Starting phenix.real_space_refine on Tue Apr 29 09:56:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dde_7868/04_2025/6dde_7868_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dde_7868/04_2025/6dde_7868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dde_7868/04_2025/6dde_7868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dde_7868/04_2025/6dde_7868.map" model { file = "/net/cci-nas-00/data/ceres_data/6dde_7868/04_2025/6dde_7868_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dde_7868/04_2025/6dde_7868_neut.cif" } resolution = 3.5 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= 0.027 sd= 0.613 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 60 5.16 5 C 5416 2.51 5 N 1457 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8489 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2097 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.61 Number of scatterers: 8489 At special positions: 0 Unit cell: (100.88, 118.56, 112.32, 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 60 16.00 O 1556 8.00 N 1457 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.70 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " 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=1, symmetry=0 Links applied TRANS " DAL D 2 " - " TYR D 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 2 " Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 16 sheets defined 35.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.834A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.989A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.191A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.648A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.723A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.529A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.710A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 4.109A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.307A pdb=" N ALA R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS R 79 " --> pdb=" O TYR R 75 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 120 removed outlier: 3.589A pdb=" N TYR R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 125 removed outlier: 4.160A pdb=" N GLN R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 120 through 125' Processing helix chain 'R' and resid 126 through 128 No H-bonds generated for 'chain 'R' and resid 126 through 128' Processing helix chain 'R' and resid 136 through 171 removed outlier: 4.077A pdb=" N LYS R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 3.758A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 205 removed outlier: 3.764A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 227 through 241 removed outlier: 3.662A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 232 " --> pdb=" O TRP R 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS R 233 " --> pdb=" O GLU R 229 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 removed outlier: 4.180A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 294 Processing helix chain 'R' and resid 294 through 306 removed outlier: 3.764A pdb=" N VAL R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 301 " --> pdb=" O HIS R 297 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.686A pdb=" N SER R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix removed outlier: 3.837A pdb=" N PHE R 338 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.082A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.082A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.823A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.636A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.529A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.690A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.809A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.563A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.569A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.937A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.653A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.653A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.538A pdb=" N ARG E 148 " --> pdb=" O THR E 129 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.728A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.796A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1110 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: 2.39 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2712 1.34 - 1.46: 2067 1.46 - 1.58: 3798 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 8664 Sorted by residual: bond pdb=" C THR E 138 " pdb=" N PRO E 139 " ideal model delta sigma weight residual 1.332 1.375 -0.044 1.34e-02 5.57e+03 1.06e+01 bond pdb=" O ETA D 5 " pdb=" CB ETA D 5 " ideal model delta sigma weight residual 1.413 1.459 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" C ASP E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.16e+00 bond pdb=" N GLU E 210 " pdb=" CA GLU E 210 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.85e+00 bond pdb=" CG LEU A 227 " pdb=" CD2 LEU A 227 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.31e+00 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11086 1.97 - 3.94: 577 3.94 - 5.92: 63 5.92 - 7.89: 27 7.89 - 9.86: 13 Bond angle restraints: 11766 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 111.91 106.14 5.77 8.90e-01 1.26e+00 4.20e+01 angle pdb=" CA ARG E 206 " pdb=" CB ARG E 206 " pdb=" CG ARG E 206 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" N GLY B 131 " pdb=" CA GLY B 131 " pdb=" C GLY B 131 " ideal model delta sigma weight residual 111.45 116.63 -5.18 1.23e+00 6.61e-01 1.77e+01 angle pdb=" N THR E 116 " pdb=" CA THR E 116 " pdb=" C THR E 116 " ideal model delta sigma weight residual 109.24 102.47 6.77 1.63e+00 3.76e-01 1.73e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 ... (remaining 11761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 4770 15.14 - 30.28: 253 30.28 - 45.41: 69 45.41 - 60.55: 9 60.55 - 75.69: 4 Dihedral angle restraints: 5105 sinusoidal: 1846 harmonic: 3259 Sorted by residual: dihedral pdb=" CA LEU B 30 " pdb=" C LEU B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA SER R 268 " pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta harmonic sigma weight residual -180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 5102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 931 0.051 - 0.102: 312 0.102 - 0.153: 90 0.153 - 0.204: 24 0.204 - 0.255: 5 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1359 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 61 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C ALA E 61 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA E 61 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP E 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.014 2.00e-02 2.50e+03 1.61e-02 6.48e+00 pdb=" CG TRP B 63 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO C 49 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.034 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1755 2.77 - 3.31: 7700 3.31 - 3.84: 14166 3.84 - 4.37: 15799 4.37 - 4.90: 27949 Nonbonded interactions: 67369 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" O LYS A 277 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.251 3.040 nonbonded pdb=" N THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.290 3.040 ... (remaining 67364 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.050 Set scattering table: 0.080 Process input model: 22.460 Find NCS groups from input model: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.010 0.673 8669 Z= 0.474 Angle : 1.055 24.760 11775 Z= 0.581 Chirality : 0.059 0.255 1362 Planarity : 0.006 0.062 1484 Dihedral : 10.869 75.688 2991 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 0.46 % Allowed : 6.00 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.56 (0.21), residues: 1103 helix: -2.51 (0.20), residues: 348 sheet: -2.14 (0.29), residues: 256 loop : -2.22 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 63 HIS 0.011 0.003 HIS E 155 PHE 0.028 0.003 PHE B 241 TYR 0.030 0.003 TYR E 163 ARG 0.018 0.001 ARG B 68 Details of bonding type rmsd link_TRANS : bond 0.00251 ( 1) link_TRANS : angle 0.43157 ( 3) hydrogen bonds : bond 0.14558 ( 383) hydrogen bonds : angle 7.60947 ( 1110) SS BOND : bond 0.38853 ( 3) SS BOND : angle 10.88787 ( 6) covalent geometry : bond 0.00636 ( 8664) covalent geometry : angle 1.02633 (11766) Misc. bond : bond 0.09878 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 362 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6898 (tm-30) REVERT: A 309 ASP cc_start: 0.7384 (t0) cc_final: 0.7153 (t0) REVERT: A 341 ASP cc_start: 0.8439 (t70) cc_final: 0.8170 (t0) REVERT: B 86 THR cc_start: 0.8060 (p) cc_final: 0.7552 (p) REVERT: B 163 ASP cc_start: 0.7499 (p0) cc_final: 0.7240 (p0) REVERT: B 221 THR cc_start: 0.8150 (m) cc_final: 0.7823 (m) REVERT: B 339 TRP cc_start: 0.8617 (m100) cc_final: 0.8210 (m100) REVERT: E 7 SER cc_start: 0.8095 (p) cc_final: 0.7554 (t) REVERT: E 130 GLN cc_start: 0.6596 (tp40) cc_final: 0.6065 (mt0) REVERT: R 112 LEU cc_start: 0.9102 (tp) cc_final: 0.8888 (tt) REVERT: R 145 SER cc_start: 0.8369 (t) cc_final: 0.7708 (m) REVERT: R 228 TRP cc_start: 0.7285 (t-100) cc_final: 0.7051 (t-100) REVERT: R 261 SER cc_start: 0.8665 (m) cc_final: 0.8283 (t) REVERT: R 263 ARG cc_start: 0.8061 (tmt90) cc_final: 0.7791 (tpt90) REVERT: R 270 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7597 (tm-30) outliers start: 4 outliers final: 1 residues processed: 365 average time/residue: 0.2290 time to fit residues: 110.0413 Evaluate side-chains 234 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 347 ASN B 110 ASN B 295 ASN E 130 GLN E 171 GLN E 174 GLN E 182 ASN R 86 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN R 150 ASN R 230 ASN R 297 HIS R 328 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.171226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142508 restraints weight = 12948.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147283 restraints weight = 6670.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150419 restraints weight = 4240.639| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8669 Z= 0.152 Angle : 0.675 10.576 11775 Z= 0.347 Chirality : 0.044 0.203 1362 Planarity : 0.004 0.041 1484 Dihedral : 5.581 67.873 1214 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.04 % Allowed : 17.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.05 (0.24), residues: 1103 helix: -0.60 (0.27), residues: 351 sheet: -1.68 (0.31), residues: 239 loop : -1.65 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE R 241 TYR 0.019 0.002 TYR R 75 ARG 0.006 0.001 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00263 ( 1) link_TRANS : angle 0.39347 ( 3) hydrogen bonds : bond 0.03709 ( 383) hydrogen bonds : angle 5.47142 ( 1110) SS BOND : bond 0.00431 ( 3) SS BOND : angle 1.49063 ( 6) covalent geometry : bond 0.00344 ( 8664) covalent geometry : angle 0.67410 (11766) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 51 LYS cc_start: 0.8610 (ttmp) cc_final: 0.8192 (tmmt) REVERT: A 216 GLU cc_start: 0.7858 (pt0) cc_final: 0.7612 (pp20) REVERT: A 254 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7638 (m) REVERT: A 302 TYR cc_start: 0.8185 (t80) cc_final: 0.7958 (t80) REVERT: A 341 ASP cc_start: 0.8706 (t70) cc_final: 0.8472 (t0) REVERT: B 82 TRP cc_start: 0.8954 (m100) cc_final: 0.8728 (m100) REVERT: B 86 THR cc_start: 0.8450 (p) cc_final: 0.8246 (p) REVERT: B 117 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7335 (tt) REVERT: B 163 ASP cc_start: 0.7875 (p0) cc_final: 0.7651 (p0) REVERT: B 280 LYS cc_start: 0.8148 (tmmt) cc_final: 0.7904 (tttt) REVERT: B 339 TRP cc_start: 0.8780 (m100) cc_final: 0.8222 (m-10) REVERT: E 115 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8315 (p) REVERT: E 130 GLN cc_start: 0.6482 (tp-100) cc_final: 0.5744 (mt0) REVERT: R 106 TYR cc_start: 0.9039 (m-80) cc_final: 0.8666 (m-10) REVERT: R 123 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7030 (t80) REVERT: R 161 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: R 165 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8204 (mtt90) REVERT: R 185 LYS cc_start: 0.8622 (ttmp) cc_final: 0.8058 (tptt) REVERT: R 228 TRP cc_start: 0.7479 (t-100) cc_final: 0.7146 (t-100) REVERT: R 263 ARG cc_start: 0.8274 (tmt90) cc_final: 0.7849 (tmt170) REVERT: R 270 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7865 (tm-30) REVERT: R 298 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7166 (pt) REVERT: R 336 TYR cc_start: 0.7124 (m-10) cc_final: 0.6859 (m-80) outliers start: 35 outliers final: 18 residues processed: 278 average time/residue: 0.2393 time to fit residues: 87.9289 Evaluate side-chains 248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 161 MET Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 92 optimal weight: 0.0030 chunk 100 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 75 GLN E 130 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.172936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144398 restraints weight = 13243.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149214 restraints weight = 6765.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152314 restraints weight = 4251.684| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8669 Z= 0.127 Angle : 0.655 8.758 11775 Z= 0.333 Chirality : 0.043 0.194 1362 Planarity : 0.004 0.039 1484 Dihedral : 5.303 71.399 1214 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.27 % Allowed : 20.21 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.47 (0.25), residues: 1103 helix: 0.09 (0.28), residues: 355 sheet: -1.41 (0.31), residues: 237 loop : -1.45 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS B 183 PHE 0.016 0.001 PHE R 241 TYR 0.024 0.002 TYR R 75 ARG 0.006 0.001 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.39387 ( 3) hydrogen bonds : bond 0.03358 ( 383) hydrogen bonds : angle 5.00279 ( 1110) SS BOND : bond 0.00463 ( 3) SS BOND : angle 0.95393 ( 6) covalent geometry : bond 0.00287 ( 8664) covalent geometry : angle 0.65509 (11766) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 51 LYS cc_start: 0.8623 (ttmp) cc_final: 0.8163 (tmmt) REVERT: A 228 SER cc_start: 0.7886 (p) cc_final: 0.7299 (m) REVERT: A 341 ASP cc_start: 0.8692 (t70) cc_final: 0.8479 (t0) REVERT: A 347 ASN cc_start: 0.9252 (m-40) cc_final: 0.8824 (m-40) REVERT: B 117 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7269 (tt) REVERT: B 234 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8303 (m-10) REVERT: B 280 LYS cc_start: 0.8244 (tmmt) cc_final: 0.8042 (tmmt) REVERT: B 308 LEU cc_start: 0.8236 (mp) cc_final: 0.7946 (mp) REVERT: B 339 TRP cc_start: 0.8759 (m100) cc_final: 0.8176 (m-10) REVERT: E 6 GLU cc_start: 0.6599 (mp0) cc_final: 0.6370 (mp0) REVERT: R 106 TYR cc_start: 0.9025 (m-80) cc_final: 0.8449 (m-10) REVERT: R 161 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8322 (tpp) REVERT: R 164 ASP cc_start: 0.8625 (t70) cc_final: 0.8358 (t70) REVERT: R 185 LYS cc_start: 0.8548 (ttmp) cc_final: 0.8032 (tptt) REVERT: R 228 TRP cc_start: 0.7502 (t-100) cc_final: 0.7145 (t-100) REVERT: R 233 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7753 (ttpt) REVERT: R 263 ARG cc_start: 0.8209 (tmt90) cc_final: 0.7795 (tmt170) REVERT: R 270 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7914 (tm-30) REVERT: R 277 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.7943 (tmm-80) REVERT: R 298 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7143 (pt) REVERT: R 336 TYR cc_start: 0.7202 (m-10) cc_final: 0.6922 (m-10) outliers start: 37 outliers final: 20 residues processed: 275 average time/residue: 0.2281 time to fit residues: 82.7712 Evaluate side-chains 244 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 161 MET Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 0.0170 chunk 82 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 156 GLN B 230 ASN E 82 GLN E 130 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140744 restraints weight = 13344.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145604 restraints weight = 6907.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148771 restraints weight = 4368.824| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8669 Z= 0.158 Angle : 0.669 8.033 11775 Z= 0.337 Chirality : 0.044 0.293 1362 Planarity : 0.004 0.039 1484 Dihedral : 5.173 70.357 1214 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.62 % Allowed : 22.40 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.19 (0.25), residues: 1103 helix: 0.52 (0.29), residues: 350 sheet: -1.30 (0.31), residues: 248 loop : -1.40 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 133 HIS 0.005 0.001 HIS R 319 PHE 0.015 0.001 PHE R 241 TYR 0.032 0.002 TYR E 178 ARG 0.007 0.001 ARG B 49 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.41789 ( 3) hydrogen bonds : bond 0.03303 ( 383) hydrogen bonds : angle 4.86630 ( 1110) SS BOND : bond 0.00297 ( 3) SS BOND : angle 1.08294 ( 6) covalent geometry : bond 0.00367 ( 8664) covalent geometry : angle 0.66871 (11766) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 51 LYS cc_start: 0.8750 (ttmp) cc_final: 0.8267 (tmmt) REVERT: A 197 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8200 (mtpp) REVERT: A 228 SER cc_start: 0.7866 (p) cc_final: 0.7384 (m) REVERT: A 341 ASP cc_start: 0.8694 (t70) cc_final: 0.8450 (t0) REVERT: A 347 ASN cc_start: 0.9325 (m-40) cc_final: 0.8962 (m-40) REVERT: B 117 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7457 (tt) REVERT: B 170 ASP cc_start: 0.7172 (t0) cc_final: 0.6963 (t0) REVERT: B 215 GLU cc_start: 0.6980 (pm20) cc_final: 0.6279 (pm20) REVERT: B 234 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8363 (m-10) REVERT: B 308 LEU cc_start: 0.8415 (mp) cc_final: 0.7934 (mp) REVERT: B 339 TRP cc_start: 0.8837 (m100) cc_final: 0.8267 (m-10) REVERT: R 161 MET cc_start: 0.8725 (tpp) cc_final: 0.8155 (tpp) REVERT: R 164 ASP cc_start: 0.8638 (t70) cc_final: 0.8348 (t70) REVERT: R 165 ARG cc_start: 0.8442 (mtt90) cc_final: 0.7735 (mtt90) REVERT: R 185 LYS cc_start: 0.8658 (ttmp) cc_final: 0.8158 (tptp) REVERT: R 211 ARG cc_start: 0.6278 (mtt90) cc_final: 0.6004 (mtt180) REVERT: R 228 TRP cc_start: 0.7474 (t-100) cc_final: 0.7140 (t-100) REVERT: R 263 ARG cc_start: 0.8227 (tmt90) cc_final: 0.7842 (tmt170) REVERT: R 277 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.7916 (tmm-80) REVERT: R 336 TYR cc_start: 0.7166 (m-10) cc_final: 0.6786 (m-10) outliers start: 40 outliers final: 27 residues processed: 266 average time/residue: 0.2271 time to fit residues: 79.8648 Evaluate side-chains 254 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 156 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.168367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140453 restraints weight = 13200.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146693 restraints weight = 7677.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.148064 restraints weight = 3969.326| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8669 Z= 0.161 Angle : 0.666 8.979 11775 Z= 0.336 Chirality : 0.044 0.284 1362 Planarity : 0.004 0.036 1484 Dihedral : 5.134 71.087 1214 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.54 % Allowed : 22.52 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.12 (0.26), residues: 1103 helix: 0.71 (0.29), residues: 348 sheet: -1.33 (0.31), residues: 254 loop : -1.41 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 133 HIS 0.006 0.001 HIS R 319 PHE 0.016 0.001 PHE R 241 TYR 0.025 0.002 TYR E 178 ARG 0.006 0.001 ARG B 49 Details of bonding type rmsd link_TRANS : bond 0.00249 ( 1) link_TRANS : angle 0.43821 ( 3) hydrogen bonds : bond 0.03264 ( 383) hydrogen bonds : angle 4.83556 ( 1110) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.96203 ( 6) covalent geometry : bond 0.00373 ( 8664) covalent geometry : angle 0.66603 (11766) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 51 LYS cc_start: 0.8821 (ttmp) cc_final: 0.8294 (tmmt) REVERT: A 216 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (pp20) REVERT: A 341 ASP cc_start: 0.8637 (t70) cc_final: 0.8389 (t0) REVERT: A 347 ASN cc_start: 0.9299 (m-40) cc_final: 0.8948 (m-40) REVERT: B 59 TYR cc_start: 0.8879 (m-80) cc_final: 0.8624 (m-80) REVERT: B 117 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7807 (tt) REVERT: B 170 ASP cc_start: 0.7314 (t0) cc_final: 0.6633 (t0) REVERT: B 172 GLU cc_start: 0.7644 (mp0) cc_final: 0.7443 (mp0) REVERT: B 234 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8450 (m-10) REVERT: B 339 TRP cc_start: 0.8912 (m100) cc_final: 0.8326 (m-10) REVERT: C 13 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8087 (mtm110) REVERT: C 38 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6023 (ttt) REVERT: E 207 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6585 (tt) REVERT: R 78 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8750 (t) REVERT: R 161 MET cc_start: 0.8569 (tpp) cc_final: 0.8083 (tpp) REVERT: R 164 ASP cc_start: 0.8518 (t70) cc_final: 0.8212 (t70) REVERT: R 165 ARG cc_start: 0.8440 (mtt90) cc_final: 0.7813 (mtt90) REVERT: R 185 LYS cc_start: 0.8734 (ttmp) cc_final: 0.8218 (tptp) REVERT: R 228 TRP cc_start: 0.7563 (t-100) cc_final: 0.7253 (t-100) REVERT: R 233 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7803 (ttmt) REVERT: R 263 ARG cc_start: 0.8179 (tmt90) cc_final: 0.7817 (tmt170) REVERT: R 270 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7495 (tm-30) REVERT: R 277 ARG cc_start: 0.8546 (tmm-80) cc_final: 0.8217 (tmm-80) REVERT: R 336 TYR cc_start: 0.7217 (m-10) cc_final: 0.6844 (m-10) outliers start: 48 outliers final: 30 residues processed: 259 average time/residue: 0.2359 time to fit residues: 82.6752 Evaluate side-chains 248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 306 GLN B 156 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141020 restraints weight = 13167.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145624 restraints weight = 7531.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148298 restraints weight = 4371.270| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8669 Z= 0.137 Angle : 0.649 8.804 11775 Z= 0.326 Chirality : 0.043 0.278 1362 Planarity : 0.004 0.035 1484 Dihedral : 5.047 72.179 1214 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.97 % Allowed : 23.44 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.94 (0.26), residues: 1103 helix: 0.96 (0.29), residues: 349 sheet: -1.36 (0.31), residues: 261 loop : -1.30 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 133 HIS 0.004 0.001 HIS R 319 PHE 0.016 0.001 PHE E 200 TYR 0.022 0.002 TYR E 178 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00224 ( 1) link_TRANS : angle 0.31588 ( 3) hydrogen bonds : bond 0.03156 ( 383) hydrogen bonds : angle 4.72975 ( 1110) SS BOND : bond 0.00542 ( 3) SS BOND : angle 0.91366 ( 6) covalent geometry : bond 0.00319 ( 8664) covalent geometry : angle 0.64914 (11766) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 51 LYS cc_start: 0.8950 (ttmp) cc_final: 0.8338 (tmmt) REVERT: A 216 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: A 228 SER cc_start: 0.7648 (p) cc_final: 0.7051 (m) REVERT: A 242 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7493 (mtp180) REVERT: A 245 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8284 (pt0) REVERT: A 341 ASP cc_start: 0.8751 (t70) cc_final: 0.8547 (t0) REVERT: A 347 ASN cc_start: 0.9378 (m-40) cc_final: 0.8982 (m-40) REVERT: B 59 TYR cc_start: 0.8801 (m-80) cc_final: 0.8366 (m-80) REVERT: B 75 GLN cc_start: 0.7345 (mt0) cc_final: 0.7025 (mm-40) REVERT: B 117 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7732 (tt) REVERT: B 169 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.6600 (m-90) REVERT: B 170 ASP cc_start: 0.7318 (t0) cc_final: 0.6405 (t0) REVERT: B 172 GLU cc_start: 0.7909 (mp0) cc_final: 0.7610 (mp0) REVERT: B 175 GLN cc_start: 0.8344 (pm20) cc_final: 0.8097 (pm20) REVERT: B 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8490 (m-10) REVERT: B 280 LYS cc_start: 0.8529 (tmmt) cc_final: 0.8256 (tttt) REVERT: B 339 TRP cc_start: 0.8986 (m100) cc_final: 0.8210 (m-10) REVERT: C 18 GLN cc_start: 0.8449 (tp40) cc_final: 0.8171 (tp40) REVERT: C 32 LYS cc_start: 0.8416 (mppt) cc_final: 0.8162 (mptt) REVERT: E 71 SER cc_start: 0.8035 (p) cc_final: 0.7686 (t) REVERT: E 93 MET cc_start: 0.7483 (ttt) cc_final: 0.7256 (ttm) REVERT: E 98 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7872 (ttp-110) REVERT: E 207 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6672 (tt) REVERT: R 78 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8920 (t) REVERT: R 161 MET cc_start: 0.8848 (tpp) cc_final: 0.8306 (tpp) REVERT: R 165 ARG cc_start: 0.8538 (mtt90) cc_final: 0.7823 (mtt90) REVERT: R 179 ARG cc_start: 0.8656 (ptm-80) cc_final: 0.8278 (ptm160) REVERT: R 185 LYS cc_start: 0.8689 (ttmp) cc_final: 0.8111 (tptp) REVERT: R 228 TRP cc_start: 0.7583 (t-100) cc_final: 0.7224 (t-100) REVERT: R 263 ARG cc_start: 0.8243 (tmt90) cc_final: 0.7750 (tmt170) REVERT: R 277 ARG cc_start: 0.8502 (tmm-80) cc_final: 0.8118 (tmm-80) REVERT: R 336 TYR cc_start: 0.7186 (m-10) cc_final: 0.6826 (m-10) outliers start: 43 outliers final: 28 residues processed: 245 average time/residue: 0.2242 time to fit residues: 73.2445 Evaluate side-chains 241 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 29 optimal weight: 0.0010 chunk 5 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.175811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149911 restraints weight = 13202.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154755 restraints weight = 7884.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.156370 restraints weight = 4383.510| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8669 Z= 0.113 Angle : 0.651 10.304 11775 Z= 0.321 Chirality : 0.042 0.255 1362 Planarity : 0.003 0.036 1484 Dihedral : 4.853 73.788 1212 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.73 % Allowed : 23.90 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.80 (0.26), residues: 1103 helix: 1.05 (0.29), residues: 355 sheet: -1.28 (0.31), residues: 261 loop : -1.22 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 133 HIS 0.003 0.001 HIS R 319 PHE 0.016 0.001 PHE E 200 TYR 0.029 0.002 TYR E 178 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00146 ( 1) link_TRANS : angle 0.25553 ( 3) hydrogen bonds : bond 0.03063 ( 383) hydrogen bonds : angle 4.58330 ( 1110) SS BOND : bond 0.00421 ( 3) SS BOND : angle 0.94240 ( 6) covalent geometry : bond 0.00259 ( 8664) covalent geometry : angle 0.65122 (11766) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 18 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7378 (ttm) REVERT: A 51 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8263 (tmmt) REVERT: A 216 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (pp20) REVERT: A 228 SER cc_start: 0.7733 (p) cc_final: 0.7251 (m) REVERT: A 245 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8219 (pt0) REVERT: A 306 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7838 (mm-40) REVERT: A 334 PHE cc_start: 0.8851 (t80) cc_final: 0.8611 (t80) REVERT: A 341 ASP cc_start: 0.8597 (t70) cc_final: 0.8383 (t0) REVERT: A 347 ASN cc_start: 0.9268 (m-40) cc_final: 0.8882 (m-40) REVERT: B 59 TYR cc_start: 0.8707 (m-80) cc_final: 0.8411 (m-80) REVERT: B 78 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8217 (mmtp) REVERT: B 95 LEU cc_start: 0.7405 (pp) cc_final: 0.7092 (pp) REVERT: B 117 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7050 (tt) REVERT: B 219 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7075 (mtt90) REVERT: B 234 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: B 280 LYS cc_start: 0.8382 (tmmt) cc_final: 0.8108 (tttt) REVERT: B 300 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 339 TRP cc_start: 0.8865 (m100) cc_final: 0.8341 (m-10) REVERT: C 21 MET cc_start: 0.7627 (mpp) cc_final: 0.7230 (mpp) REVERT: E 71 SER cc_start: 0.7917 (p) cc_final: 0.7589 (t) REVERT: E 72 ARG cc_start: 0.7567 (ptm160) cc_final: 0.7061 (mtp180) REVERT: E 93 MET cc_start: 0.7334 (ttt) cc_final: 0.7121 (ttm) REVERT: E 207 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6435 (tt) REVERT: R 78 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8691 (t) REVERT: R 165 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8158 (mtt90) REVERT: R 185 LYS cc_start: 0.8657 (ttmp) cc_final: 0.8129 (tptp) REVERT: R 228 TRP cc_start: 0.7536 (t-100) cc_final: 0.7217 (t-100) REVERT: R 233 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7941 (ttmt) REVERT: R 263 ARG cc_start: 0.8085 (tmt90) cc_final: 0.7774 (tmt170) REVERT: R 277 ARG cc_start: 0.8487 (tmm-80) cc_final: 0.8172 (tmm-80) REVERT: R 336 TYR cc_start: 0.7238 (m-10) cc_final: 0.6928 (m-10) outliers start: 41 outliers final: 24 residues processed: 248 average time/residue: 0.2300 time to fit residues: 75.2806 Evaluate side-chains 239 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.176010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.150511 restraints weight = 13028.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154794 restraints weight = 7011.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157497 restraints weight = 4273.029| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8669 Z= 0.157 Angle : 0.686 10.198 11775 Z= 0.343 Chirality : 0.043 0.272 1362 Planarity : 0.004 0.035 1484 Dihedral : 4.931 72.327 1212 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.08 % Allowed : 24.60 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.78 (0.26), residues: 1103 helix: 1.19 (0.29), residues: 346 sheet: -1.22 (0.31), residues: 261 loop : -1.30 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.029 0.001 PHE E 29 TYR 0.027 0.002 TYR E 178 ARG 0.007 0.000 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00227 ( 1) link_TRANS : angle 0.23338 ( 3) hydrogen bonds : bond 0.03159 ( 383) hydrogen bonds : angle 4.69856 ( 1110) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.96569 ( 6) covalent geometry : bond 0.00369 ( 8664) covalent geometry : angle 0.68580 (11766) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.879 Fit side-chains REVERT: A 14 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 51 LYS cc_start: 0.8868 (ttmp) cc_final: 0.8315 (tmmt) REVERT: A 216 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (pp20) REVERT: A 228 SER cc_start: 0.7818 (p) cc_final: 0.7288 (m) REVERT: A 245 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8246 (pt0) REVERT: A 334 PHE cc_start: 0.8879 (t80) cc_final: 0.8644 (t80) REVERT: A 341 ASP cc_start: 0.8794 (t70) cc_final: 0.8512 (t0) REVERT: A 347 ASN cc_start: 0.9309 (m-40) cc_final: 0.8925 (m-40) REVERT: B 34 THR cc_start: 0.6948 (t) cc_final: 0.5429 (p) REVERT: B 59 TYR cc_start: 0.8815 (m-80) cc_final: 0.8274 (m-80) REVERT: B 117 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7388 (tt) REVERT: B 169 TRP cc_start: 0.7584 (OUTLIER) cc_final: 0.6575 (m-90) REVERT: B 211 TRP cc_start: 0.8483 (m100) cc_final: 0.7837 (m100) REVERT: B 219 ARG cc_start: 0.7535 (ttm-80) cc_final: 0.7088 (mtt90) REVERT: B 234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8651 (m-10) REVERT: B 280 LYS cc_start: 0.8611 (tmmt) cc_final: 0.8359 (tttt) REVERT: B 300 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 339 TRP cc_start: 0.8991 (m100) cc_final: 0.8403 (m-10) REVERT: E 207 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6464 (tt) REVERT: R 78 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8681 (t) REVERT: R 165 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8299 (mtt90) REVERT: R 179 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8048 (ptm160) REVERT: R 185 LYS cc_start: 0.8692 (ttmp) cc_final: 0.8156 (tptp) REVERT: R 228 TRP cc_start: 0.7501 (t-100) cc_final: 0.7051 (t-100) REVERT: R 233 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8019 (ttmm) REVERT: R 263 ARG cc_start: 0.8118 (tmt90) cc_final: 0.7799 (tmt170) REVERT: R 277 ARG cc_start: 0.8518 (tmm-80) cc_final: 0.8174 (tmm-80) outliers start: 44 outliers final: 32 residues processed: 242 average time/residue: 0.2119 time to fit residues: 68.7738 Evaluate side-chains 244 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 306 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140963 restraints weight = 13368.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146178 restraints weight = 7530.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.147762 restraints weight = 4163.109| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8669 Z= 0.136 Angle : 0.680 11.611 11775 Z= 0.338 Chirality : 0.043 0.257 1362 Planarity : 0.004 0.036 1484 Dihedral : 4.926 73.278 1212 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.50 % Allowed : 25.75 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1103 helix: 1.18 (0.29), residues: 346 sheet: -1.20 (0.31), residues: 265 loop : -1.22 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 133 HIS 0.005 0.001 HIS B 183 PHE 0.027 0.001 PHE E 29 TYR 0.025 0.002 TYR E 178 ARG 0.006 0.001 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00182 ( 1) link_TRANS : angle 0.23914 ( 3) hydrogen bonds : bond 0.03131 ( 383) hydrogen bonds : angle 4.66595 ( 1110) SS BOND : bond 0.00361 ( 3) SS BOND : angle 1.46560 ( 6) covalent geometry : bond 0.00324 ( 8664) covalent geometry : angle 0.67931 (11766) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.844 Fit side-chains REVERT: A 14 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 18 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7315 (ttm) REVERT: A 51 LYS cc_start: 0.8809 (ttmp) cc_final: 0.8267 (tmmt) REVERT: A 216 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8133 (pp20) REVERT: A 228 SER cc_start: 0.7805 (p) cc_final: 0.7466 (m) REVERT: A 245 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8221 (pt0) REVERT: A 334 PHE cc_start: 0.8786 (t80) cc_final: 0.8558 (t80) REVERT: A 341 ASP cc_start: 0.8539 (t70) cc_final: 0.8326 (t0) REVERT: A 347 ASN cc_start: 0.9238 (m-40) cc_final: 0.8856 (m-40) REVERT: B 34 THR cc_start: 0.6810 (t) cc_final: 0.5182 (p) REVERT: B 59 TYR cc_start: 0.8785 (m-80) cc_final: 0.8365 (m-80) REVERT: B 75 GLN cc_start: 0.7194 (mm-40) cc_final: 0.5801 (mt0) REVERT: B 117 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7309 (tt) REVERT: B 169 TRP cc_start: 0.7379 (OUTLIER) cc_final: 0.6824 (m-90) REVERT: B 219 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7022 (mtt90) REVERT: B 234 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: B 280 LYS cc_start: 0.8423 (tmmt) cc_final: 0.8147 (tttt) REVERT: B 300 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 339 TRP cc_start: 0.8883 (m100) cc_final: 0.8492 (m100) REVERT: E 98 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7783 (ttp-110) REVERT: E 152 SER cc_start: 0.8055 (t) cc_final: 0.7701 (p) REVERT: E 207 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6271 (tt) REVERT: R 78 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8679 (t) REVERT: R 165 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8159 (mtt90) REVERT: R 179 ARG cc_start: 0.8427 (ptm-80) cc_final: 0.8073 (ptm160) REVERT: R 185 LYS cc_start: 0.8675 (ttmp) cc_final: 0.8151 (tptp) REVERT: R 228 TRP cc_start: 0.7470 (t-100) cc_final: 0.7070 (t-100) REVERT: R 233 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8043 (ttmm) REVERT: R 243 MET cc_start: 0.8449 (tpt) cc_final: 0.8220 (tmm) REVERT: R 263 ARG cc_start: 0.7941 (tmt90) cc_final: 0.7719 (tmt170) REVERT: R 277 ARG cc_start: 0.8480 (tmm-80) cc_final: 0.8174 (tmm-80) REVERT: R 336 TYR cc_start: 0.7226 (m-10) cc_final: 0.6856 (m-10) outliers start: 39 outliers final: 26 residues processed: 232 average time/residue: 0.2436 time to fit residues: 75.2770 Evaluate side-chains 241 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 256 ASN A 306 GLN B 183 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.171070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145050 restraints weight = 13220.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150741 restraints weight = 7500.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.151943 restraints weight = 4130.637| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8669 Z= 0.130 Angle : 0.686 12.046 11775 Z= 0.340 Chirality : 0.044 0.391 1362 Planarity : 0.004 0.035 1484 Dihedral : 4.960 73.662 1212 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.27 % Allowed : 25.64 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.63 (0.26), residues: 1103 helix: 1.11 (0.29), residues: 354 sheet: -0.98 (0.33), residues: 252 loop : -1.20 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.022 0.001 PHE E 29 TYR 0.025 0.002 TYR E 178 ARG 0.007 0.000 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00168 ( 1) link_TRANS : angle 0.09141 ( 3) hydrogen bonds : bond 0.03106 ( 383) hydrogen bonds : angle 4.66750 ( 1110) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.49993 ( 6) covalent geometry : bond 0.00308 ( 8664) covalent geometry : angle 0.68565 (11766) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.895 Fit side-chains REVERT: A 14 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 51 LYS cc_start: 0.8727 (ttmp) cc_final: 0.8359 (tmtt) REVERT: A 228 SER cc_start: 0.7851 (p) cc_final: 0.7528 (m) REVERT: A 245 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8185 (pt0) REVERT: A 334 PHE cc_start: 0.8777 (t80) cc_final: 0.8570 (t80) REVERT: A 347 ASN cc_start: 0.9215 (m-40) cc_final: 0.8831 (m-40) REVERT: B 34 THR cc_start: 0.6680 (t) cc_final: 0.5027 (p) REVERT: B 59 TYR cc_start: 0.8776 (m-80) cc_final: 0.8277 (m-80) REVERT: B 78 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8184 (mmtm) REVERT: B 117 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7229 (tt) REVERT: B 169 TRP cc_start: 0.7329 (OUTLIER) cc_final: 0.6861 (m-90) REVERT: B 171 ILE cc_start: 0.7627 (mm) cc_final: 0.7382 (tp) REVERT: B 219 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.7046 (mtt90) REVERT: B 234 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: B 280 LYS cc_start: 0.8389 (tmmt) cc_final: 0.8118 (tttt) REVERT: B 300 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 339 TRP cc_start: 0.8830 (m100) cc_final: 0.8448 (m100) REVERT: E 98 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7755 (ttp-110) REVERT: E 152 SER cc_start: 0.8037 (t) cc_final: 0.7656 (p) REVERT: R 165 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8169 (mtt90) REVERT: R 179 ARG cc_start: 0.8394 (ptm-80) cc_final: 0.8178 (ptm160) REVERT: R 185 LYS cc_start: 0.8645 (ttmp) cc_final: 0.8128 (tptp) REVERT: R 228 TRP cc_start: 0.7452 (t-100) cc_final: 0.7105 (t-100) REVERT: R 233 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8081 (ttmm) REVERT: R 263 ARG cc_start: 0.8039 (tmt90) cc_final: 0.7824 (tmt170) REVERT: R 270 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7712 (tm-30) REVERT: R 277 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8177 (tmm-80) REVERT: R 336 TYR cc_start: 0.7174 (m-10) cc_final: 0.6835 (m-10) outliers start: 37 outliers final: 24 residues processed: 242 average time/residue: 0.2168 time to fit residues: 70.7809 Evaluate side-chains 236 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.168629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142171 restraints weight = 13504.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148009 restraints weight = 7523.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.149041 restraints weight = 4298.290| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8669 Z= 0.158 Angle : 0.727 13.011 11775 Z= 0.359 Chirality : 0.044 0.427 1362 Planarity : 0.004 0.037 1484 Dihedral : 5.025 72.973 1212 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.27 % Allowed : 25.87 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1103 helix: 1.22 (0.29), residues: 351 sheet: -1.01 (0.32), residues: 252 loop : -1.18 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.001 PHE E 29 TYR 0.024 0.002 TYR E 178 ARG 0.007 0.000 ARG A 21 Details of bonding type rmsd link_TRANS : bond 0.00229 ( 1) link_TRANS : angle 0.11706 ( 3) hydrogen bonds : bond 0.03208 ( 383) hydrogen bonds : angle 4.69249 ( 1110) SS BOND : bond 0.00337 ( 3) SS BOND : angle 1.44700 ( 6) covalent geometry : bond 0.00377 ( 8664) covalent geometry : angle 0.72654 (11766) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.02 seconds wall clock time: 59 minutes 44.15 seconds (3584.15 seconds total)