Starting phenix.real_space_refine on Sun May 3 19:45:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ugg_64138/05_2026/9ugg_64138.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ugg_64138/05_2026/9ugg_64138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ugg_64138/05_2026/9ugg_64138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ugg_64138/05_2026/9ugg_64138.map" model { file = "/net/cci-nas-00/data/ceres_data/9ugg_64138/05_2026/9ugg_64138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ugg_64138/05_2026/9ugg_64138.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.032 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 P 8 5.49 5 S 69 5.16 5 C 9650 2.51 5 N 2473 2.21 5 O 2661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14861 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1945 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1937 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain: "C" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1953 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "D" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1964 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain: "E" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3463 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3491 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 7, 'TRANS': 427} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.39, per 1000 atoms: 0.23 Number of scatterers: 14861 At special positions: 0 Unit cell: (98.58, 124.02, 120.84, 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 69 16.00 P 8 15.00 O 2661 8.00 N 2473 7.00 C 9650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 631.5 milliseconds 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 55.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.654A pdb=" N THR A 75 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.951A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.556A pdb=" N ILE A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 4.401A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 removed outlier: 4.159A pdb=" N ALA A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 4.423A pdb=" N THR A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.803A pdb=" N THR B 75 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 76 " --> pdb=" O PRO B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 76' Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.548A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 128 through 134 Processing helix chain 'B' and resid 157 through 162 removed outlier: 4.513A pdb=" N HIS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 4.219A pdb=" N LYS B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 77 through 86 removed outlier: 3.973A pdb=" N ALA C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.707A pdb=" N ASP C 115 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'C' and resid 121 through 128 removed outlier: 4.121A pdb=" N ASP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.759A pdb=" N ALA C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.685A pdb=" N THR C 187 " --> pdb=" O GLN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 193 Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.882A pdb=" N GLN C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 78 through 89 removed outlier: 3.919A pdb=" N LEU D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 118 through 131 removed outlier: 4.015A pdb=" N MET D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.590A pdb=" N ILE D 138 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 149 through 162 removed outlier: 3.626A pdb=" N ILE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.072A pdb=" N GLY D 174 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 175' Processing helix chain 'D' and resid 177 through 195 removed outlier: 3.634A pdb=" N LYS D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 248 removed outlier: 3.684A pdb=" N SER D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 12 removed outlier: 3.562A pdb=" N LEU E 12 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.796A pdb=" N SER E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 52 through 85 removed outlier: 4.219A pdb=" N LYS E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 98 through 124 removed outlier: 3.610A pdb=" N ILE E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 138 removed outlier: 3.899A pdb=" N LEU E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP E 138 " --> pdb=" O MET E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 175 removed outlier: 3.715A pdb=" N PHE E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 161 " --> pdb=" O MET E 157 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 201 through 220 removed outlier: 4.352A pdb=" N LEU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 258 removed outlier: 3.924A pdb=" N LEU E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER E 248 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL E 249 " --> pdb=" O THR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 removed outlier: 4.055A pdb=" N VAL E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE E 276 " --> pdb=" O SER E 272 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.800A pdb=" N THR E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 550 removed outlier: 3.865A pdb=" N VAL E 524 " --> pdb=" O VAL E 520 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY E 543 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET E 550 " --> pdb=" O LEU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 566 Processing helix chain 'E' and resid 573 through 608 removed outlier: 3.702A pdb=" N ILE E 582 " --> pdb=" O LEU E 578 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE E 588 " --> pdb=" O PHE E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 615 through 643 removed outlier: 3.915A pdb=" N VAL E 619 " --> pdb=" O GLU E 615 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.744A pdb=" N ILE F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 40 removed outlier: 4.055A pdb=" N SER F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL F 29 " --> pdb=" O CYS F 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 57 through 84 removed outlier: 4.137A pdb=" N VAL F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 95 removed outlier: 4.879A pdb=" N THR F 93 " --> pdb=" O PHE F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 138 removed outlier: 3.612A pdb=" N ILE F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET F 134 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 160 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 199 through 220 removed outlier: 4.366A pdb=" N ALA F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 246 removed outlier: 4.655A pdb=" N PHE F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 4.018A pdb=" N LEU F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR F 245 " --> pdb=" O TYR F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 257 removed outlier: 3.626A pdb=" N MET F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 279 removed outlier: 3.549A pdb=" N ARG F 271 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 308 removed outlier: 4.244A pdb=" N GLY F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 301 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 550 removed outlier: 3.546A pdb=" N PHE F 529 " --> pdb=" O ALA F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 567 removed outlier: 3.591A pdb=" N ARG F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 584 removed outlier: 3.933A pdb=" N ILE F 582 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 605 Processing helix chain 'F' and resid 618 through 643 removed outlier: 3.756A pdb=" N ILE F 622 " --> pdb=" O ILE F 618 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR F 623 " --> pdb=" O VAL F 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.826A pdb=" N LEU A 25 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 13 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN A 23 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 6.227A pdb=" N ILE A 167 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 202 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 169 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 38 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 225 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 32 removed outlier: 5.232A pdb=" N SER B 26 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS B 11 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU B 30 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR B 7 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL B 32 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN B 5 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU B 9 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN B 63 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.630A pdb=" N GLY B 90 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASP B 170 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B 92 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE B 167 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 202 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA B 169 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 37 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL B 216 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY B 39 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE B 218 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU B 226 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 217 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.155A pdb=" N SER C 26 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS C 11 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 28 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 9 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU C 4 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 32 " --> pdb=" O LEU C 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.155A pdb=" N SER C 26 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS C 11 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 28 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 9 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 9 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN C 63 " --> pdb=" O LEU C 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 167 through 168 removed outlier: 6.665A pdb=" N ILE C 167 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N VAL C 202 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 38 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL C 216 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY C 39 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE C 218 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET C 41 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER C 225 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS C 219 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 32 removed outlier: 5.986A pdb=" N ALA D 24 " --> pdb=" O TYR D 13 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR D 13 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER D 26 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LYS D 11 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU D 30 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR D 7 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 32 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN D 5 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR D 7 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 65 " --> pdb=" O THR D 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 199 through 202 removed outlier: 3.515A pdb=" N LEU D 201 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE D 37 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL D 216 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY D 39 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 92 removed outlier: 5.771A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 661 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2671 1.33 - 1.45: 3799 1.45 - 1.58: 8529 1.58 - 1.70: 13 1.70 - 1.83: 122 Bond restraints: 15134 Sorted by residual: bond pdb=" CA TYR D 13 " pdb=" C TYR D 13 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.30e-02 5.92e+03 2.21e+01 bond pdb=" C LEU A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.25e-02 6.40e+03 1.99e+01 bond pdb=" CA VAL C 92 " pdb=" CB VAL C 92 " ideal model delta sigma weight residual 1.540 1.490 0.050 1.36e-02 5.41e+03 1.36e+01 bond pdb=" N PHE F 587 " pdb=" CA PHE F 587 " ideal model delta sigma weight residual 1.457 1.411 0.047 1.29e-02 6.01e+03 1.31e+01 bond pdb=" CA GLN E 542 " pdb=" C GLN E 542 " ideal model delta sigma weight residual 1.524 1.482 0.043 1.24e-02 6.50e+03 1.18e+01 ... (remaining 15129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 20098 4.05 - 8.11: 293 8.11 - 12.16: 50 12.16 - 16.22: 14 16.22 - 20.27: 3 Bond angle restraints: 20458 Sorted by residual: angle pdb=" N ASN F 221 " pdb=" CA ASN F 221 " pdb=" C ASN F 221 " ideal model delta sigma weight residual 109.96 92.24 17.72 1.68e+00 3.54e-01 1.11e+02 angle pdb=" N GLU E 181 " pdb=" CA GLU E 181 " pdb=" C GLU E 181 " ideal model delta sigma weight residual 110.30 97.94 12.36 1.50e+00 4.44e-01 6.79e+01 angle pdb=" N ARG F 253 " pdb=" CA ARG F 253 " pdb=" C ARG F 253 " ideal model delta sigma weight residual 112.90 102.43 10.47 1.31e+00 5.83e-01 6.39e+01 angle pdb=" N ALA F 616 " pdb=" CA ALA F 616 " pdb=" C ALA F 616 " ideal model delta sigma weight residual 114.12 103.20 10.92 1.39e+00 5.18e-01 6.17e+01 angle pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" C LEU A 109 " ideal model delta sigma weight residual 109.39 120.15 -10.76 1.59e+00 3.96e-01 4.58e+01 ... (remaining 20453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 8126 24.98 - 49.95: 813 49.95 - 74.93: 80 74.93 - 99.91: 17 99.91 - 124.88: 1 Dihedral angle restraints: 9037 sinusoidal: 3607 harmonic: 5430 Sorted by residual: dihedral pdb=" O2A ADP A 301 " pdb=" O3A ADP A 301 " pdb=" PA ADP A 301 " pdb=" PB ADP A 301 " ideal model delta sinusoidal sigma weight residual -60.00 64.89 -124.88 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" CA LYS A 77 " pdb=" C LYS A 77 " pdb=" N ASP A 78 " pdb=" CA ASP A 78 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA HIS C 162 " pdb=" C HIS C 162 " pdb=" N ASN C 163 " pdb=" CA ASN C 163 " ideal model delta harmonic sigma weight residual -180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 9034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2199 0.096 - 0.192: 198 0.192 - 0.288: 26 0.288 - 0.384: 6 0.384 - 0.480: 1 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CB ILE C 135 " pdb=" CA ILE C 135 " pdb=" CG1 ILE C 135 " pdb=" CG2 ILE C 135 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CA ARG E 178 " pdb=" N ARG E 178 " pdb=" C ARG E 178 " pdb=" CB ARG E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE F 182 " pdb=" CA ILE F 182 " pdb=" CG1 ILE F 182 " pdb=" CG2 ILE F 182 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2427 not shown) Planarity restraints: 2517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 89 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C LEU C 89 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU C 89 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY C 90 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 89 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C LEU A 89 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU A 89 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 90 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 144 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO F 145 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO F 145 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 145 " 0.054 5.00e-02 4.00e+02 ... (remaining 2514 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3535 2.78 - 3.31: 13629 3.31 - 3.84: 24972 3.84 - 4.37: 27105 4.37 - 4.90: 46753 Nonbonded interactions: 115994 Sorted by model distance: nonbonded pdb=" O ILE E 164 " pdb=" OG1 THR E 168 " model vdw 2.254 3.040 nonbonded pdb=" O THR C 57 " pdb=" OG1 THR C 57 " model vdw 2.296 3.040 nonbonded pdb=" O LEU E 3 " pdb=" C ARG E 4 " model vdw 2.315 3.270 nonbonded pdb=" O LEU E 296 " pdb=" OH TYR E 601 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR A 22 " pdb=" O3' ADP A 301 " model vdw 2.318 3.040 ... (remaining 115989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 249 or resid 301)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 249 or resid 301)) selection = (chain 'D' and (resid 2 through 249 or resid 301)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 3 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 16 or (resid 17 and (name N or name CA \ or name C or name O or name CB )) or resid 18 through 644)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.005 0.098 15134 Z= 0.270 Angle : 1.218 20.271 20458 Z= 0.606 Chirality : 0.060 0.480 2430 Planarity : 0.005 0.100 2517 Dihedral : 18.467 124.885 5525 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.65 % Favored : 91.19 % Rotamer: Outliers : 0.12 % Allowed : 36.54 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.67 (0.16), residues: 1850 helix: -2.28 (0.13), residues: 959 sheet: -1.83 (0.56), residues: 91 loop : -2.59 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 120 TYR 0.023 0.001 TYR F 547 PHE 0.060 0.002 PHE E 538 TRP 0.010 0.001 TRP F 138 HIS 0.004 0.001 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00507 (15134) covalent geometry : angle 1.21781 (20458) hydrogen bonds : bond 0.15490 ( 661) hydrogen bonds : angle 6.56494 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8783 (tp) cc_final: 0.8390 (mm) REVERT: B 12 THR cc_start: 0.8952 (p) cc_final: 0.8621 (p) REVERT: C 66 MET cc_start: 0.7782 (ttm) cc_final: 0.7526 (ttt) REVERT: C 93 PHE cc_start: 0.8094 (m-80) cc_final: 0.7882 (m-10) REVERT: F 153 LYS cc_start: 0.7618 (mttt) cc_final: 0.7084 (ttmt) REVERT: F 545 MET cc_start: 0.8438 (mmt) cc_final: 0.8168 (mmm) outliers start: 2 outliers final: 2 residues processed: 308 average time/residue: 0.1038 time to fit residues: 49.0861 Evaluate side-chains 273 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 542 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 192 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077445 restraints weight = 41345.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080015 restraints weight = 21520.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081751 restraints weight = 13945.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082949 restraints weight = 10317.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083788 restraints weight = 8325.596| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15134 Z= 0.156 Angle : 0.702 12.862 20458 Z= 0.341 Chirality : 0.042 0.159 2430 Planarity : 0.004 0.065 2517 Dihedral : 7.039 110.263 2052 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 4.09 % Allowed : 33.13 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.19), residues: 1850 helix: -0.78 (0.16), residues: 978 sheet: -1.67 (0.48), residues: 134 loop : -2.16 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 4 TYR 0.019 0.001 TYR F 547 PHE 0.019 0.001 PHE F 538 TRP 0.007 0.001 TRP F 201 HIS 0.003 0.001 HIS F 575 Details of bonding type rmsd covalent geometry : bond 0.00343 (15134) covalent geometry : angle 0.70233 (20458) hydrogen bonds : bond 0.03557 ( 661) hydrogen bonds : angle 4.43161 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 252 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 83 LEU cc_start: 0.9086 (tp) cc_final: 0.8748 (mm) REVERT: A 205 ASP cc_start: 0.8351 (t0) cc_final: 0.8092 (t0) REVERT: C 9 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8894 (tt) REVERT: C 66 MET cc_start: 0.8174 (ttm) cc_final: 0.7929 (ttt) REVERT: C 158 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6021 (ttm-80) REVERT: E 46 GLU cc_start: 0.9109 (mp0) cc_final: 0.8887 (mp0) REVERT: E 566 ARG cc_start: 0.9193 (ptp-170) cc_final: 0.8899 (ptp-170) REVERT: E 575 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7621 (t-90) REVERT: F 153 LYS cc_start: 0.7577 (mttt) cc_final: 0.6527 (tptt) REVERT: F 190 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8969 (tttt) REVERT: F 556 ASP cc_start: 0.8896 (t70) cc_final: 0.8696 (t0) REVERT: F 607 MET cc_start: 0.7654 (tmm) cc_final: 0.7427 (tmm) outliers start: 66 outliers final: 38 residues processed: 296 average time/residue: 0.1000 time to fit residues: 47.1829 Evaluate side-chains 277 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 HIS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 158 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 86 optimal weight: 6.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075287 restraints weight = 41797.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077830 restraints weight = 21623.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079520 restraints weight = 13939.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080705 restraints weight = 10282.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081456 restraints weight = 8314.894| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15134 Z= 0.157 Angle : 0.680 12.061 20458 Z= 0.330 Chirality : 0.042 0.159 2430 Planarity : 0.003 0.055 2517 Dihedral : 6.498 107.699 2048 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.73 % Favored : 92.22 % Rotamer: Outliers : 5.15 % Allowed : 32.44 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.20), residues: 1850 helix: -0.11 (0.16), residues: 997 sheet: -1.71 (0.46), residues: 144 loop : -2.16 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 4 TYR 0.018 0.001 TYR F 547 PHE 0.020 0.001 PHE F 538 TRP 0.009 0.001 TRP F 201 HIS 0.003 0.001 HIS F 41 Details of bonding type rmsd covalent geometry : bond 0.00350 (15134) covalent geometry : angle 0.67956 (20458) hydrogen bonds : bond 0.03375 ( 661) hydrogen bonds : angle 4.16122 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 237 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9147 (tp) cc_final: 0.8770 (mm) REVERT: A 193 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: A 205 ASP cc_start: 0.8572 (t0) cc_final: 0.8116 (t0) REVERT: B 171 GLU cc_start: 0.8218 (tp30) cc_final: 0.7746 (tp30) REVERT: C 9 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8855 (tt) REVERT: C 128 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8945 (pp20) REVERT: C 212 CYS cc_start: 0.8075 (m) cc_final: 0.7684 (m) REVERT: C 214 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8147 (ttp80) REVERT: D 41 MET cc_start: 0.8640 (ppp) cc_final: 0.8263 (tmm) REVERT: E 550 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8292 (ppp) REVERT: E 575 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7680 (t-90) REVERT: E 615 GLU cc_start: 0.8690 (pp20) cc_final: 0.8229 (pp20) REVERT: F 107 TYR cc_start: 0.8050 (t80) cc_final: 0.7837 (t80) REVERT: F 153 LYS cc_start: 0.7698 (mttt) cc_final: 0.6615 (tptt) REVERT: F 190 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8984 (tttt) REVERT: F 527 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6938 (ttm) REVERT: F 556 ASP cc_start: 0.8888 (t70) cc_final: 0.8676 (t0) REVERT: F 607 MET cc_start: 0.7722 (tmm) cc_final: 0.7482 (tmm) outliers start: 83 outliers final: 50 residues processed: 300 average time/residue: 0.1032 time to fit residues: 48.8036 Evaluate side-chains 282 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 HIS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 527 MET Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 612 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 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 = 0.3358 r_free = 0.3358 target = 0.088560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072387 restraints weight = 42204.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074862 restraints weight = 21839.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076517 restraints weight = 14099.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077597 restraints weight = 10426.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078430 restraints weight = 8498.091| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15134 Z= 0.190 Angle : 0.689 12.055 20458 Z= 0.337 Chirality : 0.042 0.219 2430 Planarity : 0.003 0.047 2517 Dihedral : 6.343 106.190 2048 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 6.64 % Allowed : 31.64 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1850 helix: 0.28 (0.17), residues: 982 sheet: -1.65 (0.47), residues: 135 loop : -2.14 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 566 TYR 0.021 0.001 TYR F 547 PHE 0.020 0.001 PHE F 538 TRP 0.009 0.001 TRP F 201 HIS 0.003 0.001 HIS F 41 Details of bonding type rmsd covalent geometry : bond 0.00427 (15134) covalent geometry : angle 0.68900 (20458) hydrogen bonds : bond 0.03389 ( 661) hydrogen bonds : angle 4.13526 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 226 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9238 (tp) cc_final: 0.8920 (mm) REVERT: A 179 LYS cc_start: 0.8928 (tptp) cc_final: 0.8619 (tptp) REVERT: A 193 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: A 205 ASP cc_start: 0.8694 (t0) cc_final: 0.8257 (t0) REVERT: B 41 MET cc_start: 0.9000 (tpp) cc_final: 0.8567 (tpp) REVERT: B 171 GLU cc_start: 0.8371 (tp30) cc_final: 0.7970 (tp30) REVERT: C 9 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8838 (tt) REVERT: C 212 CYS cc_start: 0.8246 (m) cc_final: 0.8007 (m) REVERT: C 214 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8173 (ttp80) REVERT: E 178 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8200 (ttp80) REVERT: E 550 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8435 (ppp) REVERT: E 566 ARG cc_start: 0.9245 (ptp-170) cc_final: 0.8853 (ptp-170) REVERT: E 575 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: E 585 LEU cc_start: 0.9344 (tp) cc_final: 0.9041 (tp) REVERT: E 607 MET cc_start: 0.8979 (ppp) cc_final: 0.8715 (tmm) REVERT: E 615 GLU cc_start: 0.8706 (pp20) cc_final: 0.8390 (pp20) REVERT: F 107 TYR cc_start: 0.8112 (t80) cc_final: 0.7907 (t80) REVERT: F 153 LYS cc_start: 0.7726 (mttt) cc_final: 0.6667 (tptt) REVERT: F 190 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8995 (tttt) REVERT: F 556 ASP cc_start: 0.8902 (t70) cc_final: 0.8648 (t0) REVERT: F 607 MET cc_start: 0.7784 (tmm) cc_final: 0.7504 (tmm) outliers start: 107 outliers final: 66 residues processed: 312 average time/residue: 0.0942 time to fit residues: 46.8045 Evaluate side-chains 289 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 HIS Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 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 190 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073711 restraints weight = 41560.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076199 restraints weight = 21471.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077875 restraints weight = 13815.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078957 restraints weight = 10185.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.079793 restraints weight = 8288.907| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15134 Z= 0.148 Angle : 0.669 11.331 20458 Z= 0.323 Chirality : 0.042 0.232 2430 Planarity : 0.003 0.043 2517 Dihedral : 6.131 101.523 2048 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 5.77 % Allowed : 32.20 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1850 helix: 0.38 (0.17), residues: 994 sheet: -1.72 (0.46), residues: 144 loop : -2.08 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 120 TYR 0.018 0.001 TYR F 547 PHE 0.020 0.001 PHE F 538 TRP 0.008 0.001 TRP F 201 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00337 (15134) covalent geometry : angle 0.66928 (20458) hydrogen bonds : bond 0.03242 ( 661) hydrogen bonds : angle 4.03605 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 229 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9240 (tp) cc_final: 0.8948 (mm) REVERT: A 134 GLN cc_start: 0.8752 (tp40) cc_final: 0.8522 (tp40) REVERT: A 179 LYS cc_start: 0.8759 (tptp) cc_final: 0.8432 (tptp) REVERT: A 190 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.9076 (tt0) REVERT: A 193 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: B 41 MET cc_start: 0.9004 (tpp) cc_final: 0.8567 (tpp) REVERT: B 137 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8257 (p90) REVERT: B 171 GLU cc_start: 0.8312 (tp30) cc_final: 0.7693 (tp30) REVERT: C 9 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8868 (tt) REVERT: C 128 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8918 (pp20) REVERT: C 158 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7947 (tmm-80) REVERT: C 214 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8130 (ttp80) REVERT: E 550 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8517 (ppp) REVERT: E 575 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: E 585 LEU cc_start: 0.9352 (tp) cc_final: 0.9030 (tp) REVERT: E 607 MET cc_start: 0.8979 (ppp) cc_final: 0.8729 (tmm) REVERT: E 615 GLU cc_start: 0.8672 (pp20) cc_final: 0.8376 (pp20) REVERT: F 153 LYS cc_start: 0.7722 (mttt) cc_final: 0.6665 (tptt) REVERT: F 190 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8943 (tttt) REVERT: F 553 GLU cc_start: 0.8665 (pm20) cc_final: 0.8318 (pm20) REVERT: F 556 ASP cc_start: 0.8880 (t70) cc_final: 0.8622 (t0) REVERT: F 562 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9234 (tt) REVERT: F 607 MET cc_start: 0.7788 (tmm) cc_final: 0.7510 (tmm) outliers start: 93 outliers final: 67 residues processed: 301 average time/residue: 0.1082 time to fit residues: 51.0844 Evaluate side-chains 299 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 HIS Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 527 MET Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 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 = 0.3351 r_free = 0.3351 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072404 restraints weight = 41445.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074846 restraints weight = 21504.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076496 restraints weight = 13886.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077597 restraints weight = 10244.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078363 restraints weight = 8322.139| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15134 Z= 0.179 Angle : 0.689 11.551 20458 Z= 0.333 Chirality : 0.043 0.314 2430 Planarity : 0.003 0.041 2517 Dihedral : 6.119 102.045 2048 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 6.51 % Allowed : 32.13 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1850 helix: 0.47 (0.17), residues: 985 sheet: -1.85 (0.45), residues: 150 loop : -2.04 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 120 TYR 0.018 0.001 TYR F 547 PHE 0.020 0.001 PHE F 538 TRP 0.008 0.001 TRP F 201 HIS 0.002 0.001 HIS F 575 Details of bonding type rmsd covalent geometry : bond 0.00406 (15134) covalent geometry : angle 0.68940 (20458) hydrogen bonds : bond 0.03293 ( 661) hydrogen bonds : angle 4.03624 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 229 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9248 (tp) cc_final: 0.8930 (mm) REVERT: A 106 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: A 134 GLN cc_start: 0.8811 (tp40) cc_final: 0.8565 (tp40) REVERT: A 179 LYS cc_start: 0.8820 (tptp) cc_final: 0.8470 (tptp) REVERT: A 193 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: B 41 MET cc_start: 0.9019 (tpp) cc_final: 0.8648 (tpp) REVERT: B 171 GLU cc_start: 0.8366 (tp30) cc_final: 0.7692 (tp30) REVERT: C 9 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8872 (tt) REVERT: C 37 PHE cc_start: 0.8746 (t80) cc_final: 0.8412 (t80) REVERT: C 128 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8950 (pp20) REVERT: C 158 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8174 (ttm170) REVERT: C 212 CYS cc_start: 0.7835 (m) cc_final: 0.7378 (m) REVERT: E 550 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8645 (ppp) REVERT: E 554 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8621 (mt) REVERT: E 575 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: E 607 MET cc_start: 0.8980 (ppp) cc_final: 0.8709 (tmm) REVERT: E 615 GLU cc_start: 0.8724 (pp20) cc_final: 0.8465 (pp20) REVERT: F 76 TYR cc_start: 0.7788 (m-10) cc_final: 0.7452 (m-10) REVERT: F 134 MET cc_start: 0.8525 (mtm) cc_final: 0.8294 (mtt) REVERT: F 153 LYS cc_start: 0.7729 (mttt) cc_final: 0.6677 (tptt) REVERT: F 190 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8961 (tttt) REVERT: F 553 GLU cc_start: 0.8639 (pm20) cc_final: 0.8222 (pm20) REVERT: F 556 ASP cc_start: 0.8908 (t70) cc_final: 0.8648 (t0) REVERT: F 562 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9227 (tp) REVERT: F 607 MET cc_start: 0.7774 (tmm) cc_final: 0.7494 (tmm) outliers start: 105 outliers final: 78 residues processed: 310 average time/residue: 0.1047 time to fit residues: 51.2046 Evaluate side-chains 305 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 217 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 HIS Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 567 ILE Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 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 = 0.3376 r_free = 0.3376 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073699 restraints weight = 41719.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.076207 restraints weight = 21523.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077885 restraints weight = 13858.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079039 restraints weight = 10212.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.079786 restraints weight = 8244.984| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15134 Z= 0.132 Angle : 0.671 11.621 20458 Z= 0.321 Chirality : 0.042 0.250 2430 Planarity : 0.003 0.039 2517 Dihedral : 5.962 97.830 2048 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.00 % Favored : 91.95 % Rotamer: Outliers : 5.96 % Allowed : 33.25 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1850 helix: 0.49 (0.17), residues: 995 sheet: -1.97 (0.43), residues: 160 loop : -1.92 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 120 TYR 0.017 0.001 TYR E 18 PHE 0.021 0.001 PHE F 538 TRP 0.008 0.001 TRP F 201 HIS 0.003 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00300 (15134) covalent geometry : angle 0.67057 (20458) hydrogen bonds : bond 0.03194 ( 661) hydrogen bonds : angle 3.97369 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 231 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9207 (tp) cc_final: 0.8935 (mm) REVERT: A 102 LEU cc_start: 0.9345 (mp) cc_final: 0.9131 (mp) REVERT: A 106 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: A 134 GLN cc_start: 0.8817 (tp40) cc_final: 0.8586 (tp40) REVERT: A 179 LYS cc_start: 0.8849 (tptp) cc_final: 0.8450 (tptp) REVERT: A 193 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: B 41 MET cc_start: 0.9000 (tpp) cc_final: 0.8556 (tpp) REVERT: B 137 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8402 (p90) REVERT: B 171 GLU cc_start: 0.8316 (tp30) cc_final: 0.7696 (tp30) REVERT: B 200 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8997 (tp) REVERT: C 9 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8846 (tt) REVERT: C 66 MET cc_start: 0.8116 (ttm) cc_final: 0.7903 (ttt) REVERT: C 128 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8999 (pp20) REVERT: C 158 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7893 (tmm-80) REVERT: C 212 CYS cc_start: 0.7859 (m) cc_final: 0.7083 (m) REVERT: E 88 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: E 277 ARG cc_start: 0.8786 (ptp90) cc_final: 0.8494 (ptm160) REVERT: E 550 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8647 (ppp) REVERT: E 554 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (mt) REVERT: E 575 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7634 (t-90) REVERT: E 607 MET cc_start: 0.8961 (ppp) cc_final: 0.8697 (tmm) REVERT: F 76 TYR cc_start: 0.7750 (m-10) cc_final: 0.7429 (m-10) REVERT: F 134 MET cc_start: 0.8582 (mtm) cc_final: 0.8360 (mtt) REVERT: F 153 LYS cc_start: 0.7691 (mttt) cc_final: 0.6630 (tptt) REVERT: F 190 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8973 (tttt) REVERT: F 553 GLU cc_start: 0.8636 (pm20) cc_final: 0.8218 (pm20) REVERT: F 556 ASP cc_start: 0.8885 (t70) cc_final: 0.8631 (t0) REVERT: F 562 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9226 (tt) REVERT: F 607 MET cc_start: 0.7712 (tmm) cc_final: 0.7427 (tmm) outliers start: 96 outliers final: 70 residues processed: 299 average time/residue: 0.1027 time to fit residues: 48.6270 Evaluate side-chains 306 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 HIS Chi-restraints excluded: chain E residue 576 SER Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 527 MET Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 567 ILE Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 581 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 = 0.3328 r_free = 0.3328 target = 0.086939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071024 restraints weight = 42443.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073469 restraints weight = 21779.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075113 restraints weight = 14007.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076240 restraints weight = 10327.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076968 restraints weight = 8348.409| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15134 Z= 0.196 Angle : 0.718 11.368 20458 Z= 0.345 Chirality : 0.043 0.222 2430 Planarity : 0.003 0.040 2517 Dihedral : 6.081 101.353 2048 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 6.70 % Allowed : 32.32 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1850 helix: 0.53 (0.17), residues: 983 sheet: -1.94 (0.44), residues: 151 loop : -1.93 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 120 TYR 0.017 0.001 TYR E 18 PHE 0.022 0.001 PHE F 538 TRP 0.008 0.001 TRP F 201 HIS 0.004 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00446 (15134) covalent geometry : angle 0.71778 (20458) hydrogen bonds : bond 0.03351 ( 661) hydrogen bonds : angle 4.03739 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 225 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9257 (tp) cc_final: 0.8994 (mm) REVERT: A 102 LEU cc_start: 0.9338 (mp) cc_final: 0.9087 (mp) REVERT: A 106 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: A 134 GLN cc_start: 0.8848 (tp40) cc_final: 0.8639 (tp40) REVERT: A 179 LYS cc_start: 0.8816 (tptp) cc_final: 0.8414 (tptp) REVERT: A 193 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: B 41 MET cc_start: 0.9051 (tpp) cc_final: 0.8599 (tpp) REVERT: B 137 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8493 (p90) REVERT: B 171 GLU cc_start: 0.8407 (tp30) cc_final: 0.7709 (tp30) REVERT: C 9 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8924 (tt) REVERT: C 66 MET cc_start: 0.8163 (ttm) cc_final: 0.7868 (ttt) REVERT: C 128 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.9026 (pp20) REVERT: C 212 CYS cc_start: 0.7826 (m) cc_final: 0.7427 (m) REVERT: E 88 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: E 550 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8822 (ppp) REVERT: E 554 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8607 (mt) REVERT: E 607 MET cc_start: 0.8986 (ppp) cc_final: 0.8685 (tmm) REVERT: F 76 TYR cc_start: 0.7814 (m-10) cc_final: 0.7498 (m-10) REVERT: F 134 MET cc_start: 0.8566 (mtm) cc_final: 0.8354 (mtt) REVERT: F 153 LYS cc_start: 0.7684 (mttt) cc_final: 0.6588 (tptt) REVERT: F 190 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9000 (tttt) REVERT: F 553 GLU cc_start: 0.8671 (pm20) cc_final: 0.8244 (pm20) REVERT: F 556 ASP cc_start: 0.9007 (t70) cc_final: 0.8734 (t0) REVERT: F 562 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9224 (tt) REVERT: F 607 MET cc_start: 0.7711 (tmm) cc_final: 0.7430 (tmm) outliers start: 108 outliers final: 82 residues processed: 305 average time/residue: 0.1005 time to fit residues: 49.6722 Evaluate side-chains 312 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 567 ILE Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 146 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 581 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 = 0.3305 r_free = 0.3305 target = 0.085612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069820 restraints weight = 42824.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072221 restraints weight = 22093.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073786 restraints weight = 14273.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.074915 restraints weight = 10642.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075659 restraints weight = 8610.732| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15134 Z= 0.233 Angle : 0.759 11.373 20458 Z= 0.367 Chirality : 0.044 0.255 2430 Planarity : 0.003 0.039 2517 Dihedral : 6.235 102.459 2048 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.43 % Favored : 91.51 % Rotamer: Outliers : 6.08 % Allowed : 33.00 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1850 helix: 0.50 (0.17), residues: 982 sheet: -2.11 (0.44), residues: 153 loop : -1.93 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 566 TYR 0.018 0.001 TYR F 547 PHE 0.022 0.002 PHE F 538 TRP 0.008 0.001 TRP F 201 HIS 0.003 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00528 (15134) covalent geometry : angle 0.75937 (20458) hydrogen bonds : bond 0.03502 ( 661) hydrogen bonds : angle 4.14163 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 221 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9276 (tp) cc_final: 0.9047 (mm) REVERT: A 96 PHE cc_start: 0.8699 (m-80) cc_final: 0.8334 (m-80) REVERT: A 179 LYS cc_start: 0.8813 (tptp) cc_final: 0.8405 (tptp) REVERT: A 193 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: B 41 MET cc_start: 0.9113 (tpp) cc_final: 0.8762 (tpp) REVERT: B 137 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8499 (p90) REVERT: C 9 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8925 (tt) REVERT: C 128 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.9005 (pp20) REVERT: C 212 CYS cc_start: 0.7828 (m) cc_final: 0.7212 (m) REVERT: E 88 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: E 550 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8822 (ppp) REVERT: E 554 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8592 (mt) REVERT: E 607 MET cc_start: 0.8982 (ppp) cc_final: 0.8675 (tmm) REVERT: F 76 TYR cc_start: 0.7783 (m-10) cc_final: 0.7458 (m-10) REVERT: F 134 MET cc_start: 0.8573 (mtm) cc_final: 0.8348 (mtt) REVERT: F 153 LYS cc_start: 0.7676 (mttt) cc_final: 0.6579 (tptt) REVERT: F 190 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8987 (tttt) REVERT: F 254 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8410 (tmm) REVERT: F 274 MET cc_start: 0.9397 (mmm) cc_final: 0.9179 (tpt) REVERT: F 553 GLU cc_start: 0.8602 (pm20) cc_final: 0.8192 (pm20) REVERT: F 607 MET cc_start: 0.7760 (tmm) cc_final: 0.7483 (tmm) outliers start: 98 outliers final: 79 residues processed: 292 average time/residue: 0.0969 time to fit residues: 45.6288 Evaluate side-chains 302 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 214 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 527 MET Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 567 ILE Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 115 optimal weight: 0.0060 chunk 34 optimal weight: 0.0040 chunk 130 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.7810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.089134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073311 restraints weight = 41765.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.075825 restraints weight = 21196.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077505 restraints weight = 13521.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078469 restraints weight = 9931.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079395 restraints weight = 8133.292| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15134 Z= 0.123 Angle : 0.717 12.209 20458 Z= 0.338 Chirality : 0.043 0.260 2430 Planarity : 0.003 0.039 2517 Dihedral : 5.920 94.301 2048 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.84 % Favored : 92.11 % Rotamer: Outliers : 4.40 % Allowed : 34.06 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1850 helix: 0.53 (0.17), residues: 981 sheet: -1.98 (0.44), residues: 150 loop : -1.84 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 549 TYR 0.016 0.001 TYR F 547 PHE 0.022 0.001 PHE F 538 TRP 0.009 0.001 TRP F 201 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00275 (15134) covalent geometry : angle 0.71714 (20458) hydrogen bonds : bond 0.03227 ( 661) hydrogen bonds : angle 3.98917 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7262 (mmm) cc_final: 0.6989 (tpt) REVERT: A 83 LEU cc_start: 0.9216 (tp) cc_final: 0.9007 (mm) REVERT: A 179 LYS cc_start: 0.8802 (tptp) cc_final: 0.8400 (tptp) REVERT: A 193 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: B 41 MET cc_start: 0.9105 (tpp) cc_final: 0.8630 (tpp) REVERT: B 137 HIS cc_start: 0.8749 (OUTLIER) cc_final: 0.8502 (p90) REVERT: B 171 GLU cc_start: 0.8325 (tp30) cc_final: 0.8123 (mm-30) REVERT: C 9 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8946 (tt) REVERT: C 36 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: C 37 PHE cc_start: 0.8619 (t80) cc_final: 0.8249 (t80) REVERT: C 128 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.9004 (pp20) REVERT: C 158 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7881 (tmm-80) REVERT: C 212 CYS cc_start: 0.7734 (m) cc_final: 0.7390 (m) REVERT: E 76 TYR cc_start: 0.8187 (m-80) cc_final: 0.7797 (m-10) REVERT: E 88 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: E 550 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8790 (ppp) REVERT: E 554 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8633 (mt) REVERT: E 581 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7859 (tm-30) REVERT: E 607 MET cc_start: 0.8984 (ppp) cc_final: 0.8694 (tmm) REVERT: F 76 TYR cc_start: 0.7669 (m-10) cc_final: 0.7369 (m-10) REVERT: F 134 MET cc_start: 0.8553 (mtm) cc_final: 0.8313 (mtt) REVERT: F 153 LYS cc_start: 0.7615 (mttt) cc_final: 0.6552 (tptt) REVERT: F 190 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8959 (tttt) REVERT: F 274 MET cc_start: 0.9375 (mmm) cc_final: 0.9129 (tpt) REVERT: F 553 GLU cc_start: 0.8623 (pm20) cc_final: 0.8192 (pm20) REVERT: F 607 MET cc_start: 0.7788 (tmm) cc_final: 0.7514 (tmm) outliers start: 71 outliers final: 56 residues processed: 284 average time/residue: 0.1044 time to fit residues: 46.8205 Evaluate side-chains 293 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 527 MET Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 567 ILE Chi-restraints excluded: chain F residue 612 LEU Chi-restraints excluded: chain F residue 642 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 46 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.088763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072892 restraints weight = 42018.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.075399 restraints weight = 21404.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077076 restraints weight = 13699.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078229 restraints weight = 10055.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078889 restraints weight = 8117.098| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15134 Z= 0.139 Angle : 0.717 11.994 20458 Z= 0.339 Chirality : 0.043 0.260 2430 Planarity : 0.003 0.039 2517 Dihedral : 5.822 94.325 2048 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.95 % Favored : 92.00 % Rotamer: Outliers : 4.65 % Allowed : 33.87 % Favored : 61.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.20), residues: 1850 helix: 0.57 (0.17), residues: 988 sheet: -2.02 (0.44), residues: 151 loop : -1.84 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 549 TYR 0.020 0.001 TYR F 547 PHE 0.027 0.001 PHE F 538 TRP 0.008 0.001 TRP F 201 HIS 0.002 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00320 (15134) covalent geometry : angle 0.71705 (20458) hydrogen bonds : bond 0.03193 ( 661) hydrogen bonds : angle 3.94932 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.01 seconds wall clock time: 39 minutes 31.82 seconds (2371.82 seconds total)