Starting phenix.real_space_refine on Thu Jul 2 10:11:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y27_33587/07_2026/7y27_33587.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.130 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 4, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 11, 'ASN:plan1': 1, 'HIS:plan': 1} 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: {'ASP:plan': 8, 'ARG:plan': 8, 'GLU:plan': 6, 'GLN:plan1': 2} 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: {'GLU:plan': 9, 'GLN:plan1': 2, 'ASP:plan': 2, 'ARG: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: {'ASN:plan1': 7, 'PHE:plan': 6, 'TYR:plan': 2, 'ARG:plan': 7, 'TRP:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2} 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, 'ARG:plan': 3, 'GLU: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: 1.75, per 1000 atoms: 0.21 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: 0.57 Conformation dependent library (CDL) restraints added in 475.3 milliseconds 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: 0.20 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: 1.17 Time building geometry restraints manager: 0.77 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 - 17.98: 4480 17.98 - 35.97: 293 35.97 - 53.95: 51 53.95 - 71.94: 10 71.94 - 89.92: 6 Dihedral angle restraints: 4840 sinusoidal: 1547 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 4837 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: 0.880 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 12.894 89.920 2703 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 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: 0.16 (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 ARG 0.005 0.000 ARG D 168 TYR 0.013 0.001 TYR E 180 PHE 0.011 0.001 PHE B 70 TRP 0.010 0.001 TRP E 269 HIS 0.003 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.01237 / 0.62 ( 8361) covalent geometry : angle 0.62523 / 0.33 (11440) SS BOND : bond 0.00531 / 0.28 ( 3) SS BOND : angle 1.06645 / 0.59 ( 6) hydrogen bonds : bond 0.16388 / 11.95 ( 386) hydrogen bonds : angle 5.88848 / 4.28 ( 1092) *********************** 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 : 0.205 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: 0.0736 time to fit residues: 16.6773 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3965 r_free = 0.3965 target = 0.154229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117261 restraints weight = 14307.702| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.96 r_work: 0.3359 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8364 Z= 0.137 Angle : 0.562 7.343 11446 Z= 0.300 Chirality : 0.041 0.143 1367 Planarity : 0.004 0.052 1450 Dihedral : 5.016 66.156 1211 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.78 % Allowed : 8.54 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.47 (0.26), residues: 1115 helix: 2.59 (0.27), residues: 359 sheet: 0.16 (0.31), residues: 294 loop : -1.50 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.015 0.001 TYR D 178 PHE 0.010 0.001 PHE A 199 TRP 0.012 0.001 TRP B 129 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8361) covalent geometry : angle 0.56203 / 0.30 (11440) SS BOND : bond 0.00709 / 0.37 ( 3) SS BOND : angle 0.94467 / 0.42 ( 6) hydrogen bonds : bond 0.04910 / 3.48 ( 386) hydrogen bonds : angle 4.43929 / 3.15 ( 1092) *********************** 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 : 0.323 Fit side-chains REVERT: A 259 GLN cc_start: 0.8057 (pt0) cc_final: 0.7856 (pt0) REVERT: B 43 ASN cc_start: 0.7531 (t0) cc_final: 0.7265 (t0) REVERT: B 167 PHE cc_start: 0.7619 (t80) cc_final: 0.7294 (t80) REVERT: B 188 ARG cc_start: 0.7317 (tpt-90) cc_final: 0.6544 (tpt-90) REVERT: D 159 ASN cc_start: 0.9075 (m110) cc_final: 0.8801 (m110) outliers start: 6 outliers final: 4 residues processed: 145 average time/residue: 0.0681 time to fit residues: 14.4426 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 : 0.394 ------------------------------------------------------------------------------- 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 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 80 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN B 75 GLN D 159 ASN D 171 GLN E 79 ASN E 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109220 restraints weight = 14126.263| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.09 r_work: 0.3297 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8364 Z= 0.181 Angle : 0.587 7.082 11446 Z= 0.319 Chirality : 0.042 0.141 1367 Planarity : 0.004 0.048 1450 Dihedral : 5.078 67.058 1211 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 2.07 % Allowed : 11.77 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.37 (0.26), residues: 1115 helix: 2.52 (0.27), residues: 361 sheet: 0.02 (0.31), residues: 292 loop : -1.51 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 188 TYR 0.016 0.001 TYR D 178 PHE 0.013 0.002 PHE D 165 TRP 0.013 0.001 TRP B 129 HIS 0.006 0.002 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 8361) covalent geometry : angle 0.58720 / 0.32 (11440) SS BOND : bond 0.00930 / 0.48 ( 3) SS BOND : angle 0.90064 / 0.39 ( 6) hydrogen bonds : bond 0.05819 / 4.14 ( 386) hydrogen bonds : angle 4.50700 / 3.21 ( 1092) *********************** 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 162 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.306 Fit side-chains REVERT: A 151 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: B 43 ASN cc_start: 0.7634 (t0) cc_final: 0.7390 (t0) REVERT: B 111 ASP cc_start: 0.8818 (t0) cc_final: 0.8593 (t0) REVERT: B 167 PHE cc_start: 0.7621 (t80) cc_final: 0.7297 (t80) REVERT: B 188 ARG cc_start: 0.7385 (tpt-90) cc_final: 0.6520 (tpt-90) REVERT: D 159 ASN cc_start: 0.9045 (m-40) cc_final: 0.8651 (m110) REVERT: D 232 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7612 (tttt) outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.0610 time to fit residues: 13.4851 Evaluate side-chains 155 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 3 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN D 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108272 restraints weight = 14455.755| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.94 r_work: 0.3327 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8364 Z= 0.127 Angle : 0.541 6.828 11446 Z= 0.289 Chirality : 0.040 0.136 1367 Planarity : 0.004 0.044 1450 Dihedral : 4.870 67.041 1211 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.46 % Allowed : 13.45 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.48 (0.26), residues: 1115 helix: 2.69 (0.27), residues: 360 sheet: -0.00 (0.31), residues: 297 loop : -1.47 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 168 TYR 0.014 0.001 TYR D 178 PHE 0.011 0.001 PHE A 199 TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8361) covalent geometry : angle 0.54072 / 0.29 (11440) SS BOND : bond 0.00746 / 0.39 ( 3) SS BOND : angle 0.73997 / 0.34 ( 6) hydrogen bonds : bond 0.04593 / 3.26 ( 386) hydrogen bonds : angle 4.19069 / 2.98 ( 1092) *********************** 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 156 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.263 Fit side-chains REVERT: A 151 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: B 43 ASN cc_start: 0.7621 (t0) cc_final: 0.7341 (t0) REVERT: B 167 PHE cc_start: 0.7625 (t80) cc_final: 0.7242 (t80) REVERT: B 188 ARG cc_start: 0.7279 (tpt-90) cc_final: 0.6307 (tpt-90) REVERT: B 233 ASP cc_start: 0.8864 (t0) cc_final: 0.8631 (t0) REVERT: D 159 ASN cc_start: 0.9034 (m-40) cc_final: 0.8668 (m110) REVERT: D 221 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8315 (tt) outliers start: 19 outliers final: 11 residues processed: 146 average time/residue: 0.0610 time to fit residues: 12.8961 Evaluate side-chains 148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 201 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 233 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 51 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 52 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 5 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 35 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114232 restraints weight = 14210.181| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.07 r_work: 0.3364 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1778 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= 0.102 Angle : 0.508 6.411 11446 Z= 0.268 Chirality : 0.039 0.135 1367 Planarity : 0.003 0.043 1450 Dihedral : 4.656 67.716 1211 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 14.88 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.65 (0.26), residues: 1115 helix: 2.80 (0.27), residues: 364 sheet: 0.11 (0.31), residues: 297 loop : -1.38 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.013 0.001 TYR D 178 PHE 0.012 0.001 PHE B 74 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 8361) covalent geometry : angle 0.50820 / 0.27 (11440) SS BOND : bond 0.00564 / 0.29 ( 3) SS BOND : angle 0.63571 / 0.30 ( 6) hydrogen bonds : bond 0.03749 / 2.66 ( 386) hydrogen bonds : angle 3.95221 / 2.81 ( 1092) *********************** 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 162 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.291 Fit side-chains REVERT: A 59 TYR cc_start: 0.8909 (m-80) cc_final: 0.8655 (m-80) REVERT: A 228 ASP cc_start: 0.8108 (m-30) cc_final: 0.7467 (m-30) REVERT: B 43 ASN cc_start: 0.7539 (t0) cc_final: 0.7270 (t0) REVERT: B 85 ASP cc_start: 0.7792 (p0) cc_final: 0.7506 (p0) REVERT: B 167 PHE cc_start: 0.7608 (t80) cc_final: 0.7098 (t80) REVERT: B 233 ASP cc_start: 0.8875 (t0) cc_final: 0.8456 (t0) REVERT: D 159 ASN cc_start: 0.8987 (m-40) cc_final: 0.8676 (m-40) outliers start: 15 outliers final: 13 residues processed: 154 average time/residue: 0.0612 time to fit residues: 13.4046 Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 112 SER 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 80 PHE 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 281 SER 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 77 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113045 restraints weight = 14345.031| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.88 r_work: 0.3305 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8364 Z= 0.171 Angle : 0.580 6.279 11446 Z= 0.312 Chirality : 0.042 0.224 1367 Planarity : 0.004 0.042 1450 Dihedral : 4.873 66.278 1211 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 3.10 % Allowed : 14.49 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.47 (0.26), residues: 1115 helix: 2.70 (0.26), residues: 359 sheet: -0.04 (0.30), residues: 304 loop : -1.47 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.014 0.001 TYR E 50 PHE 0.012 0.001 PHE D 165 TRP 0.009 0.001 TRP A 82 HIS 0.005 0.002 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 8361) covalent geometry : angle 0.57962 / 0.31 (11440) SS BOND : bond 0.00840 / 0.44 ( 3) SS BOND : angle 0.86724 / 0.39 ( 6) hydrogen bonds : bond 0.05360 / 3.81 ( 386) hydrogen bonds : angle 4.31380 / 3.09 ( 1092) *********************** 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 163 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.263 Fit side-chains REVERT: A 151 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: A 228 ASP cc_start: 0.8266 (m-30) cc_final: 0.7606 (m-30) REVERT: B 43 ASN cc_start: 0.7706 (t0) cc_final: 0.7439 (t0) REVERT: B 85 ASP cc_start: 0.7946 (p0) cc_final: 0.7638 (p0) REVERT: B 111 ASP cc_start: 0.8769 (t0) cc_final: 0.8381 (t0) REVERT: B 123 ASN cc_start: 0.7854 (m110) cc_final: 0.7644 (m-40) REVERT: B 167 PHE cc_start: 0.7623 (t80) cc_final: 0.7260 (t80) REVERT: B 188 ARG cc_start: 0.7329 (tpt-90) cc_final: 0.6470 (tpt-90) REVERT: B 233 ASP cc_start: 0.8983 (t0) cc_final: 0.8709 (t0) REVERT: D 159 ASN cc_start: 0.9041 (m-40) cc_final: 0.8777 (m-40) REVERT: D 221 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 24 outliers final: 16 residues processed: 150 average time/residue: 0.0697 time to fit residues: 15.2710 Evaluate side-chains 145 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 VAL 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 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 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108318 restraints weight = 14463.393| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.94 r_work: 0.3331 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8364 Z= 0.119 Angle : 0.550 12.709 11446 Z= 0.287 Chirality : 0.041 0.179 1367 Planarity : 0.004 0.041 1450 Dihedral : 4.749 67.147 1211 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.52 (0.26), residues: 1115 helix: 2.69 (0.27), residues: 364 sheet: 0.06 (0.31), residues: 297 loop : -1.48 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.012 0.001 TYR D 178 PHE 0.011 0.001 PHE B 74 TRP 0.006 0.001 TRP E 269 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8361) covalent geometry : angle 0.54971 / 0.29 (11440) SS BOND : bond 0.00677 / 0.35 ( 3) SS BOND : angle 0.71152 / 0.32 ( 6) hydrogen bonds : bond 0.04322 / 3.07 ( 386) hydrogen bonds : angle 4.11076 / 2.95 ( 1092) *********************** 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: 20 poor density : 131 time to evaluate : 0.316 Fit side-chains REVERT: A 151 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: A 228 ASP cc_start: 0.8257 (m-30) cc_final: 0.7506 (m-30) REVERT: B 43 ASN cc_start: 0.7608 (t0) cc_final: 0.7266 (t0) REVERT: B 85 ASP cc_start: 0.7840 (p0) cc_final: 0.7546 (p0) REVERT: B 94 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (tpt-90) REVERT: B 123 ASN cc_start: 0.7833 (m110) cc_final: 0.7617 (m-40) REVERT: B 167 PHE cc_start: 0.7609 (t80) cc_final: 0.7251 (t80) REVERT: B 188 ARG cc_start: 0.7249 (tpt-90) cc_final: 0.6369 (tpt-90) REVERT: D 159 ASN cc_start: 0.9025 (m-40) cc_final: 0.8242 (m110) REVERT: D 221 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8300 (tt) REVERT: E 284 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7364 (mt) outliers start: 20 outliers final: 14 residues processed: 140 average time/residue: 0.0599 time to fit residues: 12.0713 Evaluate side-chains 152 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 53 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 ARG 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 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 284 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 70 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113185 restraints weight = 14336.106| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.81 r_work: 0.3349 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8364 Z= 0.113 Angle : 0.529 6.654 11446 Z= 0.278 Chirality : 0.040 0.134 1367 Planarity : 0.004 0.040 1450 Dihedral : 4.654 67.319 1211 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 2.59 % Allowed : 16.56 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.61 (0.26), residues: 1115 helix: 2.80 (0.27), residues: 364 sheet: 0.11 (0.31), residues: 292 loop : -1.45 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.012 0.001 TYR D 178 PHE 0.011 0.001 PHE B 74 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8361) covalent geometry : angle 0.52869 / 0.28 (11440) SS BOND : bond 0.00618 / 0.32 ( 3) SS BOND : angle 0.66080 / 0.31 ( 6) hydrogen bonds : bond 0.04017 / 2.84 ( 386) hydrogen bonds : angle 3.99299 / 2.86 ( 1092) *********************** 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 156 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.302 Fit side-chains REVERT: A 151 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: A 228 ASP cc_start: 0.8204 (m-30) cc_final: 0.7445 (m-30) REVERT: B 43 ASN cc_start: 0.7586 (t0) cc_final: 0.7338 (t0) REVERT: B 85 ASP cc_start: 0.7863 (p0) cc_final: 0.7575 (p0) REVERT: B 94 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8128 (tpt-90) REVERT: B 123 ASN cc_start: 0.7830 (m110) cc_final: 0.7611 (m-40) REVERT: B 167 PHE cc_start: 0.7615 (t80) cc_final: 0.7253 (t80) REVERT: B 188 ARG cc_start: 0.7213 (tpt-90) cc_final: 0.6314 (tpt-90) REVERT: B 233 ASP cc_start: 0.8944 (t0) cc_final: 0.8640 (t0) REVERT: D 34 MET cc_start: 0.8632 (mmm) cc_final: 0.8408 (mmm) REVERT: D 159 ASN cc_start: 0.9032 (m-40) cc_final: 0.8731 (m110) REVERT: D 221 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8292 (tt) REVERT: E 284 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7426 (mt) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 0.0638 time to fit residues: 13.1457 Evaluate side-chains 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 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 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 284 ILE 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 35 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108078 restraints weight = 14312.064| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.90 r_work: 0.3328 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8364 Z= 0.128 Angle : 0.546 7.033 11446 Z= 0.288 Chirality : 0.040 0.135 1367 Planarity : 0.004 0.040 1450 Dihedral : 4.689 67.011 1211 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.72 % Allowed : 16.43 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.56 (0.26), residues: 1115 helix: 2.77 (0.27), residues: 365 sheet: 0.06 (0.31), residues: 290 loop : -1.47 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.012 0.001 TYR B 115 PHE 0.011 0.001 PHE B 74 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8361) covalent geometry : angle 0.54560 / 0.29 (11440) SS BOND : bond 0.00687 / 0.36 ( 3) SS BOND : angle 0.69026 / 0.33 ( 6) hydrogen bonds : bond 0.04383 / 3.10 ( 386) hydrogen bonds : angle 4.04660 / 2.90 ( 1092) *********************** 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 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.312 Fit side-chains REVERT: A 151 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: A 228 ASP cc_start: 0.8268 (m-30) cc_final: 0.7287 (m-30) REVERT: B 43 ASN cc_start: 0.7653 (t0) cc_final: 0.7344 (t0) REVERT: B 85 ASP cc_start: 0.7899 (p0) cc_final: 0.7613 (p0) REVERT: B 94 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7645 (tpt-90) REVERT: B 111 ASP cc_start: 0.8694 (t0) cc_final: 0.8310 (t0) REVERT: B 123 ASN cc_start: 0.7845 (m110) cc_final: 0.7627 (m-40) REVERT: B 167 PHE cc_start: 0.7600 (t80) cc_final: 0.7251 (t80) REVERT: B 188 ARG cc_start: 0.7228 (tpt-90) cc_final: 0.6324 (tpt-90) REVERT: B 233 ASP cc_start: 0.8969 (t0) cc_final: 0.8673 (t0) REVERT: D 159 ASN cc_start: 0.9018 (m-40) cc_final: 0.8569 (m110) REVERT: D 221 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8305 (tt) REVERT: E 284 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7328 (mt) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.0706 time to fit residues: 14.1017 Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 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 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 195 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 284 ILE 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 34 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115040 restraints weight = 14287.736| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.87 r_work: 0.3333 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8364 Z= 0.129 Angle : 0.546 6.732 11446 Z= 0.289 Chirality : 0.040 0.134 1367 Planarity : 0.004 0.040 1450 Dihedral : 4.693 66.965 1211 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.46 % Allowed : 16.95 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.55 (0.26), residues: 1115 helix: 2.76 (0.27), residues: 365 sheet: 0.05 (0.31), residues: 290 loop : -1.47 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.012 0.001 TYR D 178 PHE 0.011 0.001 PHE B 74 TRP 0.007 0.001 TRP A 82 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8361) covalent geometry : angle 0.54604 / 0.29 (11440) SS BOND : bond 0.00686 / 0.36 ( 3) SS BOND : angle 0.66827 / 0.32 ( 6) hydrogen bonds : bond 0.04364 / 3.09 ( 386) hydrogen bonds : angle 4.03826 / 2.90 ( 1092) ********************** 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 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.224 Fit side-chains REVERT: A 151 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: A 228 ASP cc_start: 0.8263 (m-30) cc_final: 0.7569 (m-30) REVERT: B 43 ASN cc_start: 0.7612 (t0) cc_final: 0.7271 (t0) REVERT: B 85 ASP cc_start: 0.7887 (p0) cc_final: 0.7601 (p0) REVERT: B 111 ASP cc_start: 0.8679 (t0) cc_final: 0.8302 (t0) REVERT: B 123 ASN cc_start: 0.7809 (m110) cc_final: 0.7592 (m-40) REVERT: B 167 PHE cc_start: 0.7596 (t80) cc_final: 0.7248 (t80) REVERT: B 188 ARG cc_start: 0.7215 (tpt-90) cc_final: 0.6317 (tpt-90) REVERT: B 233 ASP cc_start: 0.8963 (t0) cc_final: 0.8667 (t0) REVERT: D 159 ASN cc_start: 0.9001 (m-40) cc_final: 0.8555 (m110) REVERT: D 221 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8299 (tt) REVERT: E 284 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7405 (mt) outliers start: 19 outliers final: 15 residues processed: 138 average time/residue: 0.0707 time to fit residues: 13.9022 Evaluate side-chains 146 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 B residue 146 GLN 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 193 CYS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 284 ILE 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 51 optimal weight: 0.0980 chunk 64 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.0020 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 22 optimal weight: 0.0870 overall best weight: 0.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN E 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121995 restraints weight = 14007.121| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.68 r_work: 0.3432 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2370 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= 0.094 Angle : 0.513 7.334 11446 Z= 0.265 Chirality : 0.039 0.131 1367 Planarity : 0.003 0.040 1450 Dihedral : 4.397 68.242 1211 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.94 % Allowed : 17.72 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.78 (0.26), residues: 1115 helix: 2.93 (0.27), residues: 366 sheet: 0.35 (0.31), residues: 289 loop : -1.46 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.013 0.001 TYR D 178 PHE 0.011 0.001 PHE B 74 TRP 0.009 0.001 TRP B 96 HIS 0.002 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 8361) covalent geometry : angle 0.51310 / 0.26 (11440) SS BOND : bond 0.00343 / 0.18 ( 3) SS BOND : angle 0.60986 / 0.31 ( 6) hydrogen bonds : bond 0.02680 / 1.91 ( 386) hydrogen bonds : angle 3.69088 / 2.65 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.75 seconds wall clock time: 33 minutes 50.93 seconds (2030.93 seconds total)