Starting phenix.real_space_refine on Sat Jul 26 10:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3y_39757/07_2025/8z3y_39757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3y_39757/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3y_39757/07_2025/8z3y_39757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3y_39757/07_2025/8z3y_39757.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3y_39757/07_2025/8z3y_39757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3y_39757/07_2025/8z3y_39757.cif" } resolution = 3.2 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLU:plan': 7, '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: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 6} 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, 'GLU:plan': 5, 'ARG:plan': 2, '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, 'ARG:plan': 2, 'ASP: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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 121 Time building chain proxies: 6.06, per 1000 atoms: 0.71 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.59 Time building geometry restraints manager: 2.84 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- 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 (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: -0.53 (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 TRP 0.018 0.002 TRP R 83 HIS 0.018 0.002 HIS R 165 PHE 0.023 0.002 PHE B 234 TYR 0.018 0.002 TYR R 268 ARG 0.008 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.23136 ( 410) hydrogen bonds : angle 6.74697 ( 1167) SS BOND : bond 0.00997 ( 2) SS BOND : angle 1.60877 ( 4) covalent geometry : bond 0.00825 ( 8758) covalent geometry : angle 0.78179 (11949) *********************** 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 : 0.906 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: 0.2524 time to fit residues: 78.4332 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 : 0.909 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.0770 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 101 optimal weight: 0.1980 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.107403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.091826 restraints weight = 13207.450| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.80 r_work: 0.2967 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8760 Z= 0.115 Angle : 0.573 7.351 11953 Z= 0.302 Chirality : 0.043 0.152 1385 Planarity : 0.004 0.057 1516 Dihedral : 4.521 36.546 1245 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.77 % Allowed : 7.68 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.10 (0.25), residues: 1135 helix: 1.51 (0.27), residues: 398 sheet: 0.63 (0.31), residues: 290 loop : -1.72 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS R 269 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR S 178 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 410) hydrogen bonds : angle 4.50729 ( 1167) SS BOND : bond 0.00411 ( 2) SS BOND : angle 1.32804 ( 4) covalent geometry : bond 0.00241 ( 8758) covalent geometry : angle 0.57209 (11949) *********************** 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 225 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.879 Fit side-chains REVERT: A 28 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8322 (mtpp) REVERT: A 30 LEU cc_start: 0.8500 (mt) cc_final: 0.8276 (mp) REVERT: A 295 ASP cc_start: 0.7866 (t0) cc_final: 0.7655 (t0) REVERT: B 61 MET cc_start: 0.8360 (tmm) cc_final: 0.8102 (tmm) REVERT: B 173 THR cc_start: 0.8835 (m) cc_final: 0.8563 (p) REVERT: B 252 LEU cc_start: 0.8477 (tp) cc_final: 0.8189 (tt) REVERT: B 273 ILE cc_start: 0.8620 (mp) cc_final: 0.8337 (mp) REVERT: S 63 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7950 (t) REVERT: S 115 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8082 (p) REVERT: S 116 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8388 (t) REVERT: R 76 TYR cc_start: 0.8884 (t80) cc_final: 0.8455 (t80) REVERT: R 116 TYR cc_start: 0.8781 (t80) cc_final: 0.8304 (t80) REVERT: R 163 TYR cc_start: 0.8476 (m-80) cc_final: 0.8238 (m-80) REVERT: R 168 CYS cc_start: 0.7283 (t) cc_final: 0.6974 (t) REVERT: R 232 ILE cc_start: 0.8724 (tp) cc_final: 0.8363 (tt) REVERT: R 250 ILE cc_start: 0.8822 (tt) cc_final: 0.8610 (tt) outliers start: 15 outliers final: 6 residues processed: 214 average time/residue: 0.2470 time to fit residues: 69.5899 Evaluate side-chains 205 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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 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 56 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089102 restraints weight = 13260.702| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.77 r_work: 0.2925 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8760 Z= 0.156 Angle : 0.568 7.694 11953 Z= 0.303 Chirality : 0.043 0.150 1385 Planarity : 0.004 0.057 1516 Dihedral : 4.251 21.518 1238 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.54 % Allowed : 10.99 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.33 (0.26), residues: 1135 helix: 1.75 (0.27), residues: 399 sheet: 0.68 (0.31), residues: 299 loop : -1.63 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.002 PHE B 199 TYR 0.015 0.001 TYR R 102 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 410) hydrogen bonds : angle 4.36425 ( 1167) SS BOND : bond 0.00741 ( 2) SS BOND : angle 1.40019 ( 4) covalent geometry : bond 0.00362 ( 8758) covalent geometry : angle 0.56750 (11949) *********************** 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 224 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.987 Fit side-chains REVERT: A 30 LEU cc_start: 0.8503 (mt) cc_final: 0.8298 (mp) REVERT: A 295 ASP cc_start: 0.7911 (t0) cc_final: 0.7691 (t0) REVERT: B 52 ARG cc_start: 0.8287 (mtt90) cc_final: 0.8062 (mtt90) REVERT: B 61 MET cc_start: 0.8416 (tmm) cc_final: 0.8124 (tmm) REVERT: B 173 THR cc_start: 0.8848 (m) cc_final: 0.8592 (p) REVERT: B 181 THR cc_start: 0.8508 (p) cc_final: 0.8228 (p) REVERT: B 251 ARG cc_start: 0.8683 (mtt90) cc_final: 0.8432 (mtt90) REVERT: B 252 LEU cc_start: 0.8573 (tp) cc_final: 0.8274 (tt) REVERT: B 273 ILE cc_start: 0.8604 (mp) cc_final: 0.8300 (mp) REVERT: B 340 ASN cc_start: 0.8750 (t0) cc_final: 0.8498 (t0) REVERT: S 18 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7950 (ttt90) REVERT: R 76 TYR cc_start: 0.8907 (t80) cc_final: 0.8565 (t80) REVERT: R 168 CYS cc_start: 0.7354 (t) cc_final: 0.7078 (t) REVERT: R 232 ILE cc_start: 0.8776 (tp) cc_final: 0.8403 (tt) REVERT: R 250 ILE cc_start: 0.8823 (tt) cc_final: 0.8613 (tt) outliers start: 13 outliers final: 9 residues processed: 215 average time/residue: 0.2583 time to fit residues: 72.0835 Evaluate side-chains 205 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.105257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.089634 restraints weight = 13171.389| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.80 r_work: 0.2927 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8760 Z= 0.156 Angle : 0.561 8.290 11953 Z= 0.300 Chirality : 0.043 0.148 1385 Planarity : 0.004 0.056 1516 Dihedral : 4.214 21.402 1238 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.89 % Allowed : 11.58 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.42 (0.26), residues: 1135 helix: 1.81 (0.27), residues: 399 sheet: 0.77 (0.31), residues: 295 loop : -1.56 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.002 PHE B 199 TYR 0.016 0.001 TYR R 102 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 410) hydrogen bonds : angle 4.30813 ( 1167) SS BOND : bond 0.00709 ( 2) SS BOND : angle 1.36655 ( 4) covalent geometry : bond 0.00366 ( 8758) covalent geometry : angle 0.56089 (11949) *********************** 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 223 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.970 Fit side-chains REVERT: A 28 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8329 (mtpp) REVERT: A 30 LEU cc_start: 0.8509 (mt) cc_final: 0.8298 (mp) REVERT: A 295 ASP cc_start: 0.7924 (t0) cc_final: 0.7695 (t0) REVERT: B 61 MET cc_start: 0.8430 (tmm) cc_final: 0.8173 (tmm) REVERT: B 173 THR cc_start: 0.8855 (m) cc_final: 0.8609 (p) REVERT: B 181 THR cc_start: 0.8495 (p) cc_final: 0.8218 (p) REVERT: B 252 LEU cc_start: 0.8601 (tp) cc_final: 0.8309 (tt) REVERT: B 273 ILE cc_start: 0.8597 (mp) cc_final: 0.8351 (mt) REVERT: R 116 TYR cc_start: 0.8843 (t80) cc_final: 0.8501 (t80) REVERT: R 168 CYS cc_start: 0.7401 (t) cc_final: 0.7103 (t) REVERT: R 232 ILE cc_start: 0.8773 (tp) cc_final: 0.8398 (tt) REVERT: R 250 ILE cc_start: 0.8835 (tt) cc_final: 0.8629 (tt) outliers start: 16 outliers final: 11 residues processed: 212 average time/residue: 0.2472 time to fit residues: 68.5183 Evaluate side-chains 221 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 115 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 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 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 = 0.3291 r_free = 0.3291 target = 0.104954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089497 restraints weight = 13274.284| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.76 r_work: 0.2934 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8760 Z= 0.145 Angle : 0.549 7.527 11953 Z= 0.293 Chirality : 0.043 0.148 1385 Planarity : 0.004 0.055 1516 Dihedral : 4.168 21.185 1238 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.50 (0.26), residues: 1135 helix: 1.89 (0.27), residues: 399 sheet: 0.83 (0.31), residues: 293 loop : -1.54 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.016 0.001 TYR R 102 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 410) hydrogen bonds : angle 4.29110 ( 1167) SS BOND : bond 0.00680 ( 2) SS BOND : angle 1.23700 ( 4) covalent geometry : bond 0.00339 ( 8758) covalent geometry : angle 0.54899 (11949) *********************** 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 230 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.997 Fit side-chains REVERT: A 28 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8288 (mtpp) REVERT: A 30 LEU cc_start: 0.8506 (mt) cc_final: 0.8294 (mp) REVERT: A 295 ASP cc_start: 0.7865 (t0) cc_final: 0.7636 (t0) REVERT: B 61 MET cc_start: 0.8454 (tmm) cc_final: 0.8215 (tmm) REVERT: B 86 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 173 THR cc_start: 0.8870 (m) cc_final: 0.8627 (p) REVERT: B 181 THR cc_start: 0.8462 (p) cc_final: 0.8187 (p) REVERT: B 252 LEU cc_start: 0.8640 (tp) cc_final: 0.8334 (tt) REVERT: B 273 ILE cc_start: 0.8580 (mp) cc_final: 0.8325 (mt) REVERT: R 76 TYR cc_start: 0.8872 (t80) cc_final: 0.8634 (t80) REVERT: R 116 TYR cc_start: 0.8847 (t80) cc_final: 0.8516 (t80) REVERT: R 124 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7645 (mtt90) REVERT: R 168 CYS cc_start: 0.7386 (t) cc_final: 0.7100 (t) REVERT: R 232 ILE cc_start: 0.8762 (tp) cc_final: 0.8388 (tt) REVERT: R 250 ILE cc_start: 0.8810 (tt) cc_final: 0.8602 (tt) outliers start: 21 outliers final: 15 residues processed: 215 average time/residue: 0.2466 time to fit residues: 69.5367 Evaluate side-chains 218 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 246 ASP 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 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 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.0470 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.105471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090510 restraints weight = 13111.830| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.75 r_work: 0.2947 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8760 Z= 0.127 Angle : 0.537 7.761 11953 Z= 0.283 Chirality : 0.042 0.146 1385 Planarity : 0.004 0.053 1516 Dihedral : 4.071 20.171 1238 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.13 % Allowed : 13.24 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1135 helix: 2.02 (0.27), residues: 398 sheet: 0.89 (0.32), residues: 293 loop : -1.47 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.016 0.001 TYR R 163 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 410) hydrogen bonds : angle 4.18833 ( 1167) SS BOND : bond 0.00567 ( 2) SS BOND : angle 1.06814 ( 4) covalent geometry : bond 0.00292 ( 8758) covalent geometry : angle 0.53680 (11949) *********************** 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 222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.892 Fit side-chains REVERT: A 28 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8290 (mtpp) REVERT: A 30 LEU cc_start: 0.8537 (mt) cc_final: 0.8334 (mp) REVERT: A 295 ASP cc_start: 0.7790 (t0) cc_final: 0.7558 (t0) REVERT: B 59 TYR cc_start: 0.8302 (m-80) cc_final: 0.7938 (m-80) REVERT: B 61 MET cc_start: 0.8441 (tmm) cc_final: 0.8239 (tmm) REVERT: B 86 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 173 THR cc_start: 0.8854 (m) cc_final: 0.8619 (p) REVERT: B 181 THR cc_start: 0.8445 (p) cc_final: 0.8159 (p) REVERT: B 252 LEU cc_start: 0.8624 (tp) cc_final: 0.8310 (tt) REVERT: B 273 ILE cc_start: 0.8576 (mp) cc_final: 0.8323 (mt) REVERT: S 59 TYR cc_start: 0.8058 (m-10) cc_final: 0.7834 (m-10) REVERT: R 76 TYR cc_start: 0.8846 (t80) cc_final: 0.8634 (t80) REVERT: R 116 TYR cc_start: 0.8836 (t80) cc_final: 0.8515 (t80) REVERT: R 124 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7643 (mtt90) REVERT: R 168 CYS cc_start: 0.7371 (t) cc_final: 0.7082 (t) REVERT: R 232 ILE cc_start: 0.8732 (tp) cc_final: 0.8358 (tt) REVERT: R 250 ILE cc_start: 0.8790 (tt) cc_final: 0.8583 (tt) outliers start: 18 outliers final: 14 residues processed: 211 average time/residue: 0.2359 time to fit residues: 65.6470 Evaluate side-chains 214 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 246 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 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 83 optimal weight: 0.0470 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091696 restraints weight = 13271.987| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.77 r_work: 0.2963 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8760 Z= 0.112 Angle : 0.528 7.827 11953 Z= 0.277 Chirality : 0.042 0.191 1385 Planarity : 0.004 0.050 1516 Dihedral : 3.962 19.202 1238 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.36 % Allowed : 14.66 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.74 (0.26), residues: 1135 helix: 2.10 (0.27), residues: 398 sheet: 0.93 (0.32), residues: 293 loop : -1.38 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.016 0.001 TYR R 184 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 410) hydrogen bonds : angle 4.13239 ( 1167) SS BOND : bond 0.00508 ( 2) SS BOND : angle 0.93491 ( 4) covalent geometry : bond 0.00249 ( 8758) covalent geometry : angle 0.52761 (11949) *********************** 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 222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.850 Fit side-chains REVERT: A 28 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8276 (mtpp) REVERT: A 30 LEU cc_start: 0.8523 (mt) cc_final: 0.8323 (mp) REVERT: A 295 ASP cc_start: 0.7766 (t0) cc_final: 0.7531 (t0) REVERT: A 325 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 59 TYR cc_start: 0.8301 (m-80) cc_final: 0.7946 (m-80) REVERT: B 61 MET cc_start: 0.8408 (tmm) cc_final: 0.8198 (tmm) REVERT: B 86 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8383 (p) REVERT: B 173 THR cc_start: 0.8851 (m) cc_final: 0.8603 (p) REVERT: B 252 LEU cc_start: 0.8627 (tp) cc_final: 0.8302 (tt) REVERT: B 273 ILE cc_start: 0.8582 (mp) cc_final: 0.8325 (mt) REVERT: S 59 TYR cc_start: 0.8039 (m-10) cc_final: 0.7802 (m-10) REVERT: R 76 TYR cc_start: 0.8831 (t80) cc_final: 0.8595 (t80) REVERT: R 116 TYR cc_start: 0.8800 (t80) cc_final: 0.8296 (t80) REVERT: R 124 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7663 (mtt90) REVERT: R 168 CYS cc_start: 0.7384 (t) cc_final: 0.7091 (t) REVERT: R 232 ILE cc_start: 0.8699 (tp) cc_final: 0.8339 (tt) REVERT: R 250 ILE cc_start: 0.8780 (tt) cc_final: 0.8572 (tt) outliers start: 20 outliers final: 16 residues processed: 209 average time/residue: 0.2869 time to fit residues: 78.9879 Evaluate side-chains 219 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU 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 325 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS 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 159 PHE 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 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.105467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.090299 restraints weight = 13427.218| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.79 r_work: 0.2940 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2446 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= 0.135 Angle : 0.547 11.087 11953 Z= 0.288 Chirality : 0.042 0.148 1385 Planarity : 0.004 0.052 1516 Dihedral : 4.021 19.749 1238 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.36 % Allowed : 15.13 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.74 (0.26), residues: 1135 helix: 2.12 (0.27), residues: 399 sheet: 0.86 (0.31), residues: 295 loop : -1.37 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR R 184 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 410) hydrogen bonds : angle 4.15863 ( 1167) SS BOND : bond 0.00599 ( 2) SS BOND : angle 1.07252 ( 4) covalent geometry : bond 0.00313 ( 8758) covalent geometry : angle 0.54693 (11949) *********************** 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 227 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 1.115 Fit side-chains REVERT: A 28 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8270 (mtpp) REVERT: A 30 LEU cc_start: 0.8533 (mt) cc_final: 0.8323 (mp) REVERT: A 295 ASP cc_start: 0.7793 (t0) cc_final: 0.7545 (t0) REVERT: A 325 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8729 (p) REVERT: B 59 TYR cc_start: 0.8342 (m-80) cc_final: 0.7922 (m-80) REVERT: B 61 MET cc_start: 0.8455 (tmm) cc_final: 0.8230 (tmm) REVERT: B 86 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 173 THR cc_start: 0.8857 (m) cc_final: 0.8610 (p) REVERT: B 181 THR cc_start: 0.8409 (p) cc_final: 0.8198 (p) REVERT: B 252 LEU cc_start: 0.8634 (tp) cc_final: 0.8309 (tt) REVERT: B 273 ILE cc_start: 0.8602 (mp) cc_final: 0.8353 (mt) REVERT: S 59 TYR cc_start: 0.8049 (m-10) cc_final: 0.7801 (m-10) REVERT: R 116 TYR cc_start: 0.8837 (t80) cc_final: 0.8521 (t80) REVERT: R 124 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7644 (mtt90) REVERT: R 168 CYS cc_start: 0.7389 (t) cc_final: 0.7086 (t) REVERT: R 232 ILE cc_start: 0.8735 (tp) cc_final: 0.8370 (tt) REVERT: R 250 ILE cc_start: 0.8796 (tt) cc_final: 0.8574 (tt) outliers start: 20 outliers final: 13 residues processed: 215 average time/residue: 0.2931 time to fit residues: 82.7130 Evaluate side-chains 213 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 325 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS 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 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 74 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 266 HIS R 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090776 restraints weight = 13364.782| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.74 r_work: 0.2958 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8760 Z= 0.113 Angle : 0.542 12.070 11953 Z= 0.281 Chirality : 0.042 0.162 1385 Planarity : 0.004 0.049 1516 Dihedral : 3.922 19.099 1238 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.01 % Allowed : 16.31 % 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 (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: 0.82 (0.26), residues: 1135 helix: 2.21 (0.28), residues: 398 sheet: 0.89 (0.31), residues: 295 loop : -1.32 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR R 184 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 410) hydrogen bonds : angle 4.06146 ( 1167) SS BOND : bond 0.00519 ( 2) SS BOND : angle 0.88018 ( 4) covalent geometry : bond 0.00251 ( 8758) covalent geometry : angle 0.54205 (11949) *********************** 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 218 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.968 Fit side-chains REVERT: A 28 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8329 (mtpp) REVERT: A 295 ASP cc_start: 0.7745 (t0) cc_final: 0.7521 (t0) REVERT: A 325 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 344 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8020 (mm-30) REVERT: B 59 TYR cc_start: 0.8295 (m-80) cc_final: 0.7893 (m-80) REVERT: B 86 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8454 (p) REVERT: B 181 THR cc_start: 0.8373 (p) cc_final: 0.8152 (p) REVERT: B 196 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8527 (m) REVERT: B 273 ILE cc_start: 0.8560 (mp) cc_final: 0.8311 (mt) REVERT: S 59 TYR cc_start: 0.8033 (m-10) cc_final: 0.7821 (m-10) REVERT: S 63 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7935 (t) REVERT: R 76 TYR cc_start: 0.8894 (t80) cc_final: 0.8645 (t80) REVERT: R 116 TYR cc_start: 0.8806 (t80) cc_final: 0.8323 (t80) REVERT: R 124 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7624 (mtt90) REVERT: R 168 CYS cc_start: 0.7324 (t) cc_final: 0.7036 (t) REVERT: R 232 ILE cc_start: 0.8742 (tp) cc_final: 0.8513 (tp) REVERT: R 250 ILE cc_start: 0.8787 (tt) cc_final: 0.8577 (tt) outliers start: 17 outliers final: 11 residues processed: 210 average time/residue: 0.3390 time to fit residues: 92.3559 Evaluate side-chains 211 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 325 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 196 THR 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 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 60 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091317 restraints weight = 13278.894| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.79 r_work: 0.2946 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8760 Z= 0.123 Angle : 0.553 12.245 11953 Z= 0.287 Chirality : 0.042 0.154 1385 Planarity : 0.004 0.050 1516 Dihedral : 3.958 18.978 1238 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.01 % Allowed : 16.78 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.83 (0.26), residues: 1135 helix: 2.22 (0.27), residues: 398 sheet: 0.91 (0.32), residues: 295 loop : -1.33 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.020 0.001 TYR R 184 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 410) hydrogen bonds : angle 4.08774 ( 1167) SS BOND : bond 0.00543 ( 2) SS BOND : angle 0.95570 ( 4) covalent geometry : bond 0.00281 ( 8758) covalent geometry : angle 0.55306 (11949) ********************** 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 215 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.990 Fit side-chains REVERT: A 28 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8274 (mtpp) REVERT: A 295 ASP cc_start: 0.7763 (t0) cc_final: 0.7521 (t0) REVERT: A 325 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8770 (p) REVERT: A 344 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 59 TYR cc_start: 0.8361 (m-80) cc_final: 0.7802 (m-80) REVERT: B 86 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 181 THR cc_start: 0.8397 (p) cc_final: 0.8184 (p) REVERT: B 273 ILE cc_start: 0.8601 (mp) cc_final: 0.8357 (mt) REVERT: S 59 TYR cc_start: 0.8042 (m-10) cc_final: 0.7821 (m-10) REVERT: S 63 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.7934 (t) REVERT: R 116 TYR cc_start: 0.8815 (t80) cc_final: 0.8520 (t80) REVERT: R 124 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7640 (mtt90) REVERT: R 168 CYS cc_start: 0.7365 (t) cc_final: 0.7064 (t) REVERT: R 232 ILE cc_start: 0.8715 (tp) cc_final: 0.8460 (tp) REVERT: R 250 ILE cc_start: 0.8782 (tt) cc_final: 0.8561 (tt) outliers start: 17 outliers final: 12 residues processed: 206 average time/residue: 0.3597 time to fit residues: 100.2804 Evaluate side-chains 207 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 325 THR Chi-restraints excluded: chain B residue 86 THR 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 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090607 restraints weight = 13380.853| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.79 r_work: 0.2929 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8760 Z= 0.141 Angle : 0.570 12.281 11953 Z= 0.297 Chirality : 0.043 0.149 1385 Planarity : 0.004 0.052 1516 Dihedral : 4.050 19.783 1238 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.25 % Allowed : 16.90 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.79 (0.26), residues: 1135 helix: 2.18 (0.27), residues: 398 sheet: 0.88 (0.31), residues: 295 loop : -1.34 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.021 0.001 TYR R 184 ARG 0.008 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 410) hydrogen bonds : angle 4.15448 ( 1167) SS BOND : bond 0.00672 ( 2) SS BOND : angle 1.07934 ( 4) covalent geometry : bond 0.00327 ( 8758) covalent geometry : angle 0.57001 (11949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7303.88 seconds wall clock time: 131 minutes 54.14 seconds (7914.14 seconds total)