Starting phenix.real_space_refine on Sun May 11 17:47:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y27_33587/05_2025/7y27_33587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y27_33587/05_2025/7y27_33587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y27_33587/05_2025/7y27_33587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y27_33587/05_2025/7y27_33587.map" model { file = "/net/cci-nas-00/data/ceres_data/7y27_33587/05_2025/7y27_33587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y27_33587/05_2025/7y27_33587.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.130 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5241 2.51 5 N 1372 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8184 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2419 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1724 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 96 Chain: "D" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1683 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1901 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 2 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 147 Chain: "F" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 327 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 102 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.64 Number of scatterers: 8184 At special positions: 0 Unit cell: (93.74, 128.14, 129.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1520 8.00 N 1372 7.00 C 5241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 14 " distance=2.03 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 removed outlier: 3.894A pdb=" N LEU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.569A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 4.077A pdb=" N GLY A 131 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 132 " --> pdb=" O ARG A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'B' and resid 6 through 29 removed outlier: 3.898A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.587A pdb=" N GLN B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.595A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.124A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.794A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.519A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 71 removed outlier: 3.706A pdb=" N VAL E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE E 56 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 95 removed outlier: 3.901A pdb=" N TYR E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 106 removed outlier: 4.413A pdb=" N LEU E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 102 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 146 removed outlier: 4.306A pdb=" N CYS E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 154 removed outlier: 3.850A pdb=" N TRP E 153 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 174 removed outlier: 3.842A pdb=" N ALA E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 180 removed outlier: 3.502A pdb=" N TYR E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.610A pdb=" N LEU E 215 " --> pdb=" O TYR E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.643A pdb=" N THR E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 282 removed outlier: 3.740A pdb=" N VAL E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E 265 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 270 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix removed outlier: 3.694A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 313 removed outlier: 3.561A pdb=" N PHE E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 297 " --> pdb=" O MET E 293 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 298 " --> pdb=" O PHE E 294 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N CYS E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Proline residue: E 309 - end of helix removed outlier: 3.631A pdb=" N TYR E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.796A pdb=" N GLN E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.591A pdb=" N ASN F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.559A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS F 44 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 50 removed outlier: 3.765A pdb=" N ARG A 46 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 340 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 48 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 338 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 317 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.563A pdb=" N TYR A 59 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA A 73 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A 61 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 71 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TRP A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 69 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 74 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP A 83 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS A 89 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 3.691A pdb=" N THR A 102 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 115 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS A 121 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 138 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 123 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 125 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 134 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.947A pdb=" N ILE A 157 " --> pdb=" O TRP A 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 166 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 178 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 190 removed outlier: 6.496A pdb=" N GLY A 202 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 190 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 200 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 209 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 203 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234 removed outlier: 7.063A pdb=" N GLY A 244 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 232 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 242 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 253 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 252 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A 262 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP A 254 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A 260 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.558A pdb=" N LEU A 308 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 306 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP A 298 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG A 304 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.878A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 37 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 110 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN B 144 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 212 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS D 35 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.710A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 184 through 186 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.571A pdb=" N ASN C 5 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR C 12 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 7 " --> pdb=" O THR C 10 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1092 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: 2.35 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 3 1.20 - 1.36: 2665 1.36 - 1.51: 2456 1.51 - 1.66: 3163 1.66 - 1.82: 74 Bond restraints: 8361 Sorted by residual: bond pdb=" C10 CLR E 401 " pdb=" C9 CLR E 401 " ideal model delta sigma weight residual 1.551 1.052 0.499 2.00e-02 2.50e+03 6.24e+02 bond pdb=" C1 CLR E 401 " pdb=" C10 CLR E 401 " ideal model delta sigma weight residual 1.544 1.125 0.419 2.00e-02 2.50e+03 4.39e+02 bond pdb=" C6 CLR E 401 " pdb=" C7 CLR E 401 " ideal model delta sigma weight residual 1.492 1.089 0.403 2.00e-02 2.50e+03 4.05e+02 bond pdb=" C3 CLR E 401 " pdb=" C4 CLR E 401 " ideal model delta sigma weight residual 1.526 1.209 0.317 2.00e-02 2.50e+03 2.50e+02 bond pdb=" C13 CLR E 401 " pdb=" C17 CLR E 401 " ideal model delta sigma weight residual 1.550 1.253 0.297 2.00e-02 2.50e+03 2.21e+02 ... (remaining 8356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 11320 2.45 - 4.89: 99 4.89 - 7.34: 16 7.34 - 9.79: 3 9.79 - 12.23: 2 Bond angle restraints: 11440 Sorted by residual: angle pdb=" N ILE A 270 " pdb=" CA ILE A 270 " pdb=" C ILE A 270 " ideal model delta sigma weight residual 113.71 108.69 5.02 9.50e-01 1.11e+00 2.79e+01 angle pdb=" C4 CLR E 401 " pdb=" C5 CLR E 401 " pdb=" C6 CLR E 401 " ideal model delta sigma weight residual 120.33 108.10 12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C LEU E 105 " pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta sigma weight residual 121.97 129.29 -7.32 1.80e+00 3.09e-01 1.66e+01 angle pdb=" CA GLU A 130 " pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA PRO B 165 " pdb=" N PRO B 165 " pdb=" CD PRO B 165 " ideal model delta sigma weight residual 112.00 106.75 5.25 1.40e+00 5.10e-01 1.40e+01 ... (remaining 11435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 4560 19.35 - 38.70: 276 38.70 - 58.06: 45 58.06 - 77.41: 9 77.41 - 96.76: 6 Dihedral angle restraints: 4896 sinusoidal: 1603 harmonic: 3293 Sorted by residual: dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 14 " pdb=" CB CYS C 14 " ideal model delta sinusoidal sigma weight residual -86.00 2.41 -88.41 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 130.90 -37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA PHE E 217 " pdb=" C PHE E 217 " pdb=" N LEU E 218 " pdb=" CA LEU E 218 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 1364 0.334 - 0.668: 2 0.668 - 1.001: 0 1.001 - 1.335: 0 1.335 - 1.669: 1 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C10 CLR E 401 " pdb=" C1 CLR E 401 " pdb=" C5 CLR E 401 " pdb=" C9 CLR E 401 " both_signs ideal model delta sigma weight residual False -2.85 -1.18 -1.67 2.00e-01 2.50e+01 6.96e+01 chirality pdb=" C9 CLR E 401 " pdb=" C10 CLR E 401 " pdb=" C11 CLR E 401 " pdb=" C8 CLR E 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.10 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3 CLR E 401 " pdb=" C2 CLR E 401 " pdb=" C4 CLR E 401 " pdb=" O1 CLR E 401 " both_signs ideal model delta sigma weight residual False -2.46 -2.12 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1364 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 175 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO E 176 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 176 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 176 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 244 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ASN B 244 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN B 244 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 245 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 219 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO E 220 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 220 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 220 " 0.022 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 676 2.74 - 3.28: 7875 3.28 - 3.82: 12249 3.82 - 4.36: 12717 4.36 - 4.90: 24077 Nonbonded interactions: 57594 Sorted by model distance: nonbonded pdb=" OD1 ASP A 163 " pdb=" OG1 THR A 165 " model vdw 2.204 3.040 nonbonded pdb=" O ASN B 244 " pdb=" ND2 ASN B 244 " model vdw 2.229 3.120 nonbonded pdb=" ND2 ASN A 230 " pdb=" OD1 ASP A 246 " model vdw 2.257 3.120 nonbonded pdb=" O PHE E 275 " pdb=" OG SER E 278 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 247 " pdb=" OG1 THR A 249 " model vdw 2.266 3.040 ... (remaining 57589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.010 Find NCS groups from input model: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.012 0.499 8364 Z= 0.616 Angle : 0.626 12.233 11446 Z= 0.332 Chirality : 0.062 1.669 1367 Planarity : 0.004 0.057 1450 Dihedral : 13.374 96.759 2759 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1115 helix: 2.02 (0.28), residues: 358 sheet: 0.09 (0.31), residues: 284 loop : -1.42 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 269 HIS 0.003 0.001 HIS F 44 PHE 0.011 0.001 PHE B 70 TYR 0.013 0.001 TYR E 180 ARG 0.005 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.16388 ( 386) hydrogen bonds : angle 5.88848 ( 1092) SS BOND : bond 0.00531 ( 3) SS BOND : angle 1.06645 ( 6) covalent geometry : bond 0.01237 ( 8361) covalent geometry : angle 0.62523 (11440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 259 GLN cc_start: 0.8124 (pt0) cc_final: 0.7886 (pt0) REVERT: B 167 PHE cc_start: 0.7579 (t80) cc_final: 0.7187 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1849 time to fit residues: 41.2409 Evaluate side-chains 127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 146 GLN B 244 ASN D 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.153665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116700 restraints weight = 14198.445| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.94 r_work: 0.3347 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8364 Z= 0.145 Angle : 0.569 7.325 11446 Z= 0.304 Chirality : 0.041 0.146 1367 Planarity : 0.004 0.052 1450 Dihedral : 4.639 42.315 1267 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.78 % Allowed : 8.67 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1115 helix: 2.57 (0.27), residues: 359 sheet: 0.14 (0.31), residues: 294 loop : -1.52 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 129 HIS 0.004 0.001 HIS D 35 PHE 0.010 0.001 PHE A 199 TYR 0.015 0.001 TYR D 178 ARG 0.004 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 386) hydrogen bonds : angle 4.47795 ( 1092) SS BOND : bond 0.00724 ( 3) SS BOND : angle 0.89860 ( 6) covalent geometry : bond 0.00330 ( 8361) covalent geometry : angle 0.56909 (11440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.910 Fit side-chains REVERT: B 43 ASN cc_start: 0.7553 (t0) cc_final: 0.7290 (t0) REVERT: B 167 PHE cc_start: 0.7624 (t80) cc_final: 0.7295 (t80) REVERT: B 188 ARG cc_start: 0.7430 (tpt-90) cc_final: 0.6647 (tpt-90) REVERT: D 159 ASN cc_start: 0.9077 (m110) cc_final: 0.8806 (m110) outliers start: 6 outliers final: 4 residues processed: 145 average time/residue: 0.1679 time to fit residues: 35.2966 Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 171 GLN E 79 ASN E 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109524 restraints weight = 14286.149| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.01 r_work: 0.3300 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8364 Z= 0.171 Angle : 0.579 6.948 11446 Z= 0.315 Chirality : 0.042 0.137 1367 Planarity : 0.004 0.048 1450 Dihedral : 4.481 29.516 1267 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 2.20 % Allowed : 11.77 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1115 helix: 2.54 (0.27), residues: 361 sheet: -0.01 (0.31), residues: 297 loop : -1.50 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 129 HIS 0.006 0.002 HIS A 142 PHE 0.012 0.002 PHE D 165 TYR 0.016 0.001 TYR E 50 ARG 0.003 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.05705 ( 386) hydrogen bonds : angle 4.45982 ( 1092) SS BOND : bond 0.00872 ( 3) SS BOND : angle 0.89797 ( 6) covalent geometry : bond 0.00401 ( 8361) covalent geometry : angle 0.57869 (11440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.925 Fit side-chains REVERT: A 151 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: B 43 ASN cc_start: 0.7662 (t0) cc_final: 0.7416 (t0) REVERT: B 77 ASP cc_start: 0.8717 (t0) cc_final: 0.8504 (t0) REVERT: B 111 ASP cc_start: 0.8805 (t0) cc_final: 0.8582 (t0) REVERT: B 167 PHE cc_start: 0.7634 (t80) cc_final: 0.7239 (t80) REVERT: B 188 ARG cc_start: 0.7302 (tpt-90) cc_final: 0.6565 (tpt170) REVERT: D 159 ASN cc_start: 0.9048 (m110) cc_final: 0.8659 (m110) REVERT: D 232 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7622 (tttt) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.1667 time to fit residues: 35.6674 Evaluate side-chains 146 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3896 r_free = 0.3896 target = 0.147437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110423 restraints weight = 14305.739| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 4.04 r_work: 0.3261 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8364 Z= 0.210 Angle : 0.620 6.794 11446 Z= 0.337 Chirality : 0.043 0.142 1367 Planarity : 0.004 0.046 1450 Dihedral : 4.715 29.924 1267 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 3.23 % Allowed : 13.07 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1115 helix: 2.39 (0.27), residues: 361 sheet: -0.15 (0.31), residues: 291 loop : -1.65 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.006 0.002 HIS A 142 PHE 0.014 0.002 PHE D 165 TYR 0.017 0.002 TYR E 50 ARG 0.003 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.06234 ( 386) hydrogen bonds : angle 4.61540 ( 1092) SS BOND : bond 0.01018 ( 3) SS BOND : angle 1.00314 ( 6) covalent geometry : bond 0.00500 ( 8361) covalent geometry : angle 0.61936 (11440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.872 Fit side-chains REVERT: A 151 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: A 215 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6853 (tt0) REVERT: B 43 ASN cc_start: 0.7814 (t0) cc_final: 0.7516 (t0) REVERT: B 167 PHE cc_start: 0.7623 (t80) cc_final: 0.7195 (t80) REVERT: B 188 ARG cc_start: 0.7347 (tpt-90) cc_final: 0.6393 (tpt-90) REVERT: D 159 ASN cc_start: 0.9072 (m110) cc_final: 0.8693 (m110) REVERT: D 188 PRO cc_start: 0.8215 (Cg_exo) cc_final: 0.7899 (Cg_endo) REVERT: D 221 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8416 (tt) REVERT: D 232 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7633 (tttt) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 0.1661 time to fit residues: 34.3222 Evaluate side-chains 152 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113294 restraints weight = 14162.290| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.02 r_work: 0.3356 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8364 Z= 0.101 Angle : 0.519 6.941 11446 Z= 0.274 Chirality : 0.040 0.140 1367 Planarity : 0.003 0.043 1450 Dihedral : 4.203 29.872 1267 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 2.20 % Allowed : 15.65 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1115 helix: 2.77 (0.27), residues: 361 sheet: 0.07 (0.31), residues: 291 loop : -1.49 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS E 107 PHE 0.011 0.001 PHE B 74 TYR 0.013 0.001 TYR D 178 ARG 0.003 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 386) hydrogen bonds : angle 4.02226 ( 1092) SS BOND : bond 0.00603 ( 3) SS BOND : angle 0.64609 ( 6) covalent geometry : bond 0.00213 ( 8361) covalent geometry : angle 0.51908 (11440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.990 Fit side-chains REVERT: A 151 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: A 228 ASP cc_start: 0.8132 (m-30) cc_final: 0.7463 (m-30) REVERT: A 254 ASP cc_start: 0.8685 (t0) cc_final: 0.8125 (m-30) REVERT: B 8 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7641 (mp0) REVERT: B 43 ASN cc_start: 0.7620 (t0) cc_final: 0.7343 (t0) REVERT: B 111 ASP cc_start: 0.8745 (t0) cc_final: 0.8498 (t0) REVERT: B 167 PHE cc_start: 0.7608 (t80) cc_final: 0.7118 (t80) REVERT: D 159 ASN cc_start: 0.9014 (m110) cc_final: 0.8681 (m110) outliers start: 17 outliers final: 11 residues processed: 149 average time/residue: 0.1681 time to fit residues: 36.2625 Evaluate side-chains 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118384 restraints weight = 14250.894| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.95 r_work: 0.3378 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8364 Z= 0.098 Angle : 0.510 6.020 11446 Z= 0.268 Chirality : 0.039 0.143 1367 Planarity : 0.003 0.041 1450 Dihedral : 3.991 29.507 1267 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 2.20 % Allowed : 16.43 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1115 helix: 2.88 (0.27), residues: 364 sheet: 0.21 (0.31), residues: 290 loop : -1.39 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 96 HIS 0.003 0.001 HIS E 107 PHE 0.013 0.001 PHE B 74 TYR 0.013 0.001 TYR D 178 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 386) hydrogen bonds : angle 3.86506 ( 1092) SS BOND : bond 0.00511 ( 3) SS BOND : angle 0.64659 ( 6) covalent geometry : bond 0.00207 ( 8361) covalent geometry : angle 0.50998 (11440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8071 (m-30) cc_final: 0.7424 (m-30) REVERT: A 254 ASP cc_start: 0.8671 (t0) cc_final: 0.8109 (m-30) REVERT: B 8 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7644 (mp0) REVERT: B 43 ASN cc_start: 0.7615 (t0) cc_final: 0.7410 (t0) REVERT: B 111 ASP cc_start: 0.8721 (t0) cc_final: 0.8494 (t0) REVERT: B 167 PHE cc_start: 0.7590 (t80) cc_final: 0.7107 (t80) REVERT: D 221 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8265 (tt) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 0.1788 time to fit residues: 36.9290 Evaluate side-chains 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 0.0170 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113758 restraints weight = 14203.176| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.81 r_work: 0.3356 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8364 Z= 0.111 Angle : 0.517 5.294 11446 Z= 0.274 Chirality : 0.040 0.135 1367 Planarity : 0.004 0.040 1450 Dihedral : 3.988 29.106 1267 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 2.46 % Allowed : 16.43 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1115 helix: 2.86 (0.27), residues: 365 sheet: 0.20 (0.31), residues: 290 loop : -1.36 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS E 107 PHE 0.012 0.001 PHE B 74 TYR 0.012 0.001 TYR D 178 ARG 0.006 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 386) hydrogen bonds : angle 3.89814 ( 1092) SS BOND : bond 0.00568 ( 3) SS BOND : angle 0.63740 ( 6) covalent geometry : bond 0.00249 ( 8361) covalent geometry : angle 0.51739 (11440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.854 Fit side-chains REVERT: A 151 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: A 228 ASP cc_start: 0.8129 (m-30) cc_final: 0.7224 (m-30) REVERT: A 254 ASP cc_start: 0.8677 (t0) cc_final: 0.8084 (m-30) REVERT: B 43 ASN cc_start: 0.7683 (t0) cc_final: 0.7411 (t0) REVERT: B 94 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7584 (tpt-90) REVERT: B 167 PHE cc_start: 0.7555 (t80) cc_final: 0.7197 (t80) REVERT: B 188 ARG cc_start: 0.7202 (tpt-90) cc_final: 0.6330 (tpt-90) REVERT: D 159 ASN cc_start: 0.9060 (m-40) cc_final: 0.8652 (m110) REVERT: D 221 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8298 (tt) outliers start: 19 outliers final: 13 residues processed: 142 average time/residue: 0.1695 time to fit residues: 34.2288 Evaluate side-chains 146 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 193 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102983 restraints weight = 14540.823| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.91 r_work: 0.3255 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8364 Z= 0.235 Angle : 0.640 6.181 11446 Z= 0.348 Chirality : 0.044 0.146 1367 Planarity : 0.004 0.042 1450 Dihedral : 4.709 29.872 1267 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 3.23 % Allowed : 16.30 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1115 helix: 2.47 (0.27), residues: 361 sheet: -0.07 (0.32), residues: 283 loop : -1.58 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 82 HIS 0.006 0.002 HIS A 142 PHE 0.016 0.002 PHE B 108 TYR 0.017 0.002 TYR E 50 ARG 0.006 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.06532 ( 386) hydrogen bonds : angle 4.57692 ( 1092) SS BOND : bond 0.01053 ( 3) SS BOND : angle 1.00846 ( 6) covalent geometry : bond 0.00563 ( 8361) covalent geometry : angle 0.63980 (11440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.872 Fit side-chains REVERT: A 151 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: A 215 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6905 (tt0) REVERT: A 254 ASP cc_start: 0.8797 (t0) cc_final: 0.8069 (m-30) REVERT: B 43 ASN cc_start: 0.7762 (t0) cc_final: 0.7432 (t0) REVERT: B 94 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8055 (tpt-90) REVERT: B 123 ASN cc_start: 0.7862 (m110) cc_final: 0.7660 (m-40) REVERT: B 167 PHE cc_start: 0.7583 (t80) cc_final: 0.7207 (t80) REVERT: B 188 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.6245 (tpt-90) REVERT: D 159 ASN cc_start: 0.9070 (m-40) cc_final: 0.8688 (m110) REVERT: D 188 PRO cc_start: 0.8247 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: D 221 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8494 (tt) REVERT: E 284 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7396 (mt) outliers start: 25 outliers final: 17 residues processed: 145 average time/residue: 0.1696 time to fit residues: 35.1777 Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 96 optimal weight: 0.3980 chunk 108 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.149305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112316 restraints weight = 14643.035| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.99 r_work: 0.3296 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8364 Z= 0.152 Angle : 0.577 6.176 11446 Z= 0.309 Chirality : 0.041 0.136 1367 Planarity : 0.004 0.042 1450 Dihedral : 4.467 29.947 1267 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 17.46 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1115 helix: 2.58 (0.27), residues: 363 sheet: -0.11 (0.31), residues: 291 loop : -1.61 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.004 0.001 HIS A 142 PHE 0.011 0.001 PHE B 74 TYR 0.012 0.001 TYR E 50 ARG 0.006 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.05146 ( 386) hydrogen bonds : angle 4.26836 ( 1092) SS BOND : bond 0.00834 ( 3) SS BOND : angle 0.82537 ( 6) covalent geometry : bond 0.00353 ( 8361) covalent geometry : angle 0.57673 (11440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.859 Fit side-chains REVERT: A 151 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: A 215 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6913 (tt0) REVERT: A 254 ASP cc_start: 0.8763 (t0) cc_final: 0.8055 (m-30) REVERT: A 255 LEU cc_start: 0.8266 (tt) cc_final: 0.7993 (tt) REVERT: B 43 ASN cc_start: 0.7685 (t0) cc_final: 0.7352 (t0) REVERT: B 94 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7966 (tpt-90) REVERT: B 123 ASN cc_start: 0.7852 (m110) cc_final: 0.7642 (m-40) REVERT: B 167 PHE cc_start: 0.7572 (t80) cc_final: 0.7207 (t80) REVERT: B 188 ARG cc_start: 0.7276 (tpt-90) cc_final: 0.6536 (tpt170) REVERT: D 159 ASN cc_start: 0.9062 (m-40) cc_final: 0.8654 (m110) REVERT: D 221 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8343 (tt) REVERT: E 284 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7589 (mt) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.1722 time to fit residues: 33.9911 Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 70.0000 chunk 92 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110594 restraints weight = 14380.972| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.10 r_work: 0.3273 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8364 Z= 0.192 Angle : 0.612 6.109 11446 Z= 0.329 Chirality : 0.042 0.140 1367 Planarity : 0.004 0.041 1450 Dihedral : 4.596 29.988 1267 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.23 % Allowed : 17.72 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1115 helix: 2.45 (0.27), residues: 364 sheet: -0.13 (0.32), residues: 281 loop : -1.63 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 82 HIS 0.005 0.002 HIS D 35 PHE 0.012 0.001 PHE D 165 TYR 0.015 0.001 TYR E 50 ARG 0.006 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.05742 ( 386) hydrogen bonds : angle 4.39545 ( 1092) SS BOND : bond 0.00944 ( 3) SS BOND : angle 0.89009 ( 6) covalent geometry : bond 0.00457 ( 8361) covalent geometry : angle 0.61162 (11440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.013 Fit side-chains REVERT: A 151 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: A 215 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6903 (tt0) REVERT: A 254 ASP cc_start: 0.8780 (t0) cc_final: 0.8022 (m-30) REVERT: A 255 LEU cc_start: 0.8302 (tt) cc_final: 0.8022 (tt) REVERT: B 43 ASN cc_start: 0.7718 (t0) cc_final: 0.7374 (t0) REVERT: B 94 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7895 (tpt-90) REVERT: B 123 ASN cc_start: 0.7893 (m110) cc_final: 0.7686 (m-40) REVERT: B 167 PHE cc_start: 0.7524 (t80) cc_final: 0.7150 (t80) REVERT: B 188 ARG cc_start: 0.7286 (tpt-90) cc_final: 0.6197 (tpt-90) REVERT: D 159 ASN cc_start: 0.9049 (m-40) cc_final: 0.8628 (m110) REVERT: D 188 PRO cc_start: 0.8198 (Cg_exo) cc_final: 0.7865 (Cg_endo) REVERT: D 221 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8432 (tt) REVERT: E 284 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7481 (mt) outliers start: 25 outliers final: 19 residues processed: 139 average time/residue: 0.1726 time to fit residues: 34.2856 Evaluate side-chains 150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114198 restraints weight = 14381.042| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.83 r_work: 0.3359 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8364 Z= 0.101 Angle : 0.529 7.035 11446 Z= 0.277 Chirality : 0.039 0.133 1367 Planarity : 0.004 0.040 1450 Dihedral : 4.109 29.894 1267 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.20 % Allowed : 18.89 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1115 helix: 2.83 (0.27), residues: 365 sheet: 0.07 (0.31), residues: 289 loop : -1.49 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 96 HIS 0.003 0.001 HIS E 107 PHE 0.011 0.001 PHE B 74 TYR 0.011 0.001 TYR D 178 ARG 0.006 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 386) hydrogen bonds : angle 3.89251 ( 1092) SS BOND : bond 0.00513 ( 3) SS BOND : angle 0.59823 ( 6) covalent geometry : bond 0.00216 ( 8361) covalent geometry : angle 0.52932 (11440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4296.99 seconds wall clock time: 74 minutes 52.48 seconds (4492.48 seconds total)