B 101 ARG 0.008 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02443 ( 870) hydrogen bonds : angle 3.34023 ( 2598) covalent geometry : bond 0.00200 (15821) covalent geometry : angle 0.46153 (21195) *********************** 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 237 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 2.111 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: 0.5840 (ttt-90) cc_final: 0.5295 (mtm-85) REVERT: O 102 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8565 (mm-30) REVERT: O 119 TYR cc_start: 0.8714 (m-10) cc_final: 0.8399 (m-10) REVERT: O 120 MET cc_start: 0.8133 (ppp) cc_final: 0.7584 (ppp) REVERT: B 166 GLN cc_start: 0.8862 (mp10) cc_final: 0.8522 (mp10) REVERT: C 125 GLN cc_start: 0.8660 (mt0) cc_final: 0.8264 (tp40) REVERT: C 146 MET cc_start: 0.8781 (mtm) cc_final: 0.8414 (mtm) REVERT: H 139 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8386 (mt-10) REVERT: I 25 CYS cc_start: 0.8442 (m) cc_final: 0.8081 (p) REVERT: I 39 ASP cc_start: 0.7828 (t0) cc_final: 0.7572 (t0) REVERT: I 105 ASP cc_start: 0.8044 (t70) cc_final: 0.7806 (t0) REVERT: I 153 GLU cc_start: 0.8885 (tt0) cc_final: 0.8211 (tm-30) REVERT: I 173 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: J 106 LYS cc_start: 0.9058 (tppt) cc_final: 0.8747 (tppt) REVERT: J 116 MET cc_start: 0.8879 (mmt) cc_final: 0.8540 (mmt) REVERT: J 120 MET cc_start: 0.7921 (ptp) cc_final: 0.7302 (mpp) REVERT: J 132 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7999 (mm) REVERT: K 10 GLU cc_start: 0.8947 (tt0) cc_final: 0.8659 (tm-30) REVERT: K 173 GLN cc_start: 0.9163 (tt0) cc_final: 0.8763 (tm-30) REVERT: G 19 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8741 (mm-30) REVERT: G 97 MET cc_start: 0.8421 (mmm) cc_final: 0.8060 (mpp) REVERT: G 99 GLU cc_start: 0.9199 (tt0) cc_final: 0.8481 (tm-30) REVERT: G 102 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7597 (tt0) REVERT: G 116 MET cc_start: 0.8545 (mmm) cc_final: 0.8316 (mmm) REVERT: F 44 LEU cc_start: 0.9088 (tp) cc_final: 0.8848 (tp) REVERT: F 74 MET cc_start: 0.8167 (tpt) cc_final: 0.7938 (tpt) REVERT: F 116 MET cc_start: 0.7096 (mmp) cc_final: 0.6650 (mmt) outliers start: 18 outliers final: 11 residues processed: 226 average time/residue: 0.3484 time to fit residues: 118.3148 Evaluate side-chains 213 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 124 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 173 GLN 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 G residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 177 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 80 ASN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074038 restraints weight = 36925.032| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.90 r_work: 0.2975 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15821 Z= 0.114 Angle : 0.489 7.187 21195 Z= 0.257 Chirality : 0.036 0.226 2484 Planarity : 0.003 0.040 2682 Dihedral : 3.308 16.382 2089 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.12 % Allowed : 16.22 % Favored : 82.66 % 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: 1.99 (0.21), residues: 1881 helix: 2.01 (0.15), residues: 1420 sheet: None (None), residues: 0 loop : -0.88 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS K 82 PHE 0.021 0.001 PHE C 181 TYR 0.023 0.001 TYR B 101 ARG 0.010 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 870) hydrogen bonds : angle 3.45873 ( 2598) covalent geometry : bond 0.00271 (15821) covalent geometry : angle 0.48876 (21195) *********************** 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 226 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 2.551 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: 0.5744 (ttt-90) cc_final: 0.5229 (mtm-85) REVERT: O 102 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8555 (mm-30) REVERT: O 119 TYR cc_start: 0.8681 (m-10) cc_final: 0.8366 (m-10) REVERT: O 120 MET cc_start: 0.8102 (ppp) cc_final: 0.7548 (ppp) REVERT: B 166 GLN cc_start: 0.8844 (mp10) cc_final: 0.8508 (mp10) REVERT: B 168 ASN cc_start: 0.7705 (t0) cc_final: 0.7188 (t0) REVERT: C 125 GLN cc_start: 0.8647 (mt0) cc_final: 0.8321 (tp40) REVERT: C 146 MET cc_start: 0.8846 (mtm) cc_final: 0.8499 (mtm) REVERT: H 139 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8459 (mt-10) REVERT: I 25 CYS cc_start: 0.8425 (m) cc_final: 0.8055 (p) REVERT: I 39 ASP cc_start: 0.7846 (t0) cc_final: 0.7591 (t0) REVERT: I 105 ASP cc_start: 0.8104 (t70) cc_final: 0.7879 (t70) REVERT: I 153 GLU cc_start: 0.8910 (tt0) cc_final: 0.8197 (tm-30) REVERT: I 173 GLN cc_start: 0.8783 (tt0) cc_final: 0.8278 (tm-30) REVERT: J 106 LYS cc_start: 0.9109 (tppt) cc_final: 0.8806 (tppt) REVERT: J 120 MET cc_start: 0.7935 (ptp) cc_final: 0.7428 (mpp) REVERT: K 10 GLU cc_start: 0.8969 (tt0) cc_final: 0.8689 (tm-30) REVERT: K 173 GLN cc_start: 0.9173 (tt0) cc_final: 0.8772 (tm-30) REVERT: G 19 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8747 (mm-30) REVERT: G 99 GLU cc_start: 0.9259 (tt0) cc_final: 0.8568 (tm-30) REVERT: G 102 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7667 (tt0) REVERT: F 44 LEU cc_start: 0.9090 (tp) cc_final: 0.8853 (tp) REVERT: F 116 MET cc_start: 0.7141 (mmp) cc_final: 0.6761 (mmt) outliers start: 20 outliers final: 13 residues processed: 215 average time/residue: 0.3892 time to fit residues: 128.4196 Evaluate side-chains 214 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain C residue 53 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 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 15 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 0.0070 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.105170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074494 restraints weight = 36389.846| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.89 r_work: 0.2998 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15821 Z= 0.099 Angle : 0.484 7.561 21195 Z= 0.255 Chirality : 0.036 0.227 2484 Planarity : 0.003 0.039 2682 Dihedral : 3.294 16.026 2089 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.95 % Allowed : 16.44 % Favored : 82.61 % 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: 2.00 (0.20), residues: 1881 helix: 2.01 (0.15), residues: 1416 sheet: None (None), residues: 0 loop : -0.83 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS K 82 PHE 0.015 0.001 PHE O 114 TYR 0.026 0.001 TYR B 101 ARG 0.007 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 870) hydrogen bonds : angle 3.37505 ( 2598) covalent geometry : bond 0.00227 (15821) covalent geometry : angle 0.48393 (21195) *********************** 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 223 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.854 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: O 38 ARG cc_start: 0.5771 (ttt-90) cc_final: 0.5217 (mtm-85) REVERT: O 102 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8571 (mm-30) REVERT: O 119 TYR cc_start: 0.8641 (m-10) cc_final: 0.8282 (m-10) REVERT: O 120 MET cc_start: 0.8096 (ppp) cc_final: 0.7486 (ppp) REVERT: B 166 GLN cc_start: 0.8819 (mp10) cc_final: 0.8484 (mp10) REVERT: C 1 MET cc_start: 0.5320 (ptt) cc_final: 0.4934 (ptp) REVERT: C 125 GLN cc_start: 0.8653 (mt0) cc_final: 0.8335 (tp40) REVERT: C 146 MET cc_start: 0.8849 (mtm) cc_final: 0.8503 (mtm) REVERT: H 139 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8409 (mt-10) REVERT: I 25 CYS cc_start: 0.8420 (m) cc_final: 0.8066 (p) REVERT: I 39 ASP cc_start: 0.7839 (t0) cc_final: 0.7585 (t0) REVERT: I 105 ASP cc_start: 0.8060 (t70) cc_final: 0.7814 (t70) REVERT: I 153 GLU cc_start: 0.8891 (tt0) cc_final: 0.8167 (tm-30) REVERT: I 173 GLN cc_start: 0.8782 (tt0) cc_final: 0.8285 (tm-30) REVERT: J 106 LYS cc_start: 0.9090 (tppt) cc_final: 0.8796 (tppt) REVERT: J 120 MET cc_start: 0.7892 (ptp) cc_final: 0.7265 (mpp) REVERT: K 10 GLU cc_start: 0.8921 (tt0) cc_final: 0.8661 (tm-30) REVERT: K 173 GLN cc_start: 0.9172 (tt0) cc_final: 0.8762 (tm-30) REVERT: G 19 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8747 (mm-30) REVERT: G 102 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7619 (tt0) REVERT: G 120 MET cc_start: 0.8383 (mpp) cc_final: 0.8112 (ptp) REVERT: F 54 ASP cc_start: 0.8778 (t0) cc_final: 0.8315 (m-30) REVERT: F 74 MET cc_start: 0.7920 (tpt) cc_final: 0.7675 (tpt) REVERT: F 116 MET cc_start: 0.7111 (mmp) cc_final: 0.6750 (mmt) outliers start: 17 outliers final: 14 residues processed: 217 average time/residue: 0.2622 time to fit residues: 85.6713 Evaluate side-chains 212 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 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 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 15 THR Chi-restraints excluded: chain N residue 148 GLN 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 151 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 159 optimal weight: 0.0870 chunk 107 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN B 91 GLN N 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074064 restraints weight = 36634.278| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.90 r_work: 0.2983 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15821 Z= 0.106 Angle : 0.513 11.124 21195 Z= 0.266 Chirality : 0.036 0.236 2484 Planarity : 0.003 0.039 2682 Dihedral : 3.300 16.662 2089 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.84 % Allowed : 16.39 % Favored : 82.77 % 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: 2.03 (0.21), residues: 1881 helix: 2.02 (0.15), residues: 1416 sheet: None (None), residues: 0 loop : -0.80 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS K 82 PHE 0.014 0.001 PHE O 114 TYR 0.036 0.001 TYR G 93 ARG 0.008 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02642 ( 870) hydrogen bonds : angle 3.39281 ( 2598) covalent geometry : bond 0.00252 (15821) covalent geometry : angle 0.51262 (21195) ********************** 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 219 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 1.846 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: 0.5782 (ttt-90) cc_final: 0.5219 (mtm-85) REVERT: O 102 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8573 (mm-30) REVERT: O 119 TYR cc_start: 0.8594 (m-10) cc_final: 0.8297 (m-10) REVERT: O 120 MET cc_start: 0.8069 (ppp) cc_final: 0.7505 (ppp) REVERT: B 166 GLN cc_start: 0.8831 (mp10) cc_final: 0.8497 (mp10) REVERT: C 1 MET cc_start: 0.5300 (ptt) cc_final: 0.4912 (ptp) REVERT: C 125 GLN cc_start: 0.8651 (mt0) cc_final: 0.8331 (tp40) REVERT: C 146 MET cc_start: 0.8874 (mtm) cc_final: 0.8521 (mtm) REVERT: H 139 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8465 (mt-10) REVERT: I 25 CYS cc_start: 0.8365 (m) cc_final: 0.8038 (p) REVERT: I 39 ASP cc_start: 0.7858 (t0) cc_final: 0.7596 (t0) REVERT: I 105 ASP cc_start: 0.8058 (t70) cc_final: 0.7834 (t70) REVERT: I 153 GLU cc_start: 0.8912 (tt0) cc_final: 0.8194 (tm-30) REVERT: I 173 GLN cc_start: 0.8776 (tt0) cc_final: 0.8281 (tm-30) REVERT: J 106 LYS cc_start: 0.9089 (tppt) cc_final: 0.8827 (tppt) REVERT: J 120 MET cc_start: 0.7931 (ptp) cc_final: 0.7304 (mpp) REVERT: K 10 GLU cc_start: 0.8931 (tt0) cc_final: 0.8668 (tm-30) REVERT: K 173 GLN cc_start: 0.9177 (tt0) cc_final: 0.8768 (tm-30) REVERT: G 19 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8764 (mm-30) REVERT: G 102 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7586 (tt0) REVERT: G 120 MET cc_start: 0.8361 (mpp) cc_final: 0.8095 (ptp) REVERT: F 54 ASP cc_start: 0.8730 (t0) cc_final: 0.8313 (m-30) REVERT: F 74 MET cc_start: 0.7913 (tpt) cc_final: 0.7643 (tpt) REVERT: F 116 MET cc_start: 0.7101 (mmp) cc_final: 0.6793 (mmt) REVERT: N 17 GLU cc_start: 0.8197 (tt0) cc_final: 0.7879 (mt-10) outliers start: 15 outliers final: 14 residues processed: 213 average time/residue: 0.2559 time to fit residues: 83.3456 Evaluate side-chains 213 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 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 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 15 THR Chi-restraints excluded: chain N residue 148 GLN 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 68 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073364 restraints weight = 36581.719| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.89 r_work: 0.2974 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3325 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= 0.121 Angle : 0.524 10.840 21195 Z= 0.272 Chirality : 0.036 0.245 2484 Planarity : 0.003 0.039 2682 Dihedral : 3.327 16.678 2089 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.78 % Allowed : 16.55 % Favored : 82.66 % 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: 2.03 (0.21), residues: 1881 helix: 2.02 (0.15), residues: 1416 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS K 82 PHE 0.013 0.001 PHE O 114 TYR 0.027 0.001 TYR B 101 ARG 0.010 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 870) hydrogen bonds : angle 3.45917 ( 2598) covalent geometry : bond 0.00289 (15821) covalent geometry : angle 0.52362 (21195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.84 seconds wall clock time: 136 minutes 17.28 seconds (8177.28 seconds total)