Starting phenix.real_space_refine on Thu Sep 18 18:23:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynm_39427/09_2025/8ynm_39427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynm_39427/09_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_39427/09_2025/8ynm_39427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynm_39427/09_2025/8ynm_39427.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynm_39427/09_2025/8ynm_39427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynm_39427/09_2025/8ynm_39427.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.75, per 1000 atoms: 0.24 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: 0.92 Conformation dependent library (CDL) restraints added in 495.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 2.19 Time building geometry restraints manager: 1.26 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.280 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.000 ARG G 64 TYR 0.009 0.001 TYR K 171 PHE 0.007 0.001 PHE A 120 HIS 0.002 0.000 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00229 (15821) covalent geometry : angle 0.39468 (21195) hydrogen bonds : bond 0.16335 ( 870) hydrogen bonds : angle 4.67929 ( 2598) *********************** 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 : 0.682 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: 0.1412 time to fit residues: 76.8790 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 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 = 0.3721 r_free = 0.3721 target = 0.107481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078962 restraints weight = 37086.144| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.33 r_work: 0.3086 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15821 Z= 0.122 Angle : 0.510 7.477 21195 Z= 0.266 Chirality : 0.036 0.171 2484 Planarity : 0.004 0.063 2682 Dihedral : 3.447 12.868 2089 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.12 % Allowed : 8.45 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.20), residues: 1881 helix: 1.76 (0.14), residues: 1409 sheet: None (None), residues: 0 loop : -0.84 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 64 TYR 0.013 0.001 TYR N 93 PHE 0.011 0.001 PHE F 114 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00279 (15821) covalent geometry : angle 0.51041 (21195) hydrogen bonds : bond 0.03806 ( 870) hydrogen bonds : angle 3.94181 ( 2598) *********************** 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 270 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.561 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: 0.5813 (ttt-90) cc_final: 0.5285 (mtm-85) REVERT: O 102 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8494 (mm-30) REVERT: O 116 MET cc_start: 0.9126 (mmp) cc_final: 0.8921 (mmm) REVERT: O 142 ASN cc_start: 0.8847 (t0) cc_final: 0.8596 (t0) REVERT: B 80 ASN cc_start: 0.9067 (t0) cc_final: 0.8824 (p0) REVERT: B 86 MET cc_start: 0.8681 (mmm) cc_final: 0.8433 (tpp) REVERT: B 125 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8647 (mm-40) REVERT: B 137 MET cc_start: 0.8513 (mtt) cc_final: 0.8255 (mtm) REVERT: B 166 GLN cc_start: 0.8805 (mp10) cc_final: 0.8605 (mp10) REVERT: B 168 ASN cc_start: 0.8028 (t0) cc_final: 0.7763 (t0) REVERT: C 125 GLN cc_start: 0.8563 (mt0) cc_final: 0.8218 (tp40) REVERT: C 146 MET cc_start: 0.9076 (mtm) cc_final: 0.8875 (mtm) REVERT: H 14 ASP cc_start: 0.8683 (m-30) cc_final: 0.8365 (m-30) REVERT: H 16 ASP cc_start: 0.8400 (p0) cc_final: 0.7797 (m-30) REVERT: I 39 ASP cc_start: 0.7768 (t0) cc_final: 0.7551 (t0) REVERT: I 153 GLU cc_start: 0.8868 (tt0) cc_final: 0.8509 (tm-30) REVERT: K 10 GLU cc_start: 0.9022 (tt0) cc_final: 0.8756 (tm-30) REVERT: G 99 GLU cc_start: 0.9162 (tt0) cc_final: 0.8696 (tm-30) REVERT: G 102 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8241 (pt0) REVERT: F 44 LEU cc_start: 0.9021 (tp) cc_final: 0.8661 (tp) REVERT: N 119 TYR cc_start: 0.8106 (m-80) cc_final: 0.7704 (m-10) REVERT: N 158 ASN cc_start: 0.8355 (m-40) cc_final: 0.8026 (m110) outliers start: 20 outliers final: 13 residues processed: 259 average time/residue: 0.1306 time to fit residues: 50.1147 Evaluate side-chains 221 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 74 MET 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 I residue 79 VAL 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 135 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 154 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.109273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.080750 restraints weight = 37635.832| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.38 r_work: 0.3095 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2435 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= 0.104 Angle : 0.485 12.498 21195 Z= 0.251 Chirality : 0.035 0.177 2484 Planarity : 0.003 0.043 2682 Dihedral : 3.381 12.738 2089 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.06 % Allowed : 11.02 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.20), residues: 1881 helix: 1.82 (0.15), residues: 1406 sheet: None (None), residues: 0 loop : -0.88 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 85 TYR 0.017 0.001 TYR C 29 PHE 0.010 0.001 PHE F 131 HIS 0.006 0.000 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00234 (15821) covalent geometry : angle 0.48491 (21195) hydrogen bonds : bond 0.03206 ( 870) hydrogen bonds : angle 3.72741 ( 2598) *********************** 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 250 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.641 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: 0.5839 (ttt-90) cc_final: 0.5285 (mtm-85) REVERT: O 102 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8503 (mm-30) REVERT: O 142 ASN cc_start: 0.8836 (t0) cc_final: 0.8600 (t0) REVERT: A 5 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8859 (ttp-170) REVERT: A 43 MET cc_start: 0.8807 (mmp) cc_final: 0.8553 (mmm) REVERT: B 80 ASN cc_start: 0.9072 (t0) cc_final: 0.8840 (p0) REVERT: B 152 LEU cc_start: 0.9051 (tp) cc_final: 0.8710 (tt) REVERT: B 166 GLN cc_start: 0.8837 (mp10) cc_final: 0.8588 (mp10) REVERT: B 168 ASN cc_start: 0.7987 (t0) cc_final: 0.7665 (t0) REVERT: C 125 GLN cc_start: 0.8553 (mt0) cc_final: 0.8119 (tp40) REVERT: C 146 MET cc_start: 0.9029 (mtm) cc_final: 0.8800 (mtm) REVERT: H 14 ASP cc_start: 0.8620 (m-30) cc_final: 0.8388 (m-30) REVERT: H 16 ASP cc_start: 0.8445 (p0) cc_final: 0.7850 (m-30) REVERT: I 39 ASP cc_start: 0.7729 (t0) cc_final: 0.7496 (t0) REVERT: I 54 ASP cc_start: 0.8573 (t0) cc_final: 0.8369 (t0) REVERT: I 153 GLU cc_start: 0.8818 (tt0) cc_final: 0.8464 (tm-30) REVERT: J 106 LYS cc_start: 0.9143 (tppt) cc_final: 0.8872 (tppt) REVERT: J 116 MET cc_start: 0.9110 (mmt) cc_final: 0.8605 (mmt) REVERT: J 120 MET cc_start: 0.8199 (ptp) cc_final: 0.7827 (mpp) REVERT: K 10 GLU cc_start: 0.8999 (tt0) cc_final: 0.8744 (tm-30) REVERT: K 173 GLN cc_start: 0.9026 (tt0) cc_final: 0.8702 (tm-30) REVERT: G 99 GLU cc_start: 0.9130 (tt0) cc_final: 0.8670 (tm-30) REVERT: G 102 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8199 (pt0) REVERT: F 1 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7332 (tmm) REVERT: F 44 LEU cc_start: 0.9079 (tp) cc_final: 0.8817 (tp) REVERT: N 119 TYR cc_start: 0.8224 (m-80) cc_final: 0.7898 (m-10) REVERT: N 158 ASN cc_start: 0.8372 (m-40) cc_final: 0.8045 (m110) outliers start: 19 outliers final: 12 residues processed: 243 average time/residue: 0.1228 time to fit residues: 45.2090 Evaluate side-chains 215 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 74 MET 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 I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 133 ASP 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 1 MET Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 153 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN K 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073007 restraints weight = 36521.112| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.90 r_work: 0.2962 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15821 Z= 0.123 Angle : 0.491 10.183 21195 Z= 0.256 Chirality : 0.036 0.192 2484 Planarity : 0.003 0.039 2682 Dihedral : 3.394 13.027 2089 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.68 % Allowed : 12.42 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.20), residues: 1881 helix: 1.85 (0.15), residues: 1407 sheet: None (None), residues: 0 loop : -0.91 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 122 TYR 0.020 0.001 TYR B 101 PHE 0.022 0.001 PHE C 181 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00292 (15821) covalent geometry : angle 0.49100 (21195) hydrogen bonds : bond 0.03232 ( 870) hydrogen bonds : angle 3.70058 ( 2598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.708 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: 0.5697 (ttt-90) cc_final: 0.5176 (mtm-85) REVERT: O 102 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8527 (mm-30) REVERT: O 119 TYR cc_start: 0.9004 (m-80) cc_final: 0.8791 (m-10) REVERT: O 142 ASN cc_start: 0.8971 (t0) cc_final: 0.8754 (t0) REVERT: A 5 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8635 (ttm170) REVERT: A 43 MET cc_start: 0.8939 (mmp) cc_final: 0.8691 (mmm) REVERT: B 80 ASN cc_start: 0.9205 (t0) cc_final: 0.8798 (p0) REVERT: B 166 GLN cc_start: 0.8855 (mp10) cc_final: 0.8541 (mp10) REVERT: B 168 ASN cc_start: 0.7752 (t0) cc_final: 0.7250 (t0) REVERT: C 125 GLN cc_start: 0.8691 (mt0) cc_final: 0.8246 (tp40) REVERT: C 146 MET cc_start: 0.8853 (mtm) cc_final: 0.8511 (mtm) REVERT: H 14 ASP cc_start: 0.8549 (m-30) cc_final: 0.8119 (m-30) REVERT: H 16 ASP cc_start: 0.8700 (p0) cc_final: 0.8103 (m-30) REVERT: I 39 ASP cc_start: 0.7953 (t0) cc_final: 0.7739 (t0) REVERT: I 54 ASP cc_start: 0.8791 (t0) cc_final: 0.8567 (t0) REVERT: I 153 GLU cc_start: 0.8904 (tt0) cc_final: 0.8295 (tm-30) REVERT: J 106 LYS cc_start: 0.9164 (tppt) cc_final: 0.8791 (tppt) REVERT: J 120 MET cc_start: 0.7993 (ptp) cc_final: 0.7345 (mpp) REVERT: K 10 GLU cc_start: 0.8999 (tt0) cc_final: 0.8691 (tm-30) REVERT: K 173 GLN cc_start: 0.9203 (tt0) cc_final: 0.8788 (tm-30) REVERT: G 39 ASP cc_start: 0.8788 (t0) cc_final: 0.8552 (t0) REVERT: G 99 GLU cc_start: 0.9271 (tt0) cc_final: 0.8510 (tm-30) REVERT: G 102 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7777 (pt0) REVERT: F 44 LEU cc_start: 0.9093 (tp) cc_final: 0.8845 (tp) REVERT: F 116 MET cc_start: 0.7203 (mmp) cc_final: 0.6768 (mmt) outliers start: 30 outliers final: 18 residues processed: 233 average time/residue: 0.1186 time to fit residues: 41.3376 Evaluate side-chains 221 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 O residue 166 THR Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 27 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 J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain N residue 168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 2 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 43 optimal weight: 0.0670 chunk 14 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.072569 restraints weight = 36762.972| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.90 r_work: 0.2953 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15821 Z= 0.130 Angle : 0.490 7.047 21195 Z= 0.256 Chirality : 0.036 0.203 2484 Planarity : 0.003 0.037 2682 Dihedral : 3.448 14.330 2089 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.73 % Allowed : 14.09 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.20), residues: 1881 helix: 1.86 (0.15), residues: 1414 sheet: None (None), residues: 0 loop : -0.96 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 85 TYR 0.022 0.001 TYR N 93 PHE 0.014 0.001 PHE A 120 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00311 (15821) covalent geometry : angle 0.49043 (21195) hydrogen bonds : bond 0.03248 ( 870) hydrogen bonds : angle 3.69310 ( 2598) *********************** 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 251 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.492 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: 0.5750 (ttt-90) cc_final: 0.5204 (mtm-85) REVERT: O 102 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8496 (mm-30) REVERT: O 119 TYR cc_start: 0.8947 (m-80) cc_final: 0.8729 (m-10) REVERT: O 120 MET cc_start: 0.8202 (ppp) cc_final: 0.7769 (ppp) REVERT: A 5 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8503 (ttm170) REVERT: B 80 ASN cc_start: 0.9220 (t0) cc_final: 0.8828 (p0) REVERT: B 166 GLN cc_start: 0.8839 (mp10) cc_final: 0.8523 (mp10) REVERT: B 168 ASN cc_start: 0.7750 (t0) cc_final: 0.7242 (t0) REVERT: C 125 GLN cc_start: 0.8682 (mt0) cc_final: 0.8241 (tp40) REVERT: C 146 MET cc_start: 0.8849 (mtm) cc_final: 0.8485 (mtm) REVERT: H 14 ASP cc_start: 0.8532 (m-30) cc_final: 0.8216 (m-30) REVERT: H 16 ASP cc_start: 0.8654 (p0) cc_final: 0.8207 (m-30) REVERT: I 39 ASP cc_start: 0.8001 (t0) cc_final: 0.7791 (t0) REVERT: I 54 ASP cc_start: 0.8826 (t0) cc_final: 0.8612 (t0) REVERT: I 153 GLU cc_start: 0.8897 (tt0) cc_final: 0.8271 (tm-30) REVERT: J 106 LYS cc_start: 0.9153 (tppt) cc_final: 0.8799 (tppt) REVERT: J 120 MET cc_start: 0.7878 (ptp) cc_final: 0.7235 (mpp) REVERT: K 10 GLU cc_start: 0.9017 (tt0) cc_final: 0.8696 (tm-30) REVERT: K 173 GLN cc_start: 0.9218 (tt0) cc_final: 0.8796 (tm-30) REVERT: G 57 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8369 (tm-30) REVERT: G 102 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7732 (pt0) REVERT: G 116 MET cc_start: 0.8506 (mmm) cc_final: 0.8212 (mmm) REVERT: F 44 LEU cc_start: 0.9104 (tp) cc_final: 0.8853 (tp) REVERT: F 74 MET cc_start: 0.8099 (tpt) cc_final: 0.7626 (tpt) outliers start: 31 outliers final: 21 residues processed: 234 average time/residue: 0.1232 time to fit residues: 43.4197 Evaluate side-chains 227 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 1 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 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain N residue 168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073295 restraints weight = 36318.463| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.87 r_work: 0.2964 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15821 Z= 0.112 Angle : 0.483 6.573 21195 Z= 0.254 Chirality : 0.036 0.215 2484 Planarity : 0.003 0.034 2682 Dihedral : 3.429 13.093 2089 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 14.49 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.20), residues: 1881 helix: 1.88 (0.15), residues: 1416 sheet: None (None), residues: 0 loop : -0.94 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 85 TYR 0.023 0.001 TYR B 101 PHE 0.026 0.001 PHE O 114 HIS 0.006 0.000 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00264 (15821) covalent geometry : angle 0.48336 (21195) hydrogen bonds : bond 0.02955 ( 870) hydrogen bonds : angle 3.59061 ( 2598) *********************** 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 241 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.520 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: 0.5749 (ttt-90) cc_final: 0.5203 (mtm-85) REVERT: O 93 TYR cc_start: 0.6565 (t80) cc_final: 0.6204 (t80) REVERT: O 102 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8510 (mm-30) REVERT: O 119 TYR cc_start: 0.8951 (m-80) cc_final: 0.8658 (m-10) REVERT: O 120 MET cc_start: 0.8123 (ppp) cc_final: 0.7622 (ppp) REVERT: A 43 MET cc_start: 0.8906 (mmp) cc_final: 0.8695 (mmm) REVERT: A 106 TYR cc_start: 0.8231 (t80) cc_final: 0.7854 (t80) REVERT: B 80 ASN cc_start: 0.9228 (t0) cc_final: 0.8892 (p0) REVERT: B 166 GLN cc_start: 0.8845 (mp10) cc_final: 0.8524 (mp10) REVERT: B 168 ASN cc_start: 0.7729 (t0) cc_final: 0.7229 (t0) REVERT: C 125 GLN cc_start: 0.8666 (mt0) cc_final: 0.8252 (tp40) REVERT: C 146 MET cc_start: 0.8837 (mtm) cc_final: 0.8486 (mtm) REVERT: H 14 ASP cc_start: 0.8503 (m-30) cc_final: 0.8261 (t70) REVERT: H 86 ASN cc_start: 0.7552 (m-40) cc_final: 0.7304 (m-40) REVERT: I 39 ASP cc_start: 0.7972 (t0) cc_final: 0.7752 (t0) REVERT: I 54 ASP cc_start: 0.8820 (t0) cc_final: 0.8613 (t0) REVERT: I 153 GLU cc_start: 0.8889 (tt0) cc_final: 0.8235 (tm-30) REVERT: I 173 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: J 106 LYS cc_start: 0.9123 (tppt) cc_final: 0.8791 (tppt) REVERT: J 120 MET cc_start: 0.7942 (ptp) cc_final: 0.7306 (mpp) REVERT: J 132 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8061 (mm) REVERT: K 10 GLU cc_start: 0.8994 (tt0) cc_final: 0.8686 (tm-30) REVERT: K 173 GLN cc_start: 0.9207 (tt0) cc_final: 0.8793 (tm-30) REVERT: G 102 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7717 (tt0) REVERT: G 120 MET cc_start: 0.8397 (mpp) cc_final: 0.8135 (ptp) REVERT: F 44 LEU cc_start: 0.9102 (tp) cc_final: 0.8860 (tp) REVERT: F 74 MET cc_start: 0.8229 (tpt) cc_final: 0.8025 (tpt) outliers start: 31 outliers final: 23 residues processed: 227 average time/residue: 0.1135 time to fit residues: 39.1080 Evaluate side-chains 228 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 139 LEU 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 I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 169 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 126 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 113 optimal weight: 0.0050 chunk 185 optimal weight: 6.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 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 = 0.3669 r_free = 0.3669 target = 0.103682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073331 restraints weight = 36124.133| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.87 r_work: 0.2966 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15821 Z= 0.108 Angle : 0.479 6.794 21195 Z= 0.251 Chirality : 0.036 0.221 2484 Planarity : 0.003 0.034 2682 Dihedral : 3.399 15.165 2089 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.62 % Allowed : 14.93 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.20), residues: 1881 helix: 1.91 (0.15), residues: 1416 sheet: None (None), residues: 0 loop : -0.93 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 85 TYR 0.025 0.001 TYR B 101 PHE 0.021 0.001 PHE O 114 HIS 0.006 0.000 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00253 (15821) covalent geometry : angle 0.47868 (21195) hydrogen bonds : bond 0.02865 ( 870) hydrogen bonds : angle 3.52930 ( 2598) *********************** 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 241 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.636 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: 0.5769 (ttt-90) cc_final: 0.5206 (mtm-85) REVERT: O 102 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8544 (mm-30) REVERT: O 119 TYR cc_start: 0.8859 (m-80) cc_final: 0.8619 (m-10) REVERT: O 120 MET cc_start: 0.8155 (ppp) cc_final: 0.7593 (ppp) REVERT: A 43 MET cc_start: 0.8926 (mmp) cc_final: 0.8700 (mmm) REVERT: B 80 ASN cc_start: 0.9215 (t0) cc_final: 0.8905 (p0) REVERT: B 166 GLN cc_start: 0.8851 (mp10) cc_final: 0.8531 (mp10) REVERT: C 125 GLN cc_start: 0.8650 (mt0) cc_final: 0.8255 (tp40) REVERT: C 137 MET cc_start: 0.8315 (ppp) cc_final: 0.8084 (ppp) REVERT: C 146 MET cc_start: 0.8843 (mtm) cc_final: 0.8479 (mtm) REVERT: I 39 ASP cc_start: 0.7975 (t0) cc_final: 0.7759 (t0) REVERT: I 54 ASP cc_start: 0.8805 (t0) cc_final: 0.8593 (t0) REVERT: I 153 GLU cc_start: 0.8872 (tt0) cc_final: 0.8211 (tm-30) REVERT: I 173 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: J 106 LYS cc_start: 0.9108 (tppt) cc_final: 0.8795 (tppt) REVERT: J 120 MET cc_start: 0.7964 (ptp) cc_final: 0.7332 (mpp) REVERT: K 10 GLU cc_start: 0.8984 (tt0) cc_final: 0.8672 (tm-30) REVERT: K 173 GLN cc_start: 0.9201 (tt0) cc_final: 0.8781 (tm-30) REVERT: G 99 GLU cc_start: 0.9242 (tt0) cc_final: 0.8510 (tm-30) REVERT: G 102 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7710 (tt0) REVERT: G 120 MET cc_start: 0.8385 (mpp) cc_final: 0.8141 (ptp) REVERT: F 44 LEU cc_start: 0.9099 (tp) cc_final: 0.8859 (tp) REVERT: F 74 MET cc_start: 0.8209 (tpt) cc_final: 0.7980 (tpt) REVERT: F 116 MET cc_start: 0.7285 (mmp) cc_final: 0.6753 (mmt) outliers start: 29 outliers final: 20 residues processed: 222 average time/residue: 0.1220 time to fit residues: 41.2744 Evaluate side-chains 225 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain N residue 169 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 170 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073573 restraints weight = 36466.369| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.86 r_work: 0.2971 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3125 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= 0.109 Angle : 0.496 7.128 21195 Z= 0.259 Chirality : 0.036 0.230 2484 Planarity : 0.003 0.033 2682 Dihedral : 3.408 15.248 2089 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.34 % Allowed : 15.44 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.21), residues: 1881 helix: 1.92 (0.15), residues: 1419 sheet: None (None), residues: 0 loop : -0.90 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 85 TYR 0.024 0.001 TYR B 101 PHE 0.017 0.001 PHE O 114 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00259 (15821) covalent geometry : angle 0.49568 (21195) hydrogen bonds : bond 0.02819 ( 870) hydrogen bonds : angle 3.49845 ( 2598) *********************** 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 234 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.700 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: 0.5723 (ttt-90) cc_final: 0.5180 (mtm-85) REVERT: O 102 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8585 (mm-30) REVERT: O 119 TYR cc_start: 0.8854 (m-80) cc_final: 0.8595 (m-10) REVERT: O 120 MET cc_start: 0.8128 (ppp) cc_final: 0.7538 (ppp) REVERT: A 43 MET cc_start: 0.8942 (mmp) cc_final: 0.8705 (mmm) REVERT: B 80 ASN cc_start: 0.9227 (t0) cc_final: 0.8945 (p0) REVERT: B 166 GLN cc_start: 0.8842 (mp10) cc_final: 0.8515 (mp10) REVERT: C 1 MET cc_start: 0.5322 (ptt) cc_final: 0.4861 (ptp) REVERT: C 125 GLN cc_start: 0.8640 (mt0) cc_final: 0.8301 (tp40) REVERT: C 137 MET cc_start: 0.8260 (ppp) cc_final: 0.7998 (ppp) REVERT: C 146 MET cc_start: 0.8859 (mtm) cc_final: 0.8496 (mtm) REVERT: I 39 ASP cc_start: 0.8009 (t0) cc_final: 0.7788 (t0) REVERT: I 54 ASP cc_start: 0.8814 (t0) cc_final: 0.8606 (t0) REVERT: I 153 GLU cc_start: 0.8898 (tt0) cc_final: 0.8212 (tm-30) REVERT: I 173 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: J 106 LYS cc_start: 0.9123 (tppt) cc_final: 0.8817 (tppt) REVERT: J 120 MET cc_start: 0.7915 (ptp) cc_final: 0.7364 (mpp) REVERT: J 132 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8084 (mm) REVERT: K 10 GLU cc_start: 0.8990 (tt0) cc_final: 0.8677 (tm-30) REVERT: K 17 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8231 (mt-10) REVERT: K 173 GLN cc_start: 0.9200 (tt0) cc_final: 0.8773 (tm-30) REVERT: G 99 GLU cc_start: 0.9245 (tt0) cc_final: 0.8539 (tm-30) REVERT: G 102 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7713 (tt0) REVERT: G 120 MET cc_start: 0.8377 (mpp) cc_final: 0.8137 (ptp) REVERT: F 44 LEU cc_start: 0.9096 (tp) cc_final: 0.8875 (tp) REVERT: F 74 MET cc_start: 0.8235 (tpt) cc_final: 0.8004 (tpt) REVERT: F 116 MET cc_start: 0.7291 (mmp) cc_final: 0.6847 (mmt) outliers start: 24 outliers final: 18 residues processed: 220 average time/residue: 0.1150 time to fit residues: 38.6793 Evaluate side-chains 220 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain C residue 90 LEU 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 I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 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 = 0.3680 r_free = 0.3680 target = 0.104281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073906 restraints weight = 36457.694| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.87 r_work: 0.2982 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3199 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= 0.105 Angle : 0.498 7.888 21195 Z= 0.260 Chirality : 0.036 0.236 2484 Planarity : 0.003 0.032 2682 Dihedral : 3.383 15.090 2089 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.17 % Allowed : 16.39 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.21), residues: 1881 helix: 1.92 (0.15), residues: 1419 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 85 TYR 0.026 0.001 TYR B 101 PHE 0.017 0.001 PHE O 114 HIS 0.005 0.000 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00244 (15821) covalent geometry : angle 0.49753 (21195) hydrogen bonds : bond 0.02736 ( 870) hydrogen bonds : angle 3.46342 ( 2598) *********************** 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 229 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.703 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: 0.5781 (ttt-90) cc_final: 0.5209 (mtm-85) REVERT: O 102 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8595 (mm-30) REVERT: O 119 TYR cc_start: 0.8831 (m-80) cc_final: 0.8561 (m-10) REVERT: O 120 MET cc_start: 0.8129 (ppp) cc_final: 0.7523 (ppp) REVERT: A 43 MET cc_start: 0.8944 (mmp) cc_final: 0.8706 (mmm) REVERT: B 80 ASN cc_start: 0.9252 (t0) cc_final: 0.8992 (p0) REVERT: B 166 GLN cc_start: 0.8847 (mp10) cc_final: 0.8521 (mp10) REVERT: C 1 MET cc_start: 0.5343 (ptt) cc_final: 0.4920 (ptp) REVERT: C 125 GLN cc_start: 0.8635 (mt0) cc_final: 0.8311 (tp40) REVERT: C 137 MET cc_start: 0.8245 (ppp) cc_final: 0.7976 (ppp) REVERT: C 146 MET cc_start: 0.8862 (mtm) cc_final: 0.8508 (mtm) REVERT: H 139 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8492 (mt-10) REVERT: I 39 ASP cc_start: 0.7999 (t0) cc_final: 0.7771 (t0) REVERT: I 153 GLU cc_start: 0.8894 (tt0) cc_final: 0.8187 (tm-30) REVERT: I 173 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: J 106 LYS cc_start: 0.9132 (tppt) cc_final: 0.8830 (tppt) REVERT: J 120 MET cc_start: 0.7975 (ptp) cc_final: 0.7365 (mpp) REVERT: K 10 GLU cc_start: 0.8973 (tt0) cc_final: 0.8705 (tm-30) REVERT: K 173 GLN cc_start: 0.9190 (tt0) cc_final: 0.8776 (tm-30) REVERT: G 99 GLU cc_start: 0.9215 (tt0) cc_final: 0.8497 (tm-30) REVERT: G 102 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7695 (tt0) REVERT: G 120 MET cc_start: 0.8375 (mpp) cc_final: 0.8135 (ptp) REVERT: F 54 ASP cc_start: 0.8727 (t0) cc_final: 0.8267 (m-30) REVERT: F 74 MET cc_start: 0.8258 (tpt) cc_final: 0.8040 (tpt) REVERT: F 116 MET cc_start: 0.7233 (mmp) cc_final: 0.6871 (mmt) outliers start: 21 outliers final: 19 residues processed: 216 average time/residue: 0.1111 time to fit residues: 37.5433 Evaluate side-chains 220 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 184 optimal weight: 2.9990 chunk 84 optimal weight: 0.0040 chunk 180 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** K 82 HIS ** 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 = 0.3643 r_free = 0.3643 target = 0.101903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071500 restraints weight = 36728.159| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.86 r_work: 0.2930 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15821 Z= 0.166 Angle : 0.563 7.524 21195 Z= 0.291 Chirality : 0.038 0.234 2484 Planarity : 0.003 0.035 2682 Dihedral : 3.563 16.105 2089 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.40 % Allowed : 16.39 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.21), residues: 1881 helix: 1.86 (0.15), residues: 1415 sheet: None (None), residues: 0 loop : -0.86 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 85 TYR 0.027 0.002 TYR B 101 PHE 0.014 0.001 PHE O 114 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00404 (15821) covalent geometry : angle 0.56296 (21195) hydrogen bonds : bond 0.03527 ( 870) hydrogen bonds : angle 3.75773 ( 2598) ********************** 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 231 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.678 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: 0.5802 (ttt-90) cc_final: 0.5183 (mtm-85) REVERT: O 102 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8506 (mm-30) REVERT: O 119 TYR cc_start: 0.8841 (m-80) cc_final: 0.8557 (m-10) REVERT: O 120 MET cc_start: 0.8104 (ppp) cc_final: 0.7514 (ppp) REVERT: A 43 MET cc_start: 0.8968 (mmp) cc_final: 0.8693 (mmm) REVERT: B 80 ASN cc_start: 0.9257 (t0) cc_final: 0.8975 (p0) REVERT: B 166 GLN cc_start: 0.8847 (mp10) cc_final: 0.8521 (mp10) REVERT: B 168 ASN cc_start: 0.7684 (t0) cc_final: 0.7158 (t0) REVERT: C 125 GLN cc_start: 0.8655 (mt0) cc_final: 0.8313 (tp40) REVERT: C 137 MET cc_start: 0.8290 (ppp) cc_final: 0.7984 (ppp) REVERT: C 146 MET cc_start: 0.8971 (mtm) cc_final: 0.8629 (mtm) REVERT: I 153 GLU cc_start: 0.8910 (tt0) cc_final: 0.8228 (tm-30) REVERT: I 173 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: J 106 LYS cc_start: 0.9184 (tppt) cc_final: 0.8876 (tppt) REVERT: J 120 MET cc_start: 0.7991 (ptp) cc_final: 0.7400 (mpp) REVERT: K 10 GLU cc_start: 0.9021 (tt0) cc_final: 0.8703 (tm-30) REVERT: K 173 GLN cc_start: 0.9213 (tt0) cc_final: 0.8786 (tm-30) REVERT: G 99 GLU cc_start: 0.9261 (tt0) cc_final: 0.8581 (tm-30) REVERT: G 102 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7734 (tt0) REVERT: F 54 ASP cc_start: 0.8751 (t0) cc_final: 0.8260 (m-30) REVERT: F 74 MET cc_start: 0.8267 (tpt) cc_final: 0.8029 (tpt) REVERT: F 116 MET cc_start: 0.7254 (mmp) cc_final: 0.6903 (mmt) outliers start: 25 outliers final: 21 residues processed: 217 average time/residue: 0.1151 time to fit residues: 38.9957 Evaluate side-chains 224 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 90 LEU 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 I residue 97 MET Chi-restraints excluded: chain I residue 173 GLN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN C 91 GLN ** K 82 HIS ** 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 = 0.3667 r_free = 0.3667 target = 0.103432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072936 restraints weight = 36323.904| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.87 r_work: 0.2965 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3281 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= 0.116 Angle : 0.540 8.636 21195 Z= 0.279 Chirality : 0.036 0.236 2484 Planarity : 0.003 0.033 2682 Dihedral : 3.506 15.146 2089 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.34 % Allowed : 16.44 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.20), residues: 1881 helix: 1.88 (0.15), residues: 1419 sheet: None (None), residues: 0 loop : -0.90 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 85 TYR 0.028 0.001 TYR B 101 PHE 0.016 0.001 PHE O 114 HIS 0.005 0.000 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00276 (15821) covalent geometry : angle 0.54012 (21195) hydrogen bonds : bond 0.02958 ( 870) hydrogen bonds : angle 3.55997 ( 2598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.40 seconds wall clock time: 60 minutes 42.80 seconds (3642.80 seconds total)