Starting phenix.real_space_refine on Wed Sep 17 11:54:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3y_39757/09_2025/8z3y_39757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3y_39757/09_2025/8z3y_39757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z3y_39757/09_2025/8z3y_39757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3y_39757/09_2025/8z3y_39757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z3y_39757/09_2025/8z3y_39757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3y_39757/09_2025/8z3y_39757.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5478 2.51 5 N 1470 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8557 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1857 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2464 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 333 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "S" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1669 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2234 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 11, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 121 Time building chain proxies: 1.92, per 1000 atoms: 0.22 Number of scatterers: 8557 At special positions: 0 Unit cell: (90.28, 122.84, 129.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1558 8.00 N 1470 7.00 C 5478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 349.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.668A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 27 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 29 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.692A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.556A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.512A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.714A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.682A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.506A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.509A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.548A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.614A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.528A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.713A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.527A pdb=" N GLN R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 79 Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 5.274A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 149 removed outlier: 3.568A pdb=" N ASN R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 177 through 189 removed outlier: 3.566A pdb=" N MET R 181 " --> pdb=" O TRP R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 209 Processing helix chain 'R' and resid 215 through 252 removed outlier: 3.841A pdb=" N LYS R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 275 removed outlier: 5.909A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 303 removed outlier: 3.758A pdb=" N ASN R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 223 removed outlier: 4.746A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.665A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.705A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.819A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.725A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.714A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.346A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.521A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.547A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.526A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 145 Processing sheet with id=AB5, first strand: chain 'R' and resid 160 through 161 removed outlier: 4.202A pdb=" N HIS R 165 " --> pdb=" O ASP R 161 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1368 1.30 - 1.43: 2520 1.43 - 1.56: 4798 1.56 - 1.69: 1 1.69 - 1.82: 71 Bond restraints: 8758 Sorted by residual: bond pdb=" C GLU R 170 " pdb=" N LYS R 171 " ideal model delta sigma weight residual 1.331 1.479 -0.148 1.51e-02 4.39e+03 9.59e+01 bond pdb=" C PHE R 172 " pdb=" O PHE R 172 " ideal model delta sigma weight residual 1.244 1.184 0.059 9.30e-03 1.16e+04 4.09e+01 bond pdb=" C PHE R 169 " pdb=" N GLU R 170 " ideal model delta sigma weight residual 1.331 1.418 -0.087 1.55e-02 4.16e+03 3.14e+01 bond pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 1.527 1.465 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" C GLU A 392 " pdb=" O GLU A 392 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.28e-02 6.10e+03 2.12e+01 ... (remaining 8753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11614 2.03 - 4.06: 272 4.06 - 6.09: 47 6.09 - 8.13: 12 8.13 - 10.16: 4 Bond angle restraints: 11949 Sorted by residual: angle pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" C ASP R 81 " ideal model delta sigma weight residual 111.74 121.20 -9.46 1.35e+00 5.49e-01 4.91e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 111.39 120.00 -8.61 1.38e+00 5.25e-01 3.89e+01 angle pdb=" N ASN R 164 " pdb=" CA ASN R 164 " pdb=" C ASN R 164 " ideal model delta sigma weight residual 111.24 119.56 -8.32 1.38e+00 5.25e-01 3.63e+01 angle pdb=" N SER R 276 " pdb=" CA SER R 276 " pdb=" C SER R 276 " ideal model delta sigma weight residual 113.01 119.76 -6.75 1.20e+00 6.94e-01 3.16e+01 angle pdb=" O GLU R 170 " pdb=" C GLU R 170 " pdb=" N LYS R 171 " ideal model delta sigma weight residual 123.27 116.58 6.69 1.22e+00 6.72e-01 3.00e+01 ... (remaining 11944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4649 16.16 - 32.32: 360 32.32 - 48.49: 55 48.49 - 64.65: 10 64.65 - 80.81: 7 Dihedral angle restraints: 5081 sinusoidal: 1737 harmonic: 3344 Sorted by residual: dihedral pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " pdb=" CZ ARG A 38 " pdb=" NH1 ARG A 38 " ideal model delta sinusoidal sigma weight residual 0.00 76.47 -76.47 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" N PHE R 169 " pdb=" C PHE R 169 " pdb=" CA PHE R 169 " pdb=" CB PHE R 169 " ideal model delta harmonic sigma weight residual 122.80 136.48 -13.68 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" C HIS R 165 " pdb=" N HIS R 165 " pdb=" CA HIS R 165 " pdb=" CB HIS R 165 " ideal model delta harmonic sigma weight residual -122.60 -109.34 -13.26 0 2.50e+00 1.60e-01 2.81e+01 ... (remaining 5078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1345 0.115 - 0.231: 30 0.231 - 0.346: 4 0.346 - 0.462: 4 0.462 - 0.577: 2 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CA PHE R 169 " pdb=" N PHE R 169 " pdb=" C PHE R 169 " pdb=" CB PHE R 169 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" CA ASP R 81 " pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CB ASP R 81 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 1382 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 38 " 1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 38 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 38 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 38 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 38 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 169 " 0.032 2.00e-02 2.50e+03 6.13e-02 3.76e+01 pdb=" C PHE R 169 " -0.106 2.00e-02 2.50e+03 pdb=" O PHE R 169 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU R 170 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 170 " -0.025 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C GLU R 170 " 0.080 2.00e-02 2.50e+03 pdb=" O GLU R 170 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS R 171 " -0.025 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 82 2.63 - 3.20: 7352 3.20 - 3.77: 12366 3.77 - 4.33: 16838 4.33 - 4.90: 29186 Nonbonded interactions: 65824 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.065 3.040 nonbonded pdb=" NH2 ARG A 241 " pdb=" OD1 ASP A 272 " model vdw 2.208 3.120 nonbonded pdb=" OD1 ASN A 249 " pdb=" NZ LYS B 57 " model vdw 2.213 3.120 nonbonded pdb=" NH1 ARG R 247 " pdb=" OE1 GLU R 261 " model vdw 2.231 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.242 3.040 ... (remaining 65819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.008 0.148 8760 Z= 0.449 Angle : 0.782 10.158 11953 Z= 0.463 Chirality : 0.059 0.577 1385 Planarity : 0.014 0.482 1516 Dihedral : 12.261 80.810 2919 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.47 % Allowed : 0.83 % Favored : 98.70 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.24), residues: 1135 helix: 0.78 (0.27), residues: 390 sheet: 0.61 (0.33), residues: 254 loop : -1.87 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 314 TYR 0.018 0.002 TYR R 268 PHE 0.023 0.002 PHE B 234 TRP 0.018 0.002 TRP R 83 HIS 0.018 0.002 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00825 ( 8758) covalent geometry : angle 0.78179 (11949) SS BOND : bond 0.00997 ( 2) SS BOND : angle 1.60877 ( 4) hydrogen bonds : bond 0.23136 ( 410) hydrogen bonds : angle 6.74697 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 236 time to evaluate : 0.271 Fit side-chains REVERT: A 42 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8086 (mtm-85) REVERT: A 55 THR cc_start: 0.8287 (m) cc_final: 0.8086 (m) REVERT: A 221 LYS cc_start: 0.8204 (mptt) cc_final: 0.7747 (mptt) REVERT: A 295 ASP cc_start: 0.8061 (t0) cc_final: 0.7829 (t0) REVERT: B 59 TYR cc_start: 0.8181 (m-80) cc_final: 0.7918 (m-80) REVERT: B 189 SER cc_start: 0.8735 (t) cc_final: 0.8453 (m) REVERT: B 252 LEU cc_start: 0.8641 (tp) cc_final: 0.8272 (tt) REVERT: B 273 ILE cc_start: 0.8761 (mp) cc_final: 0.8351 (mp) REVERT: R 74 VAL cc_start: 0.8582 (t) cc_final: 0.8337 (p) REVERT: R 76 TYR cc_start: 0.8787 (t80) cc_final: 0.8318 (t80) REVERT: R 168 CYS cc_start: 0.5973 (t) cc_final: 0.5686 (t) REVERT: R 232 ILE cc_start: 0.8496 (tp) cc_final: 0.8137 (tt) REVERT: R 250 ILE cc_start: 0.8820 (tt) cc_final: 0.8576 (tt) outliers start: 4 outliers final: 4 residues processed: 239 average time/residue: 0.1061 time to fit residues: 32.7995 Evaluate side-chains 195 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain R residue 161 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 230 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089802 restraints weight = 13325.326| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.79 r_work: 0.2945 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8760 Z= 0.144 Angle : 0.598 7.692 11953 Z= 0.316 Chirality : 0.044 0.157 1385 Planarity : 0.004 0.059 1516 Dihedral : 4.666 37.295 1245 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.77 % Allowed : 7.80 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.25), residues: 1135 helix: 1.44 (0.27), residues: 398 sheet: 0.54 (0.31), residues: 294 loop : -1.69 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.018 0.001 TYR S 178 PHE 0.013 0.002 PHE B 234 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8758) covalent geometry : angle 0.59747 (11949) SS BOND : bond 0.00602 ( 2) SS BOND : angle 1.45380 ( 4) hydrogen bonds : bond 0.05495 ( 410) hydrogen bonds : angle 4.66254 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.326 Fit side-chains REVERT: A 30 LEU cc_start: 0.8532 (mt) cc_final: 0.8306 (mp) REVERT: A 285 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 295 ASP cc_start: 0.7940 (t0) cc_final: 0.7733 (t0) REVERT: B 61 MET cc_start: 0.8428 (tmm) cc_final: 0.8172 (tmm) REVERT: B 173 THR cc_start: 0.8849 (m) cc_final: 0.8578 (p) REVERT: B 252 LEU cc_start: 0.8535 (tp) cc_final: 0.8227 (tt) REVERT: B 273 ILE cc_start: 0.8614 (mp) cc_final: 0.8331 (mp) REVERT: S 7 SER cc_start: 0.8783 (p) cc_final: 0.8521 (m) REVERT: S 115 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8079 (p) REVERT: S 116 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8451 (t) REVERT: S 149 SER cc_start: 0.8780 (p) cc_final: 0.8579 (p) REVERT: R 74 VAL cc_start: 0.8598 (t) cc_final: 0.8377 (p) REVERT: R 76 TYR cc_start: 0.8912 (t80) cc_final: 0.8473 (t80) REVERT: R 168 CYS cc_start: 0.7316 (t) cc_final: 0.7022 (t) REVERT: R 232 ILE cc_start: 0.8772 (tp) cc_final: 0.8409 (tt) REVERT: R 250 ILE cc_start: 0.8829 (tt) cc_final: 0.8620 (tt) outliers start: 15 outliers final: 6 residues processed: 206 average time/residue: 0.0997 time to fit residues: 26.8745 Evaluate side-chains 194 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain R residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.088931 restraints weight = 13164.841| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.77 r_work: 0.2927 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8760 Z= 0.156 Angle : 0.570 7.994 11953 Z= 0.304 Chirality : 0.043 0.152 1385 Planarity : 0.004 0.057 1516 Dihedral : 4.296 21.672 1238 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.01 % Allowed : 9.93 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.25), residues: 1135 helix: 1.69 (0.27), residues: 399 sheet: 0.70 (0.31), residues: 298 loop : -1.66 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.015 0.001 TYR R 102 PHE 0.014 0.002 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8758) covalent geometry : angle 0.57002 (11949) SS BOND : bond 0.00727 ( 2) SS BOND : angle 1.36955 ( 4) hydrogen bonds : bond 0.05486 ( 410) hydrogen bonds : angle 4.37642 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.316 Fit side-chains REVERT: A 30 LEU cc_start: 0.8512 (mt) cc_final: 0.8302 (mp) REVERT: A 295 ASP cc_start: 0.7922 (t0) cc_final: 0.7701 (t0) REVERT: B 52 ARG cc_start: 0.8288 (mtt90) cc_final: 0.8059 (mtt90) REVERT: B 61 MET cc_start: 0.8434 (tmm) cc_final: 0.8165 (tmm) REVERT: B 173 THR cc_start: 0.8849 (m) cc_final: 0.8595 (p) REVERT: B 181 THR cc_start: 0.8519 (p) cc_final: 0.8231 (p) REVERT: B 252 LEU cc_start: 0.8588 (tp) cc_final: 0.8302 (tt) REVERT: B 273 ILE cc_start: 0.8608 (mp) cc_final: 0.8266 (mp) REVERT: B 340 ASN cc_start: 0.8761 (t0) cc_final: 0.8516 (t0) REVERT: S 7 SER cc_start: 0.8776 (p) cc_final: 0.8567 (m) REVERT: S 116 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8468 (t) REVERT: S 129 THR cc_start: 0.8413 (t) cc_final: 0.8103 (p) REVERT: S 149 SER cc_start: 0.8800 (p) cc_final: 0.8573 (p) REVERT: R 28 ILE cc_start: 0.8074 (mt) cc_final: 0.7861 (mt) REVERT: R 76 TYR cc_start: 0.8925 (t80) cc_final: 0.8567 (t80) REVERT: R 168 CYS cc_start: 0.7407 (t) cc_final: 0.7137 (t) REVERT: R 232 ILE cc_start: 0.8782 (tp) cc_final: 0.8405 (tt) outliers start: 17 outliers final: 12 residues processed: 208 average time/residue: 0.0992 time to fit residues: 27.2509 Evaluate side-chains 213 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 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 390 GLN R 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088382 restraints weight = 13416.190| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.80 r_work: 0.2916 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8760 Z= 0.163 Angle : 0.568 7.971 11953 Z= 0.303 Chirality : 0.044 0.151 1385 Planarity : 0.004 0.056 1516 Dihedral : 4.253 21.608 1238 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 11.82 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1135 helix: 1.75 (0.27), residues: 399 sheet: 0.79 (0.31), residues: 295 loop : -1.62 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.016 0.001 TYR R 102 PHE 0.015 0.002 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8758) covalent geometry : angle 0.56791 (11949) SS BOND : bond 0.00738 ( 2) SS BOND : angle 1.32584 ( 4) hydrogen bonds : bond 0.05489 ( 410) hydrogen bonds : angle 4.33086 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.282 Fit side-chains REVERT: A 30 LEU cc_start: 0.8513 (mt) cc_final: 0.8298 (mp) REVERT: A 295 ASP cc_start: 0.7937 (t0) cc_final: 0.7702 (t0) REVERT: B 61 MET cc_start: 0.8469 (tmm) cc_final: 0.8234 (tmm) REVERT: B 173 THR cc_start: 0.8861 (m) cc_final: 0.8606 (p) REVERT: B 181 THR cc_start: 0.8510 (p) cc_final: 0.8227 (p) REVERT: B 252 LEU cc_start: 0.8628 (tp) cc_final: 0.8275 (tt) REVERT: B 273 ILE cc_start: 0.8617 (mp) cc_final: 0.8364 (mt) REVERT: S 149 SER cc_start: 0.8809 (p) cc_final: 0.8585 (p) REVERT: R 28 ILE cc_start: 0.8104 (mt) cc_final: 0.7879 (mt) REVERT: R 168 CYS cc_start: 0.7387 (t) cc_final: 0.7088 (t) REVERT: R 232 ILE cc_start: 0.8791 (tp) cc_final: 0.8408 (tt) outliers start: 19 outliers final: 16 residues processed: 201 average time/residue: 0.1000 time to fit residues: 26.6195 Evaluate side-chains 212 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089239 restraints weight = 13302.073| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.76 r_work: 0.2963 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8760 Z= 0.111 Angle : 0.515 7.141 11953 Z= 0.275 Chirality : 0.042 0.146 1385 Planarity : 0.004 0.049 1516 Dihedral : 4.002 20.009 1238 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.01 % Allowed : 12.88 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1135 helix: 1.99 (0.27), residues: 398 sheet: 0.90 (0.32), residues: 293 loop : -1.51 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.016 0.001 TYR S 178 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP R 73 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8758) covalent geometry : angle 0.51480 (11949) SS BOND : bond 0.00488 ( 2) SS BOND : angle 0.94743 ( 4) hydrogen bonds : bond 0.04373 ( 410) hydrogen bonds : angle 4.09215 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.351 Fit side-chains REVERT: A 10 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7945 (mtmm) REVERT: A 28 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8278 (mtpp) REVERT: A 295 ASP cc_start: 0.7853 (t0) cc_final: 0.7623 (t0) REVERT: A 344 GLU cc_start: 0.8227 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 86 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 173 THR cc_start: 0.8856 (m) cc_final: 0.8620 (p) REVERT: B 181 THR cc_start: 0.8394 (p) cc_final: 0.8081 (p) REVERT: B 252 LEU cc_start: 0.8617 (tp) cc_final: 0.8312 (tt) REVERT: B 273 ILE cc_start: 0.8585 (mp) cc_final: 0.8329 (mt) REVERT: S 59 TYR cc_start: 0.8032 (m-10) cc_final: 0.7800 (m-10) REVERT: S 149 SER cc_start: 0.8767 (p) cc_final: 0.8548 (p) REVERT: R 116 TYR cc_start: 0.8821 (t80) cc_final: 0.8332 (t80) REVERT: R 124 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7623 (mtt90) REVERT: R 168 CYS cc_start: 0.7345 (t) cc_final: 0.7035 (t) REVERT: R 232 ILE cc_start: 0.8725 (tp) cc_final: 0.8358 (tt) outliers start: 17 outliers final: 11 residues processed: 210 average time/residue: 0.1088 time to fit residues: 29.7402 Evaluate side-chains 204 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 62 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090488 restraints weight = 13395.901| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.77 r_work: 0.2952 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8760 Z= 0.121 Angle : 0.523 7.422 11953 Z= 0.279 Chirality : 0.042 0.148 1385 Planarity : 0.004 0.050 1516 Dihedral : 3.990 19.239 1238 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.36 % Allowed : 14.18 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1135 helix: 2.10 (0.27), residues: 398 sheet: 0.90 (0.32), residues: 293 loop : -1.48 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.016 0.001 TYR R 163 PHE 0.013 0.001 PHE R 93 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8758) covalent geometry : angle 0.52287 (11949) SS BOND : bond 0.00550 ( 2) SS BOND : angle 1.02542 ( 4) hydrogen bonds : bond 0.04615 ( 410) hydrogen bonds : angle 4.08274 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.256 Fit side-chains REVERT: A 28 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8285 (mtpp) REVERT: A 295 ASP cc_start: 0.7808 (t0) cc_final: 0.7581 (t0) REVERT: A 344 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 59 TYR cc_start: 0.8276 (m-80) cc_final: 0.8030 (m-80) REVERT: B 86 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 173 THR cc_start: 0.8839 (m) cc_final: 0.8602 (p) REVERT: B 181 THR cc_start: 0.8416 (p) cc_final: 0.8125 (p) REVERT: B 252 LEU cc_start: 0.8650 (tp) cc_final: 0.8336 (tt) REVERT: B 273 ILE cc_start: 0.8590 (mp) cc_final: 0.8343 (mt) REVERT: S 59 TYR cc_start: 0.8037 (m-10) cc_final: 0.7809 (m-10) REVERT: S 149 SER cc_start: 0.8820 (p) cc_final: 0.8598 (p) REVERT: R 116 TYR cc_start: 0.8839 (t80) cc_final: 0.8343 (t80) REVERT: R 124 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7664 (mtt90) REVERT: R 168 CYS cc_start: 0.7409 (t) cc_final: 0.7097 (t) REVERT: R 232 ILE cc_start: 0.8742 (tp) cc_final: 0.8367 (tt) outliers start: 20 outliers final: 17 residues processed: 208 average time/residue: 0.1205 time to fit residues: 32.2918 Evaluate side-chains 217 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 390 GLN ** B 75 GLN ** 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 = 0.3297 r_free = 0.3297 target = 0.104758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089684 restraints weight = 13499.746| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.77 r_work: 0.2932 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8760 Z= 0.145 Angle : 0.553 9.529 11953 Z= 0.292 Chirality : 0.042 0.147 1385 Planarity : 0.004 0.054 1516 Dihedral : 4.076 20.485 1238 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.36 % Allowed : 14.89 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1135 helix: 2.11 (0.27), residues: 399 sheet: 0.85 (0.32), residues: 295 loop : -1.45 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.016 0.001 TYR R 163 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8758) covalent geometry : angle 0.55274 (11949) SS BOND : bond 0.00696 ( 2) SS BOND : angle 1.17141 ( 4) hydrogen bonds : bond 0.05036 ( 410) hydrogen bonds : angle 4.13593 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.351 Fit side-chains REVERT: A 295 ASP cc_start: 0.7810 (t0) cc_final: 0.7575 (t0) REVERT: A 344 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8005 (mm-30) REVERT: B 59 TYR cc_start: 0.8321 (m-80) cc_final: 0.7962 (m-80) REVERT: B 86 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 173 THR cc_start: 0.8861 (m) cc_final: 0.8616 (p) REVERT: B 181 THR cc_start: 0.8457 (p) cc_final: 0.8178 (p) REVERT: B 252 LEU cc_start: 0.8651 (tp) cc_final: 0.8283 (tt) REVERT: B 273 ILE cc_start: 0.8578 (mp) cc_final: 0.8339 (mt) REVERT: S 149 SER cc_start: 0.8819 (p) cc_final: 0.8598 (p) REVERT: R 76 TYR cc_start: 0.8832 (t80) cc_final: 0.8595 (t80) REVERT: R 116 TYR cc_start: 0.8860 (t80) cc_final: 0.8540 (t80) REVERT: R 124 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7658 (mtt90) REVERT: R 168 CYS cc_start: 0.7404 (t) cc_final: 0.7108 (t) REVERT: R 232 ILE cc_start: 0.8768 (tp) cc_final: 0.8389 (tt) outliers start: 20 outliers final: 16 residues processed: 216 average time/residue: 0.1195 time to fit residues: 33.2913 Evaluate side-chains 220 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091368 restraints weight = 13314.968| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.76 r_work: 0.2957 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8760 Z= 0.112 Angle : 0.527 9.085 11953 Z= 0.277 Chirality : 0.041 0.147 1385 Planarity : 0.004 0.051 1516 Dihedral : 3.932 19.143 1238 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.60 % Allowed : 15.60 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1135 helix: 2.22 (0.27), residues: 398 sheet: 0.91 (0.32), residues: 294 loop : -1.40 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.015 0.001 TYR R 163 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8758) covalent geometry : angle 0.52719 (11949) SS BOND : bond 0.00474 ( 2) SS BOND : angle 0.88248 ( 4) hydrogen bonds : bond 0.04330 ( 410) hydrogen bonds : angle 4.01263 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.313 Fit side-chains REVERT: A 10 LYS cc_start: 0.8297 (mtmm) cc_final: 0.8075 (mtmm) REVERT: A 28 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8430 (mtpp) REVERT: A 295 ASP cc_start: 0.7755 (t0) cc_final: 0.7530 (t0) REVERT: A 344 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8041 (mm-30) REVERT: B 59 TYR cc_start: 0.8305 (m-80) cc_final: 0.7931 (m-80) REVERT: B 86 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 173 THR cc_start: 0.8872 (m) cc_final: 0.8652 (p) REVERT: B 181 THR cc_start: 0.8379 (p) cc_final: 0.8143 (p) REVERT: B 252 LEU cc_start: 0.8663 (tp) cc_final: 0.8354 (tt) REVERT: B 273 ILE cc_start: 0.8575 (mp) cc_final: 0.8333 (mt) REVERT: S 149 SER cc_start: 0.8781 (p) cc_final: 0.8568 (p) REVERT: R 28 ILE cc_start: 0.7961 (mt) cc_final: 0.7731 (tt) REVERT: R 116 TYR cc_start: 0.8829 (t80) cc_final: 0.8350 (t80) REVERT: R 124 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7662 (mtt90) REVERT: R 168 CYS cc_start: 0.7364 (t) cc_final: 0.7073 (t) REVERT: R 232 ILE cc_start: 0.8756 (tp) cc_final: 0.8394 (tt) outliers start: 22 outliers final: 18 residues processed: 210 average time/residue: 0.1152 time to fit residues: 31.1827 Evaluate side-chains 221 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.0040 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.091773 restraints weight = 13224.950| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.77 r_work: 0.2973 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8760 Z= 0.109 Angle : 0.525 8.926 11953 Z= 0.276 Chirality : 0.041 0.147 1385 Planarity : 0.004 0.048 1516 Dihedral : 3.881 18.468 1238 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.13 % Allowed : 16.08 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1135 helix: 2.26 (0.27), residues: 398 sheet: 0.95 (0.32), residues: 295 loop : -1.37 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.016 0.001 TYR R 184 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8758) covalent geometry : angle 0.52517 (11949) SS BOND : bond 0.00513 ( 2) SS BOND : angle 0.84655 ( 4) hydrogen bonds : bond 0.04241 ( 410) hydrogen bonds : angle 3.98749 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8354 (mtpp) REVERT: A 295 ASP cc_start: 0.7777 (t0) cc_final: 0.7541 (t0) REVERT: A 344 GLU cc_start: 0.8207 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 59 TYR cc_start: 0.8325 (m-80) cc_final: 0.7902 (m-80) REVERT: B 86 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8401 (p) REVERT: B 173 THR cc_start: 0.8877 (m) cc_final: 0.8633 (p) REVERT: B 252 LEU cc_start: 0.8610 (tp) cc_final: 0.8312 (tt) REVERT: B 273 ILE cc_start: 0.8560 (mp) cc_final: 0.8322 (mt) REVERT: S 149 SER cc_start: 0.8766 (p) cc_final: 0.8554 (p) REVERT: R 28 ILE cc_start: 0.7903 (mt) cc_final: 0.7687 (tt) REVERT: R 116 TYR cc_start: 0.8804 (t80) cc_final: 0.8323 (t80) REVERT: R 124 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7640 (mtt90) REVERT: R 168 CYS cc_start: 0.7330 (t) cc_final: 0.6987 (t) REVERT: R 232 ILE cc_start: 0.8722 (tp) cc_final: 0.8357 (tt) outliers start: 18 outliers final: 16 residues processed: 211 average time/residue: 0.1215 time to fit residues: 32.8821 Evaluate side-chains 214 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 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 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN R 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090753 restraints weight = 13221.745| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.76 r_work: 0.2963 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8760 Z= 0.119 Angle : 0.531 8.710 11953 Z= 0.281 Chirality : 0.042 0.148 1385 Planarity : 0.004 0.049 1516 Dihedral : 3.923 18.654 1238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.36 % Allowed : 15.60 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1135 helix: 2.27 (0.27), residues: 398 sheet: 0.94 (0.32), residues: 295 loop : -1.35 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 49 TYR 0.019 0.001 TYR A 391 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8758) covalent geometry : angle 0.53122 (11949) SS BOND : bond 0.00539 ( 2) SS BOND : angle 0.91582 ( 4) hydrogen bonds : bond 0.04464 ( 410) hydrogen bonds : angle 4.00393 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.334 Fit side-chains REVERT: A 28 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8345 (mtpp) REVERT: A 295 ASP cc_start: 0.7780 (t0) cc_final: 0.7553 (t0) REVERT: A 344 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 59 TYR cc_start: 0.8361 (m-80) cc_final: 0.7814 (m-80) REVERT: B 86 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8371 (p) REVERT: B 173 THR cc_start: 0.8869 (m) cc_final: 0.8614 (p) REVERT: B 181 THR cc_start: 0.8382 (p) cc_final: 0.8133 (p) REVERT: B 252 LEU cc_start: 0.8622 (tp) cc_final: 0.8320 (tt) REVERT: B 273 ILE cc_start: 0.8571 (mp) cc_final: 0.8330 (mt) REVERT: S 149 SER cc_start: 0.8766 (p) cc_final: 0.8547 (p) REVERT: R 28 ILE cc_start: 0.7912 (mt) cc_final: 0.7666 (tt) REVERT: R 116 TYR cc_start: 0.8806 (t80) cc_final: 0.8272 (t80) REVERT: R 124 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7648 (mtt90) REVERT: R 168 CYS cc_start: 0.7299 (t) cc_final: 0.6978 (t) REVERT: R 232 ILE cc_start: 0.8736 (tp) cc_final: 0.8372 (tt) outliers start: 20 outliers final: 18 residues processed: 216 average time/residue: 0.1218 time to fit residues: 33.8693 Evaluate side-chains 228 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 182 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 104 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN R 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091005 restraints weight = 13179.888| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.76 r_work: 0.2962 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8760 Z= 0.121 Angle : 0.537 8.591 11953 Z= 0.285 Chirality : 0.042 0.147 1385 Planarity : 0.004 0.049 1516 Dihedral : 3.932 18.652 1238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.36 % Allowed : 15.96 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.26), residues: 1135 helix: 2.27 (0.27), residues: 398 sheet: 0.95 (0.32), residues: 295 loop : -1.34 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 49 TYR 0.020 0.001 TYR R 184 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8758) covalent geometry : angle 0.53655 (11949) SS BOND : bond 0.00595 ( 2) SS BOND : angle 0.91855 ( 4) hydrogen bonds : bond 0.04476 ( 410) hydrogen bonds : angle 4.02012 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.54 seconds wall clock time: 41 minutes 33.30 seconds (2493.30 seconds total)