Starting phenix.real_space_refine on Sat Mar 7 13:37:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lsx_23508/03_2026/7lsx_23508.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lsx_23508/03_2026/7lsx_23508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lsx_23508/03_2026/7lsx_23508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lsx_23508/03_2026/7lsx_23508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lsx_23508/03_2026/7lsx_23508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lsx_23508/03_2026/7lsx_23508.map" } resolution = 3.61 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= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 79 5.16 5 C 14125 2.51 5 N 3717 2.21 5 O 4296 1.98 5 H 22176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44393 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3850 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 234} Chain: "B" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 3791 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "C" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3676 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "D" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3700 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "E" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 3827 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3614 Classifications: {'peptide': 234} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "G" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3796 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "H" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1490 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "I" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3131 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 3 Chain: "J" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2740 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 2 Chain: "K" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2937 Classifications: {'peptide': 182} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Chain: "O" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3768 Classifications: {'peptide': 240} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 221} Chain breaks: 1 Chain: "P" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 4073 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 1 Time building chain proxies: 7.67, per 1000 atoms: 0.17 Number of scatterers: 44393 At special positions: 0 Unit cell: (150.52, 121.9, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 O 4296 8.00 N 3717 7.00 C 14125 6.00 H 22176 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 22 sheets defined 42.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.719A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.589A pdb=" N THR A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.732A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.678A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.537A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.908A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.861A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.694A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.726A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.650A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 removed outlier: 4.079A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.506A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.555A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.916A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.019A pdb=" N ASN D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.511A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 4.198A pdb=" N ILE E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.694A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 232 through 247 Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 29 through 32 Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.662A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.546A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 185 through 199 removed outlier: 4.029A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.038A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.637A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.713A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.785A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.073A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'H' and resid 53 through 59 removed outlier: 4.360A pdb=" N ASN H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 77 Processing helix chain 'H' and resid 78 through 95 removed outlier: 3.641A pdb=" N THR H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 111 removed outlier: 3.679A pdb=" N ASP H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.628A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 146 No H-bonds generated for 'chain 'I' and resid 144 through 146' Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.752A pdb=" N ALA I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 152 Processing helix chain 'J' and resid 159 through 173 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 92 Processing helix chain 'K' and resid 93 through 95 No H-bonds generated for 'chain 'K' and resid 93 through 95' Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.837A pdb=" N PHE K 138 " --> pdb=" O TYR K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 148 removed outlier: 4.758A pdb=" N HIS K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'O' and resid 39 through 47 removed outlier: 3.559A pdb=" N LEU O 42 " --> pdb=" O PRO O 39 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP O 43 " --> pdb=" O GLN O 40 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL O 44 " --> pdb=" O ASP O 41 " (cutoff:3.500A) Proline residue: O 45 - end of helix No H-bonds generated for 'chain 'O' and resid 39 through 47' Processing helix chain 'O' and resid 55 through 61 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 143 through 159 removed outlier: 3.938A pdb=" N GLY O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 206 Processing helix chain 'O' and resid 231 through 247 removed outlier: 4.291A pdb=" N GLN O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP O 245 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 263 Processing helix chain 'O' and resid 270 through 275 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 13 through 26 Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 94 through 102 removed outlier: 3.659A pdb=" N ILE P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 110 Processing helix chain 'P' and resid 126 through 130 removed outlier: 3.864A pdb=" N VAL P 130 " --> pdb=" O GLU P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 156 Processing helix chain 'P' and resid 182 through 193 removed outlier: 4.312A pdb=" N PHE P 186 " --> pdb=" O ASP P 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 231 Processing helix chain 'P' and resid 238 through 242 removed outlier: 4.520A pdb=" N VAL P 241 " --> pdb=" O PRO P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 254 removed outlier: 4.355A pdb=" N TYR P 253 " --> pdb=" O GLN P 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.848A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.507A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.015A pdb=" N LEU C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 77 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS C 68 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 75 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 70 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 147 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.267A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.664A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.538A pdb=" N ASP E 148 " --> pdb=" O GLY E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.579A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 132 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.626A pdb=" N SER G 37 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 50 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.401A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.433A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 243 through 246 removed outlier: 3.863A pdb=" N CYS J 20 " --> pdb=" O GLY J 17 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 43 through 46 Processing sheet with id=AC1, first strand: chain 'K' and resid 130 through 133 removed outlier: 3.929A pdb=" N ILE K 4 " --> pdb=" O HIS K 133 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP K 185 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.268A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN K 101 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 35 through 37 removed outlier: 6.635A pdb=" N ILE O 124 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU O 73 " --> pdb=" O PHE O 122 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE O 122 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS O 75 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE O 120 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR O 77 " --> pdb=" O TYR O 118 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR O 118 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER O 134 " --> pdb=" O PRO O 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE O 52 " --> pdb=" O ILE O 166 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE O 165 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU O 217 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL O 167 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA O 219 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY O 169 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 30 through 35 removed outlier: 7.105A pdb=" N VAL P 72 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA P 35 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU P 70 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU P 71 " --> pdb=" O GLN P 84 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS P 3 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE P 83 " --> pdb=" O CYS P 3 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL P 5 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLN P 85 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU P 4 " --> pdb=" O CYS P 116 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP P 118 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU P 6 " --> pdb=" O TRP P 118 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N SER P 120 " --> pdb=" O LEU P 6 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE P 115 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS P 208 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE P 117 " --> pdb=" O CYS P 208 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N CYS P 210 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP P 119 " --> pdb=" O CYS P 210 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA P 212 " --> pdb=" O ASP P 119 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU P 121 " --> pdb=" O ALA P 212 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3267 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: 12.81 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22142 1.03 - 1.23: 36 1.23 - 1.42: 9383 1.42 - 1.61: 13123 1.61 - 1.81: 124 Bond restraints: 44808 Sorted by residual: bond pdb=" N ASP A 212 " pdb=" H ASP A 212 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" N GLY A 215 " pdb=" H GLY A 215 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N THR A 216 " pdb=" H THR A 216 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" N ALA A 213 " pdb=" CA ALA A 213 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.17e-02 7.31e+03 5.82e+00 bond pdb=" CA ALA A 213 " pdb=" CB ALA A 213 " ideal model delta sigma weight residual 1.537 1.497 0.040 1.76e-02 3.23e+03 5.12e+00 ... (remaining 44803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.96: 81041 6.96 - 13.92: 2 13.92 - 20.89: 0 20.89 - 27.85: 0 27.85 - 34.81: 3 Bond angle restraints: 81046 Sorted by residual: angle pdb=" C ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 109.00 74.19 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 110.00 75.39 34.61 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 109.00 75.21 33.79 3.00e+00 1.11e-01 1.27e+02 angle pdb=" N LEU A 214 " pdb=" CA LEU A 214 " pdb=" C LEU A 214 " ideal model delta sigma weight residual 111.28 103.03 8.25 1.09e+00 8.42e-01 5.73e+01 angle pdb=" CA THR A 216 " pdb=" C THR A 216 " pdb=" O THR A 216 " ideal model delta sigma weight residual 120.36 116.04 4.32 1.08e+00 8.57e-01 1.60e+01 ... (remaining 81041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19424 17.96 - 35.91: 1195 35.91 - 53.87: 319 53.87 - 71.83: 96 71.83 - 89.79: 21 Dihedral angle restraints: 21055 sinusoidal: 11493 harmonic: 9562 Sorted by residual: dihedral pdb=" CA PHE I 37 " pdb=" C PHE I 37 " pdb=" N ASN I 38 " pdb=" CA ASN I 38 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP P 260 " pdb=" C ASP P 260 " pdb=" N LYS P 261 " pdb=" CA LYS P 261 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN G 21 " pdb=" C ASN G 21 " pdb=" N PHE G 22 " pdb=" CA PHE G 22 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 21052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3110 0.067 - 0.135: 351 0.135 - 0.202: 6 0.202 - 0.269: 0 0.269 - 0.336: 1 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA ALA P 69 " pdb=" N ALA P 69 " pdb=" C ALA P 69 " pdb=" CB ALA P 69 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA LEU A 214 " pdb=" N LEU A 214 " pdb=" C LEU A 214 " pdb=" CB LEU A 214 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA ILE I 32 " pdb=" N ILE I 32 " pdb=" C ILE I 32 " pdb=" CB ILE I 32 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 3465 not shown) Planarity restraints: 6640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 211 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ILE A 211 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 211 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 212 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 7 " -0.010 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" N ASN J 8 " 0.032 2.00e-02 2.50e+03 pdb=" CA ASN J 8 " -0.008 2.00e-02 2.50e+03 pdb=" H ASN J 8 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 252 " -0.131 9.50e-02 1.11e+02 4.45e-02 3.30e+00 pdb=" NE ARG O 252 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG O 252 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG O 252 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG O 252 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG O 252 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG O 252 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG O 252 " -0.010 2.00e-02 2.50e+03 pdb="HH22 ARG O 252 " 0.008 2.00e-02 2.50e+03 ... (remaining 6637 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1670 2.17 - 2.77: 89237 2.77 - 3.38: 126234 3.38 - 3.99: 164107 3.99 - 4.60: 257261 Nonbonded interactions: 638509 Sorted by model distance: nonbonded pdb=" OE2 GLU G 51 " pdb=" HD1 HIS G 204 " model vdw 1.557 2.450 nonbonded pdb=" HD1 HIS B 94 " pdb=" OG SER I 90 " model vdw 1.563 2.450 nonbonded pdb=" H LYS C 231 " pdb=" OE2 GLU C 234 " model vdw 1.585 2.450 nonbonded pdb=" HH TYR G 126 " pdb=" OE2 GLU H 87 " model vdw 1.593 2.450 nonbonded pdb=" OE2 GLU G 32 " pdb="HH12 ARG G 169 " model vdw 1.595 2.450 ... (remaining 638504 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 0.700 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 43.890 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.003 0.051 22632 Z= 0.143 Angle : 0.553 8.250 30616 Z= 0.318 Chirality : 0.041 0.336 3468 Planarity : 0.003 0.059 3932 Dihedral : 12.740 89.786 8369 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.77 (0.16), residues: 2792 helix: 1.51 (0.17), residues: 1002 sheet: 0.12 (0.20), residues: 608 loop : -0.01 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 252 TYR 0.023 0.001 TYR K 135 PHE 0.024 0.001 PHE J 44 TRP 0.013 0.001 TRP B 159 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00289 (22632) covalent geometry : angle 0.55262 (30616) hydrogen bonds : bond 0.17154 ( 1159) hydrogen bonds : angle 7.23950 ( 3267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7747 (m-80) cc_final: 0.7504 (m-80) REVERT: B 57 MET cc_start: 0.8191 (mtm) cc_final: 0.7811 (mtm) REVERT: B 119 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8691 (tm-30) REVERT: C 122 TYR cc_start: 0.8119 (m-10) cc_final: 0.7816 (m-10) REVERT: E 206 GLN cc_start: 0.9516 (tp-100) cc_final: 0.8932 (tp-100) REVERT: H 70 GLU cc_start: 0.8539 (tp30) cc_final: 0.7894 (tp30) REVERT: O 8 ASP cc_start: 0.7638 (m-30) cc_final: 0.7313 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3691 time to fit residues: 126.1512 Evaluate side-chains 173 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN G 118 GLN I 64 HIS J 89 GLN K 78 GLN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.110515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.086877 restraints weight = 162692.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091622 restraints weight = 62856.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094633 restraints weight = 33429.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.096578 restraints weight = 21174.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.097762 restraints weight = 14956.598| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22632 Z= 0.169 Angle : 0.556 7.916 30616 Z= 0.305 Chirality : 0.043 0.323 3468 Planarity : 0.004 0.048 3932 Dihedral : 4.864 23.159 3057 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.29 % Allowed : 4.11 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.67 (0.16), residues: 2792 helix: 1.50 (0.16), residues: 1021 sheet: 0.02 (0.20), residues: 627 loop : -0.16 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 252 TYR 0.021 0.001 TYR G 126 PHE 0.018 0.001 PHE B 157 TRP 0.015 0.001 TRP B 159 HIS 0.011 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00358 (22632) covalent geometry : angle 0.55557 (30616) hydrogen bonds : bond 0.04719 ( 1159) hydrogen bonds : angle 5.75531 ( 3267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.8117 (mtm) cc_final: 0.7685 (mtm) REVERT: B 119 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8681 (tm-30) REVERT: F 146 GLU cc_start: 0.6850 (tt0) cc_final: 0.6566 (tt0) REVERT: H 70 GLU cc_start: 0.8602 (tp30) cc_final: 0.8038 (tp30) REVERT: H 86 MET cc_start: 0.8660 (ttm) cc_final: 0.8408 (ttm) REVERT: H 87 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8273 (mm-30) REVERT: I 39 ASN cc_start: 0.8185 (m-40) cc_final: 0.7675 (t0) REVERT: I 208 GLU cc_start: 0.7232 (tp30) cc_final: 0.6438 (mm-30) REVERT: K 127 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6485 (tm-30) REVERT: O 8 ASP cc_start: 0.7704 (m-30) cc_final: 0.7270 (p0) outliers start: 7 outliers final: 5 residues processed: 187 average time/residue: 0.3771 time to fit residues: 112.0605 Evaluate side-chains 168 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain O residue 168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 256 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.0980 chunk 186 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 266 optimal weight: 0.0170 chunk 34 optimal weight: 0.5980 overall best weight: 0.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN K 133 HIS O 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070764 restraints weight = 159175.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075537 restraints weight = 61448.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078673 restraints weight = 33043.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080667 restraints weight = 21094.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082069 restraints weight = 15131.302| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 22632 Z= 0.105 Angle : 0.506 6.084 30616 Z= 0.272 Chirality : 0.042 0.325 3468 Planarity : 0.004 0.046 3932 Dihedral : 4.638 21.854 3057 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.41 % Allowed : 5.31 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.77 (0.16), residues: 2792 helix: 1.64 (0.16), residues: 1026 sheet: -0.00 (0.19), residues: 630 loop : -0.12 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.017 0.001 TYR C 122 PHE 0.018 0.001 PHE F 179 TRP 0.010 0.001 TRP B 159 HIS 0.009 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00229 (22632) covalent geometry : angle 0.50591 (30616) hydrogen bonds : bond 0.03846 ( 1159) hydrogen bonds : angle 5.23637 ( 3267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 MET cc_start: 0.8197 (mmm) cc_final: 0.7622 (mmm) REVERT: B 119 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8655 (tm-30) REVERT: C 9 ARG cc_start: 0.7667 (mtt90) cc_final: 0.7410 (mtm-85) REVERT: F 146 GLU cc_start: 0.6823 (tt0) cc_final: 0.6462 (tt0) REVERT: H 70 GLU cc_start: 0.8571 (tp30) cc_final: 0.7950 (tp30) REVERT: H 86 MET cc_start: 0.8621 (ttm) cc_final: 0.8320 (ttm) REVERT: H 87 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8306 (mm-30) REVERT: I 39 ASN cc_start: 0.8285 (m-40) cc_final: 0.7635 (t0) REVERT: I 93 GLU cc_start: 0.8770 (tp30) cc_final: 0.7949 (tm-30) REVERT: I 208 GLU cc_start: 0.7171 (tp30) cc_final: 0.6446 (mm-30) REVERT: K 49 GLU cc_start: 0.8002 (pm20) cc_final: 0.7799 (pm20) REVERT: K 112 ASN cc_start: 0.8825 (t0) cc_final: 0.8617 (t0) REVERT: O 7 ASN cc_start: 0.8963 (t0) cc_final: 0.8743 (t0) REVERT: O 8 ASP cc_start: 0.7796 (m-30) cc_final: 0.7176 (p0) REVERT: O 248 PHE cc_start: 0.7823 (m-80) cc_final: 0.7495 (m-10) outliers start: 10 outliers final: 8 residues processed: 189 average time/residue: 0.3605 time to fit residues: 109.3871 Evaluate side-chains 174 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 206 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN K 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.106506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085047 restraints weight = 162198.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.089774 restraints weight = 65538.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.092873 restraints weight = 35984.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094874 restraints weight = 23084.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.096119 restraints weight = 16471.702| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22632 Z= 0.174 Angle : 0.520 6.994 30616 Z= 0.281 Chirality : 0.042 0.330 3468 Planarity : 0.004 0.047 3932 Dihedral : 4.628 22.377 3057 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.53 % Allowed : 6.58 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.66 (0.16), residues: 2792 helix: 1.67 (0.16), residues: 1027 sheet: -0.19 (0.20), residues: 637 loop : -0.22 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.017 0.001 TYR J 96 PHE 0.016 0.001 PHE F 179 TRP 0.011 0.001 TRP G 218 HIS 0.010 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00384 (22632) covalent geometry : angle 0.51952 (30616) hydrogen bonds : bond 0.03616 ( 1159) hydrogen bonds : angle 5.10660 ( 3267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7025 (t80) REVERT: B 119 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8658 (tm-30) REVERT: H 70 GLU cc_start: 0.8620 (tp30) cc_final: 0.8102 (tp30) REVERT: H 86 MET cc_start: 0.8665 (ttm) cc_final: 0.8386 (ttm) REVERT: H 87 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8221 (mm-30) REVERT: I 39 ASN cc_start: 0.8293 (m-40) cc_final: 0.7700 (t0) REVERT: I 93 GLU cc_start: 0.8703 (tp30) cc_final: 0.7983 (tm-30) REVERT: I 208 GLU cc_start: 0.7287 (tp30) cc_final: 0.6641 (mm-30) REVERT: K 112 ASN cc_start: 0.8742 (t0) cc_final: 0.8528 (t0) REVERT: K 127 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6463 (tm-30) REVERT: O 8 ASP cc_start: 0.7705 (m-30) cc_final: 0.7094 (p0) REVERT: P 209 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8225 (p) outliers start: 13 outliers final: 10 residues processed: 174 average time/residue: 0.3730 time to fit residues: 102.5445 Evaluate side-chains 172 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 220 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083328 restraints weight = 162476.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.088093 restraints weight = 62988.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091166 restraints weight = 33908.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.093177 restraints weight = 21635.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.094452 restraints weight = 15344.250| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22632 Z= 0.175 Angle : 0.519 6.399 30616 Z= 0.280 Chirality : 0.042 0.333 3468 Planarity : 0.004 0.048 3932 Dihedral : 4.633 21.547 3057 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.74 % Allowed : 7.49 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.57 (0.16), residues: 2792 helix: 1.62 (0.16), residues: 1030 sheet: -0.27 (0.20), residues: 632 loop : -0.29 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 9 TYR 0.028 0.001 TYR B 82 PHE 0.015 0.001 PHE F 179 TRP 0.011 0.001 TRP G 218 HIS 0.011 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00389 (22632) covalent geometry : angle 0.51924 (30616) hydrogen bonds : bond 0.03491 ( 1159) hydrogen bonds : angle 4.97612 ( 3267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7088 (t80) REVERT: B 57 MET cc_start: 0.8159 (mtm) cc_final: 0.7780 (mtm) REVERT: B 119 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 146 GLU cc_start: 0.6853 (tt0) cc_final: 0.6551 (tt0) REVERT: H 70 GLU cc_start: 0.8660 (tp30) cc_final: 0.8080 (tp30) REVERT: H 87 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8200 (mm-30) REVERT: I 39 ASN cc_start: 0.8432 (m-40) cc_final: 0.7900 (t0) REVERT: I 93 GLU cc_start: 0.8773 (tp30) cc_final: 0.8010 (tm-30) REVERT: I 208 GLU cc_start: 0.7348 (tp30) cc_final: 0.6744 (mm-30) REVERT: K 115 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7277 (mt-10) REVERT: O 8 ASP cc_start: 0.7839 (m-30) cc_final: 0.7008 (p0) outliers start: 18 outliers final: 15 residues processed: 173 average time/residue: 0.3675 time to fit residues: 101.5666 Evaluate side-chains 171 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 180 MET Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084887 restraints weight = 162301.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089693 restraints weight = 63339.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092857 restraints weight = 34312.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.094901 restraints weight = 21862.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.096156 restraints weight = 15490.514| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22632 Z= 0.142 Angle : 0.500 6.079 30616 Z= 0.268 Chirality : 0.041 0.329 3468 Planarity : 0.004 0.046 3932 Dihedral : 4.527 21.126 3057 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.70 % Allowed : 8.19 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.67 (0.16), residues: 2792 helix: 1.73 (0.16), residues: 1030 sheet: -0.24 (0.20), residues: 631 loop : -0.25 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 14 TYR 0.015 0.001 TYR J 96 PHE 0.015 0.001 PHE F 179 TRP 0.010 0.001 TRP G 218 HIS 0.009 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00316 (22632) covalent geometry : angle 0.49982 (30616) hydrogen bonds : bond 0.03305 ( 1159) hydrogen bonds : angle 4.84138 ( 3267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7074 (t80) REVERT: B 57 MET cc_start: 0.8269 (mtm) cc_final: 0.7776 (mtm) REVERT: B 119 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8672 (tm-30) REVERT: F 146 GLU cc_start: 0.6836 (tt0) cc_final: 0.6555 (tt0) REVERT: H 70 GLU cc_start: 0.8658 (tp30) cc_final: 0.8074 (tp30) REVERT: H 86 MET cc_start: 0.8621 (ttm) cc_final: 0.8343 (ttm) REVERT: H 87 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8245 (mm-30) REVERT: I 39 ASN cc_start: 0.8437 (m-40) cc_final: 0.7878 (t0) REVERT: I 93 GLU cc_start: 0.8774 (tp30) cc_final: 0.7967 (tm-30) REVERT: I 208 GLU cc_start: 0.7334 (tp30) cc_final: 0.6773 (mm-30) REVERT: K 127 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6474 (tm-30) REVERT: O 8 ASP cc_start: 0.7946 (m-30) cc_final: 0.6967 (p0) outliers start: 17 outliers final: 16 residues processed: 178 average time/residue: 0.3496 time to fit residues: 99.7374 Evaluate side-chains 170 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 180 MET Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 200 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.088682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070278 restraints weight = 165545.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074652 restraints weight = 65311.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077557 restraints weight = 35439.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079448 restraints weight = 22772.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080719 restraints weight = 16359.257| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22632 Z= 0.165 Angle : 0.511 6.090 30616 Z= 0.274 Chirality : 0.041 0.332 3468 Planarity : 0.004 0.048 3932 Dihedral : 4.517 21.188 3057 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.78 % Allowed : 8.56 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.64 (0.16), residues: 2792 helix: 1.75 (0.16), residues: 1030 sheet: -0.30 (0.20), residues: 630 loop : -0.29 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 259 TYR 0.016 0.001 TYR C 122 PHE 0.014 0.001 PHE F 179 TRP 0.011 0.001 TRP G 218 HIS 0.009 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00365 (22632) covalent geometry : angle 0.51133 (30616) hydrogen bonds : bond 0.03282 ( 1159) hydrogen bonds : angle 4.82176 ( 3267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 119 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 146 GLU cc_start: 0.6828 (tt0) cc_final: 0.6544 (tt0) REVERT: H 70 GLU cc_start: 0.8666 (tp30) cc_final: 0.7958 (tp30) REVERT: H 86 MET cc_start: 0.8609 (ttm) cc_final: 0.8309 (ttm) REVERT: H 87 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8315 (mm-30) REVERT: I 93 GLU cc_start: 0.8790 (tp30) cc_final: 0.7844 (tm-30) REVERT: I 208 GLU cc_start: 0.7316 (tp30) cc_final: 0.7105 (tp30) REVERT: K 115 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7275 (mt-10) REVERT: O 8 ASP cc_start: 0.7819 (m-30) cc_final: 0.6942 (p0) outliers start: 19 outliers final: 18 residues processed: 171 average time/residue: 0.3747 time to fit residues: 102.3212 Evaluate side-chains 175 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain O residue 180 MET Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 255 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 154 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN O 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083567 restraints weight = 162723.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.088278 restraints weight = 63805.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091339 restraints weight = 34728.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093237 restraints weight = 22364.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.094614 restraints weight = 16209.435| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22632 Z= 0.182 Angle : 0.519 6.123 30616 Z= 0.279 Chirality : 0.041 0.332 3468 Planarity : 0.004 0.047 3932 Dihedral : 4.535 21.244 3057 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.90 % Allowed : 9.05 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.62 (0.16), residues: 2792 helix: 1.76 (0.16), residues: 1031 sheet: -0.34 (0.20), residues: 627 loop : -0.31 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 93 TYR 0.017 0.001 TYR J 96 PHE 0.013 0.001 PHE F 179 TRP 0.011 0.001 TRP G 218 HIS 0.009 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00404 (22632) covalent geometry : angle 0.51904 (30616) hydrogen bonds : bond 0.03299 ( 1159) hydrogen bonds : angle 4.82773 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7180 (t80) REVERT: B 119 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8634 (tm-30) REVERT: H 70 GLU cc_start: 0.8671 (tp30) cc_final: 0.8027 (tp30) REVERT: H 86 MET cc_start: 0.8623 (ttm) cc_final: 0.8369 (ttm) REVERT: H 87 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8279 (mm-30) REVERT: I 7 ASP cc_start: 0.7600 (m-30) cc_final: 0.7316 (t0) REVERT: I 93 GLU cc_start: 0.8777 (tp30) cc_final: 0.7976 (tm-30) REVERT: K 127 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6501 (tm-30) REVERT: O 8 ASP cc_start: 0.7771 (m-30) cc_final: 0.6933 (p0) outliers start: 22 outliers final: 20 residues processed: 174 average time/residue: 0.3814 time to fit residues: 105.3490 Evaluate side-chains 176 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain O residue 180 MET Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 261 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068594 restraints weight = 160429.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073247 restraints weight = 62602.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076339 restraints weight = 34056.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078272 restraints weight = 21931.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079617 restraints weight = 15925.113| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22632 Z= 0.119 Angle : 0.498 9.145 30616 Z= 0.264 Chirality : 0.041 0.330 3468 Planarity : 0.004 0.046 3932 Dihedral : 4.426 21.154 3057 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.74 % Allowed : 9.42 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.80 (0.16), residues: 2792 helix: 1.89 (0.16), residues: 1031 sheet: -0.24 (0.20), residues: 629 loop : -0.20 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 14 TYR 0.018 0.001 TYR C 122 PHE 0.015 0.001 PHE F 179 TRP 0.010 0.001 TRP G 218 HIS 0.008 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00267 (22632) covalent geometry : angle 0.49788 (30616) hydrogen bonds : bond 0.03113 ( 1159) hydrogen bonds : angle 4.69109 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 78 MET cc_start: 0.8202 (mmm) cc_final: 0.7815 (mmm) REVERT: B 119 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8605 (tm-30) REVERT: H 70 GLU cc_start: 0.8628 (tp30) cc_final: 0.7917 (tp30) REVERT: H 86 MET cc_start: 0.8557 (ttm) cc_final: 0.8281 (ttm) REVERT: H 87 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8315 (mm-30) REVERT: I 7 ASP cc_start: 0.7587 (m-30) cc_final: 0.7245 (t0) REVERT: I 93 GLU cc_start: 0.8819 (tp30) cc_final: 0.7891 (tm-30) REVERT: K 127 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6479 (tm-30) REVERT: O 8 ASP cc_start: 0.7831 (m-30) cc_final: 0.6891 (p0) outliers start: 18 outliers final: 16 residues processed: 173 average time/residue: 0.3791 time to fit residues: 104.1717 Evaluate side-chains 176 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain O residue 180 MET Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.081069 restraints weight = 158264.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085522 restraints weight = 62605.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088410 restraints weight = 34149.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090252 restraints weight = 21989.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.091440 restraints weight = 15821.994| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22632 Z= 0.229 Angle : 0.547 7.082 30616 Z= 0.295 Chirality : 0.042 0.333 3468 Planarity : 0.004 0.047 3932 Dihedral : 4.563 22.717 3057 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.78 % Allowed : 9.26 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.58 (0.16), residues: 2792 helix: 1.75 (0.16), residues: 1031 sheet: -0.36 (0.20), residues: 627 loop : -0.36 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 14 TYR 0.019 0.001 TYR J 96 PHE 0.013 0.002 PHE O 248 TRP 0.011 0.001 TRP B 159 HIS 0.009 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00509 (22632) covalent geometry : angle 0.54698 (30616) hydrogen bonds : bond 0.03370 ( 1159) hydrogen bonds : angle 4.85842 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 MET cc_start: 0.8504 (mmm) cc_final: 0.8146 (mmm) REVERT: B 119 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8592 (tm-30) REVERT: H 70 GLU cc_start: 0.8700 (tp30) cc_final: 0.8080 (tp30) REVERT: H 86 MET cc_start: 0.8624 (ttm) cc_final: 0.8370 (ttm) REVERT: H 112 ASN cc_start: 0.8599 (t0) cc_final: 0.8366 (t0) REVERT: I 7 ASP cc_start: 0.7634 (m-30) cc_final: 0.7360 (t0) REVERT: I 93 GLU cc_start: 0.8772 (tp30) cc_final: 0.8020 (tm-30) REVERT: K 127 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6529 (tm-30) REVERT: O 8 ASP cc_start: 0.7760 (m-30) cc_final: 0.6915 (p0) outliers start: 19 outliers final: 17 residues processed: 164 average time/residue: 0.3812 time to fit residues: 98.9669 Evaluate side-chains 170 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain O residue 180 MET Chi-restraints excluded: chain P residue 209 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 5 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083993 restraints weight = 163154.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088607 restraints weight = 66136.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091598 restraints weight = 36621.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.093542 restraints weight = 23848.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094827 restraints weight = 17218.243| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22632 Z= 0.172 Angle : 0.521 7.151 30616 Z= 0.279 Chirality : 0.041 0.333 3468 Planarity : 0.004 0.048 3932 Dihedral : 4.522 22.436 3057 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.78 % Allowed : 9.30 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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 are not related in a simple way. whole: 0.62 (0.16), residues: 2792 helix: 1.79 (0.16), residues: 1031 sheet: -0.36 (0.20), residues: 629 loop : -0.33 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 252 TYR 0.016 0.001 TYR J 96 PHE 0.013 0.001 PHE O 248 TRP 0.011 0.001 TRP G 218 HIS 0.009 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00384 (22632) covalent geometry : angle 0.52096 (30616) hydrogen bonds : bond 0.03239 ( 1159) hydrogen bonds : angle 4.77644 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5690.93 seconds wall clock time: 98 minutes 50.50 seconds (5930.50 seconds total)