Starting phenix.real_space_refine on Tue Sep 24 14:42:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/09_2024/7y27_33587.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/09_2024/7y27_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/09_2024/7y27_33587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/09_2024/7y27_33587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/09_2024/7y27_33587.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/09_2024/7y27_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-5461/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: 5.33, per 1000 atoms: 0.65 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 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: 1.12 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: 2.46 Time building geometry restraints manager: 2.72 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: 0.900 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- 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 8361 Z= 0.802 Angle : 0.625 12.233 11440 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.918 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: 0.1876 time to fit residues: 41.8574 Evaluate side-chains 127 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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: 30.0000 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 8361 Z= 0.224 Angle : 0.569 7.325 11440 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.842 Fit side-chains REVERT: B 43 ASN cc_start: 0.7326 (t0) cc_final: 0.7085 (t0) REVERT: B 167 PHE cc_start: 0.7699 (t80) cc_final: 0.7414 (t80) REVERT: B 188 ARG cc_start: 0.7423 (tpt-90) cc_final: 0.6559 (tpt-90) REVERT: D 159 ASN cc_start: 0.8963 (m110) cc_final: 0.8716 (m110) outliers start: 6 outliers final: 4 residues processed: 145 average time/residue: 0.1723 time to fit residues: 35.9865 Evaluate side-chains 144 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8361 Z= 0.183 Angle : 0.523 6.967 11440 Z= 0.281 Chirality : 0.040 0.146 1367 Planarity : 0.004 0.047 1450 Dihedral : 4.227 31.624 1267 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 1.68 % Allowed : 11.51 % Favored : 86.80 % 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: 0.59 (0.26), residues: 1115 helix: 2.76 (0.27), residues: 360 sheet: 0.17 (0.31), residues: 294 loop : -1.45 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 129 HIS 0.003 0.001 HIS A 142 PHE 0.010 0.001 PHE A 199 TYR 0.014 0.001 TYR D 178 ARG 0.003 0.000 ARG D 168 *********************** 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 156 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.924 Fit side-chains REVERT: B 43 ASN cc_start: 0.7337 (t0) cc_final: 0.7110 (t0) REVERT: B 111 ASP cc_start: 0.8428 (t0) cc_final: 0.8182 (t0) REVERT: B 167 PHE cc_start: 0.7716 (t80) cc_final: 0.7415 (t80) REVERT: B 188 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.6293 (tpt-90) REVERT: D 159 ASN cc_start: 0.8927 (m110) cc_final: 0.8558 (m110) outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.1637 time to fit residues: 34.8848 Evaluate side-chains 141 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 PHE Chi-restraints excluded: chain D residue 180 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.0970 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 ASN E 79 ASN E 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8361 Z= 0.452 Angle : 0.690 7.629 11440 Z= 0.376 Chirality : 0.046 0.155 1367 Planarity : 0.005 0.047 1450 Dihedral : 4.919 29.901 1267 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 3.49 % Allowed : 13.32 % 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 (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: 0.05 (0.25), residues: 1115 helix: 2.22 (0.26), residues: 361 sheet: -0.17 (0.32), residues: 283 loop : -1.64 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 82 HIS 0.007 0.002 HIS A 142 PHE 0.019 0.002 PHE D 165 TYR 0.020 0.002 TYR E 50 ARG 0.003 0.001 ARG A 314 *********************** 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 162 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.889 Fit side-chains REVERT: A 151 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: A 215 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6946 (tt0) REVERT: A 254 ASP cc_start: 0.8689 (t0) cc_final: 0.7845 (m-30) REVERT: B 43 ASN cc_start: 0.7620 (t0) cc_final: 0.7332 (t0) REVERT: B 167 PHE cc_start: 0.7740 (t80) cc_final: 0.7404 (t80) REVERT: B 188 ARG cc_start: 0.7522 (tpt-90) cc_final: 0.6477 (tpt-90) REVERT: D 159 ASN cc_start: 0.9012 (m-40) cc_final: 0.8621 (m110) REVERT: D 188 PRO cc_start: 0.8417 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: D 221 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8527 (tt) REVERT: D 232 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7687 (tttt) REVERT: E 183 LEU cc_start: 0.8607 (tt) cc_final: 0.8401 (tp) outliers start: 27 outliers final: 20 residues processed: 147 average time/residue: 0.1674 time to fit residues: 35.2074 Evaluate side-chains 148 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 273 ILE 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 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 218 MET 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 231 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 279 SER 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 61 optimal weight: 3.9990 chunk 1 optimal weight: 50.0000 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8361 Z= 0.247 Angle : 0.580 6.475 11440 Z= 0.311 Chirality : 0.042 0.138 1367 Planarity : 0.004 0.045 1450 Dihedral : 4.614 29.888 1267 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 3.23 % Allowed : 15.39 % 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: 0.25 (0.26), residues: 1115 helix: 2.54 (0.27), residues: 359 sheet: -0.17 (0.31), residues: 295 loop : -1.60 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS A 142 PHE 0.012 0.001 PHE B 74 TYR 0.015 0.001 TYR D 178 ARG 0.003 0.000 ARG A 251 *********************** 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 160 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.881 Fit side-chains REVERT: A 215 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6904 (tt0) REVERT: A 228 ASP cc_start: 0.7984 (m-30) cc_final: 0.7359 (m-30) REVERT: A 254 ASP cc_start: 0.8612 (t0) cc_final: 0.7864 (m-30) REVERT: B 43 ASN cc_start: 0.7613 (t0) cc_final: 0.7319 (t0) REVERT: B 167 PHE cc_start: 0.7710 (t80) cc_final: 0.7242 (t80) REVERT: D 159 ASN cc_start: 0.8980 (m-40) cc_final: 0.8639 (m110) REVERT: D 188 PRO cc_start: 0.8304 (Cg_exo) cc_final: 0.8022 (Cg_endo) REVERT: D 232 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7725 (tttt) outliers start: 25 outliers final: 18 residues processed: 146 average time/residue: 0.1652 time to fit residues: 34.6191 Evaluate side-chains 154 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 168 ARG 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 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 97 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8361 Z= 0.143 Angle : 0.520 6.208 11440 Z= 0.273 Chirality : 0.039 0.138 1367 Planarity : 0.004 0.042 1450 Dihedral : 4.192 29.709 1267 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 2.07 % Allowed : 16.17 % Favored : 81.76 % 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: 0.52 (0.26), residues: 1115 helix: 2.75 (0.27), residues: 364 sheet: 0.01 (0.31), residues: 289 loop : -1.48 (0.28), residues: 462 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 0.014 0.001 PHE B 74 TYR 0.014 0.001 TYR D 178 ARG 0.004 0.000 ARG D 18 *********************** 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 161 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.926 Fit side-chains REVERT: A 228 ASP cc_start: 0.7810 (m-30) cc_final: 0.7143 (m-30) REVERT: A 254 ASP cc_start: 0.8582 (t0) cc_final: 0.7885 (m-30) REVERT: B 43 ASN cc_start: 0.7420 (t0) cc_final: 0.7139 (t0) REVERT: B 111 ASP cc_start: 0.8421 (t0) cc_final: 0.8188 (t0) REVERT: B 167 PHE cc_start: 0.7704 (t80) cc_final: 0.7389 (t80) REVERT: B 188 ARG cc_start: 0.7255 (tpt-90) cc_final: 0.6291 (tpt-90) REVERT: B 233 ASP cc_start: 0.8716 (t0) cc_final: 0.8418 (t0) REVERT: D 159 ASN cc_start: 0.8938 (m-40) cc_final: 0.8136 (m110) REVERT: D 221 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8257 (tt) outliers start: 16 outliers final: 11 residues processed: 152 average time/residue: 0.1614 time to fit residues: 35.1888 Evaluate side-chains 143 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8361 Z= 0.187 Angle : 0.536 6.041 11440 Z= 0.284 Chirality : 0.040 0.136 1367 Planarity : 0.004 0.040 1450 Dihedral : 4.161 29.958 1267 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 2.33 % Allowed : 17.34 % 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 (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: 2.75 (0.27), residues: 364 sheet: 0.01 (0.31), residues: 291 loop : -1.44 (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 A 142 PHE 0.011 0.001 PHE B 74 TYR 0.014 0.001 TYR D 178 ARG 0.007 0.000 ARG D 18 *********************** 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 fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.930 Fit side-chains REVERT: A 228 ASP cc_start: 0.7831 (m-30) cc_final: 0.6880 (m-30) REVERT: A 254 ASP cc_start: 0.8634 (t0) cc_final: 0.7909 (m-30) REVERT: A 255 LEU cc_start: 0.8162 (tt) cc_final: 0.7876 (tt) REVERT: B 43 ASN cc_start: 0.7429 (t0) cc_final: 0.7139 (t0) REVERT: B 94 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7529 (tpt-90) REVERT: B 111 ASP cc_start: 0.8442 (t0) cc_final: 0.8221 (t0) REVERT: B 123 ASN cc_start: 0.7646 (m110) cc_final: 0.7419 (m-40) REVERT: B 167 PHE cc_start: 0.7697 (t80) cc_final: 0.7393 (t80) REVERT: B 188 ARG cc_start: 0.7264 (tpt-90) cc_final: 0.6286 (tpt-90) REVERT: D 159 ASN cc_start: 0.8927 (m-40) cc_final: 0.8577 (m110) REVERT: D 221 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8298 (tt) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.1760 time to fit residues: 35.4951 Evaluate side-chains 144 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU 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 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8361 Z= 0.138 Angle : 0.504 6.767 11440 Z= 0.264 Chirality : 0.039 0.135 1367 Planarity : 0.003 0.039 1450 Dihedral : 3.905 29.529 1267 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 2.33 % Allowed : 17.72 % Favored : 79.95 % 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: 0.69 (0.26), residues: 1115 helix: 2.86 (0.27), residues: 366 sheet: 0.22 (0.31), residues: 289 loop : -1.44 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.002 0.001 HIS E 107 PHE 0.011 0.001 PHE B 74 TYR 0.014 0.001 TYR D 178 ARG 0.006 0.000 ARG D 18 *********************** 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 152 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.872 Fit side-chains REVERT: A 228 ASP cc_start: 0.7688 (m-30) cc_final: 0.6828 (m-30) REVERT: A 254 ASP cc_start: 0.8612 (t0) cc_final: 0.7930 (m-30) REVERT: A 255 LEU cc_start: 0.8089 (tt) cc_final: 0.7856 (tt) REVERT: B 43 ASN cc_start: 0.7396 (t0) cc_final: 0.7188 (t0) REVERT: B 94 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7484 (tpt-90) REVERT: B 167 PHE cc_start: 0.7690 (t80) cc_final: 0.7358 (t80) REVERT: B 188 ARG cc_start: 0.7183 (tpt-90) cc_final: 0.6179 (tpt-90) REVERT: D 159 ASN cc_start: 0.8898 (m110) cc_final: 0.8449 (m110) REVERT: D 221 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8224 (tt) outliers start: 18 outliers final: 11 residues processed: 143 average time/residue: 0.1738 time to fit residues: 35.1961 Evaluate side-chains 139 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 201 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 195 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 94 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.0000 chunk 106 optimal weight: 7.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8361 Z= 0.152 Angle : 0.509 6.563 11440 Z= 0.267 Chirality : 0.039 0.135 1367 Planarity : 0.003 0.039 1450 Dihedral : 3.855 29.075 1267 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.07 % Allowed : 17.72 % Favored : 80.21 % 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: 367 sheet: 0.23 (0.31), residues: 292 loop : -1.40 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.002 0.001 HIS A 142 PHE 0.011 0.001 PHE B 74 TYR 0.013 0.001 TYR D 178 ARG 0.007 0.000 ARG D 18 *********************** 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 143 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.892 Fit side-chains REVERT: A 228 ASP cc_start: 0.7714 (m-30) cc_final: 0.6877 (m-30) REVERT: A 254 ASP cc_start: 0.8620 (t0) cc_final: 0.7911 (m-30) REVERT: A 255 LEU cc_start: 0.8139 (tt) cc_final: 0.7909 (tt) REVERT: B 8 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7573 (mp0) REVERT: B 43 ASN cc_start: 0.7405 (t0) cc_final: 0.7111 (t0) REVERT: B 94 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7543 (tpt-90) REVERT: B 167 PHE cc_start: 0.7670 (t80) cc_final: 0.7357 (t80) REVERT: B 188 ARG cc_start: 0.7175 (tpt-90) cc_final: 0.6174 (tpt-90) REVERT: D 159 ASN cc_start: 0.8922 (m110) cc_final: 0.8447 (m110) REVERT: D 221 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8261 (tt) outliers start: 16 outliers final: 13 residues processed: 135 average time/residue: 0.1632 time to fit residues: 31.7468 Evaluate side-chains 140 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 201 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 257 MET 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 64 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.0670 chunk 102 optimal weight: 0.0000 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.0050 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8361 Z= 0.134 Angle : 0.497 7.029 11440 Z= 0.259 Chirality : 0.039 0.133 1367 Planarity : 0.003 0.039 1450 Dihedral : 3.650 28.181 1267 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.81 % Allowed : 17.98 % Favored : 80.21 % 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: 0.87 (0.26), residues: 1115 helix: 2.95 (0.27), residues: 366 sheet: 0.35 (0.31), residues: 293 loop : -1.33 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.002 0.000 HIS D 35 PHE 0.010 0.001 PHE B 74 TYR 0.013 0.001 TYR D 178 ARG 0.006 0.000 ARG D 18 ********************** 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 152 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 0.966 Fit side-chains REVERT: A 228 ASP cc_start: 0.7668 (m-30) cc_final: 0.6909 (m-30) REVERT: A 254 ASP cc_start: 0.8598 (t0) cc_final: 0.7859 (m-30) REVERT: A 255 LEU cc_start: 0.8141 (tt) cc_final: 0.7879 (tt) REVERT: B 43 ASN cc_start: 0.7327 (t0) cc_final: 0.6817 (t0) REVERT: B 94 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7465 (tpt-90) REVERT: B 167 PHE cc_start: 0.7650 (t80) cc_final: 0.7346 (t80) REVERT: B 188 ARG cc_start: 0.6897 (tpt-90) cc_final: 0.5917 (tpt-90) REVERT: D 159 ASN cc_start: 0.8889 (m110) cc_final: 0.8409 (m110) REVERT: D 221 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8174 (tt) outliers start: 14 outliers final: 11 residues processed: 145 average time/residue: 0.1587 time to fit residues: 33.8308 Evaluate side-chains 139 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 221 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 257 MET 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 27 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116298 restraints weight = 14132.428| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.80 r_work: 0.3391 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8361 Z= 0.160 Angle : 0.514 6.609 11440 Z= 0.270 Chirality : 0.040 0.205 1367 Planarity : 0.003 0.039 1450 Dihedral : 3.682 27.694 1267 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.81 % Allowed : 18.37 % 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: 0.86 (0.26), residues: 1115 helix: 2.95 (0.27), residues: 367 sheet: 0.34 (0.31), residues: 294 loop : -1.35 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.002 0.001 HIS E 107 PHE 0.030 0.001 PHE E 294 TYR 0.012 0.001 TYR D 178 ARG 0.007 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.89 seconds wall clock time: 38 minutes 5.01 seconds (2285.01 seconds total)