Starting phenix.real_space_refine on Tue Mar 3 22:24:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r81_4749/03_2026/6r81_4749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r81_4749/03_2026/6r81_4749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2026/6r81_4749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2026/6r81_4749.map" model { file = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2026/6r81_4749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2026/6r81_4749_neut.cif" } resolution = 3.9 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= 0.010 sd= 0.063 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 5668 2.51 5 N 1479 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8861 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4405 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4392 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8861 At special positions: 0 Unit cell: (75.26, 90.1, 137.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 6 15.00 Mg 2 11.99 O 1671 8.00 N 1479 7.00 C 5668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 358.1 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 64.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.598A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 57 removed outlier: 4.403A pdb=" N LYS A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 3.670A pdb=" N THR A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 79 removed outlier: 4.036A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 109 removed outlier: 4.104A pdb=" N TYR A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.175A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 159 removed outlier: 3.918A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.512A pdb=" N VAL A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.746A pdb=" N ALA A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 4.187A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.503A pdb=" N GLN A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.658A pdb=" N TYR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 269 removed outlier: 4.216A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.876A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.527A pdb=" N VAL A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 320 removed outlier: 3.856A pdb=" N GLN A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N MET A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.550A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.519A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 removed outlier: 4.033A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.720A pdb=" N ALA A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.634A pdb=" N GLN A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 removed outlier: 4.314A pdb=" N ASN A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.600A pdb=" N ARG B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 58 removed outlier: 4.404A pdb=" N LYS B 28 " --> pdb=" O PRO B 24 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.674A pdb=" N THR B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 79 removed outlier: 4.217A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 4.101A pdb=" N TYR B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.175A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 159 removed outlier: 3.911A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.515A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.758A pdb=" N ALA B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.198A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.508A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 221 through 234 removed outlier: 3.658A pdb=" N TYR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 269 removed outlier: 4.219A pdb=" N ALA B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.878A pdb=" N SER B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.535A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 320 removed outlier: 3.861A pdb=" N GLN B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.759A pdb=" N PHE B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.520A pdb=" N ARG B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 removed outlier: 4.034A pdb=" N SER B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 559 through 567 removed outlier: 3.723A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 removed outlier: 3.634A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.739A pdb=" N GLU B 585 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 4.819A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 346 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA A 395 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 502 removed outlier: 6.166A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 545 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364 removed outlier: 4.818A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 346 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 395 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 502 removed outlier: 6.161A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 545 " --> pdb=" O VAL B 369 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1122 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: 1.37 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1451 1.26 - 1.40: 2010 1.40 - 1.54: 5398 1.54 - 1.68: 68 1.68 - 1.82: 68 Bond restraints: 8995 Sorted by residual: bond pdb=" CA SER A 480 " pdb=" C SER A 480 " ideal model delta sigma weight residual 1.532 1.410 0.121 1.15e-02 7.56e+03 1.11e+02 bond pdb=" C THR B 381 " pdb=" O THR B 381 " ideal model delta sigma weight residual 1.237 1.125 0.111 1.19e-02 7.06e+03 8.73e+01 bond pdb=" C LYS B 380 " pdb=" O LYS B 380 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.26e-02 6.30e+03 8.35e+01 bond pdb=" CA THR B 382 " pdb=" C THR B 382 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.34e-02 5.57e+03 6.60e+01 bond pdb=" C ILE A 477 " pdb=" O ILE A 477 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.23e-02 6.61e+03 6.45e+01 ... (remaining 8990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 12005 5.04 - 10.08: 158 10.08 - 15.12: 14 15.12 - 20.16: 5 20.16 - 25.20: 2 Bond angle restraints: 12184 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" C SER A 480 " pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta sigma weight residual 114.40 89.20 25.20 1.25e+00 6.40e-01 4.06e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.39 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.58 17.29 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.05 15.78 1.00e+00 1.00e+00 2.49e+02 ... (remaining 12179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4731 17.89 - 35.78: 582 35.78 - 53.66: 122 53.66 - 71.55: 27 71.55 - 89.44: 16 Dihedral angle restraints: 5478 sinusoidal: 2207 harmonic: 3271 Sorted by residual: dihedral pdb=" C SER A 480 " pdb=" N SER A 480 " pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta harmonic sigma weight residual -122.60 -92.81 -29.79 0 2.50e+00 1.60e-01 1.42e+02 dihedral pdb=" CA ASN A 118 " pdb=" C ASN A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 132.04 47.96 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ASN B 118 " pdb=" C ASN B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual 180.00 132.39 47.61 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 5475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1411 0.147 - 0.294: 51 0.294 - 0.440: 6 0.440 - 0.587: 0 0.587 - 0.734: 1 Chirality restraints: 1469 Sorted by residual: chirality pdb=" CA ARG A 475 " pdb=" N ARG A 475 " pdb=" C ARG A 475 " pdb=" CB ARG A 475 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA MET B 59 " pdb=" N MET B 59 " pdb=" C MET B 59 " pdb=" CB MET B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA SER B 60 " pdb=" N SER B 60 " pdb=" C SER B 60 " pdb=" CB SER B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1466 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 58 " 0.045 2.00e-02 2.50e+03 9.41e-02 8.85e+01 pdb=" C SER B 58 " -0.162 2.00e-02 2.50e+03 pdb=" O SER B 58 " 0.064 2.00e-02 2.50e+03 pdb=" N MET B 59 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 480 " -0.027 2.00e-02 2.50e+03 5.23e-02 2.73e+01 pdb=" C SER A 480 " 0.090 2.00e-02 2.50e+03 pdb=" O SER A 480 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY A 481 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 474 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLU A 474 " 0.089 2.00e-02 2.50e+03 pdb=" O GLU A 474 " -0.033 2.00e-02 2.50e+03 pdb=" N ARG A 475 " -0.030 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 20 2.21 - 2.88: 3609 2.88 - 3.56: 13195 3.56 - 4.23: 19913 4.23 - 4.90: 32086 Nonbonded interactions: 68823 Sorted by model distance: nonbonded pdb=" O GLY B 374 " pdb=" NZ LYS B 380 " model vdw 1.538 3.120 nonbonded pdb=" OG SER A 480 " pdb=" N GLY A 481 " model vdw 1.887 3.120 nonbonded pdb=" O ARG B 432 " pdb=" SG CYS B 436 " model vdw 1.912 3.400 nonbonded pdb=" N GLY B 374 " pdb=" CE LYS B 380 " model vdw 1.919 3.520 nonbonded pdb=" O ARG A 432 " pdb=" SG CYS A 436 " model vdw 1.933 3.400 ... (remaining 68818 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 269 or resid 282 through 586 or resid 603)) selection = (chain 'B' and (resid 9 through 269 or resid 282 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.380 Find NCS groups from input model: 0.150 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.013 0.643 8999 Z= 0.974 Angle : 1.495 25.197 12184 Z= 0.951 Chirality : 0.073 0.734 1469 Planarity : 0.009 0.094 1518 Dihedral : 16.775 89.439 3374 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.47 % Favored : 88.08 % Rotamer: Outliers : 1.25 % Allowed : 14.35 % Favored : 84.41 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.18), residues: 1133 helix: -3.59 (0.12), residues: 597 sheet: -2.99 (0.64), residues: 50 loop : -3.28 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 414 TYR 0.023 0.003 TYR B 570 PHE 0.027 0.004 PHE A 57 TRP 0.021 0.004 TRP B 413 HIS 0.012 0.003 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.01117 ( 8995) covalent geometry : angle 1.49527 (12184) hydrogen bonds : bond 0.31090 ( 389) hydrogen bonds : angle 10.47500 ( 1122) Misc. bond : bond 0.33492 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4646 (t0) REVERT: A 101 GLU cc_start: 0.9225 (tp30) cc_final: 0.8826 (tp30) REVERT: A 158 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8898 (tp) REVERT: A 231 MET cc_start: 0.9205 (ttm) cc_final: 0.8862 (tpp) REVERT: A 262 LEU cc_start: 0.9229 (mm) cc_final: 0.8995 (mm) REVERT: A 295 MET cc_start: 0.9061 (tpp) cc_final: 0.8647 (tmm) REVERT: A 299 GLN cc_start: 0.9568 (mm-40) cc_final: 0.9005 (mm-40) REVERT: A 474 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 478 MET cc_start: 0.8990 (mmm) cc_final: 0.8457 (mmm) REVERT: B 145 PHE cc_start: 0.9396 (t80) cc_final: 0.8624 (t80) REVERT: B 158 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 231 MET cc_start: 0.9226 (ttm) cc_final: 0.8879 (tpp) REVERT: B 288 LEU cc_start: 0.8945 (tt) cc_final: 0.8741 (tt) REVERT: B 295 MET cc_start: 0.9109 (tpp) cc_final: 0.8486 (tmm) REVERT: B 299 GLN cc_start: 0.9470 (mm-40) cc_final: 0.8910 (mm-40) REVERT: B 413 TRP cc_start: 0.8688 (t60) cc_final: 0.7630 (t60) outliers start: 12 outliers final: 3 residues processed: 221 average time/residue: 0.0769 time to fit residues: 24.8436 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 518 GLN B 196 GLN B 518 GLN ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.106120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080625 restraints weight = 26671.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.083728 restraints weight = 14522.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.085847 restraints weight = 9672.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087313 restraints weight = 7265.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088256 restraints weight = 5933.523| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8999 Z= 0.152 Angle : 0.805 9.388 12184 Z= 0.412 Chirality : 0.045 0.140 1469 Planarity : 0.005 0.055 1518 Dihedral : 9.748 82.888 1301 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.74 % Favored : 91.09 % Rotamer: Outliers : 3.53 % Allowed : 20.27 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.23), residues: 1133 helix: -1.80 (0.19), residues: 610 sheet: -1.94 (0.68), residues: 50 loop : -2.64 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 475 TYR 0.015 0.002 TYR B 350 PHE 0.018 0.002 PHE A 74 TRP 0.011 0.002 TRP B 104 HIS 0.009 0.002 HIS A 567 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8995) covalent geometry : angle 0.80511 (12184) hydrogen bonds : bond 0.04982 ( 389) hydrogen bonds : angle 6.08837 ( 1122) Misc. bond : bond 0.00128 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9184 (t80) cc_final: 0.8655 (t80) REVERT: A 231 MET cc_start: 0.9088 (ttm) cc_final: 0.8736 (tpp) REVERT: A 258 LEU cc_start: 0.9565 (tt) cc_final: 0.9237 (tt) REVERT: A 262 LEU cc_start: 0.9171 (mm) cc_final: 0.8827 (mm) REVERT: A 295 MET cc_start: 0.9260 (tpp) cc_final: 0.9013 (tmm) REVERT: A 299 GLN cc_start: 0.9520 (mm-40) cc_final: 0.9058 (mm110) REVERT: A 460 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7069 (t80) REVERT: A 567 HIS cc_start: 0.7487 (t70) cc_final: 0.7168 (t-90) REVERT: B 77 GLN cc_start: 0.9102 (mt0) cc_final: 0.8687 (mt0) REVERT: B 145 PHE cc_start: 0.9261 (t80) cc_final: 0.8728 (t80) REVERT: B 219 SER cc_start: 0.8108 (t) cc_final: 0.7806 (p) REVERT: B 231 MET cc_start: 0.9162 (ttm) cc_final: 0.8906 (tpp) REVERT: B 262 LEU cc_start: 0.9163 (mm) cc_final: 0.8793 (mm) REVERT: B 295 MET cc_start: 0.9289 (tpp) cc_final: 0.8935 (tmm) REVERT: B 299 GLN cc_start: 0.9431 (mm-40) cc_final: 0.9030 (mm110) REVERT: B 460 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7368 (t80) REVERT: B 567 HIS cc_start: 0.7273 (t70) cc_final: 0.7018 (t70) REVERT: B 580 MET cc_start: 0.8315 (mtp) cc_final: 0.8067 (mtt) outliers start: 34 outliers final: 10 residues processed: 243 average time/residue: 0.0782 time to fit residues: 27.7939 Evaluate side-chains 204 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 460 PHE Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.0050 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.098897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072685 restraints weight = 26040.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.075707 restraints weight = 14430.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077768 restraints weight = 9766.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.079212 restraints weight = 7441.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.080078 restraints weight = 6155.796| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8999 Z= 0.146 Angle : 0.740 7.796 12184 Z= 0.377 Chirality : 0.044 0.180 1469 Planarity : 0.004 0.050 1518 Dihedral : 8.967 80.031 1287 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.85 % Allowed : 23.80 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.24), residues: 1133 helix: -1.06 (0.21), residues: 612 sheet: -1.81 (0.62), residues: 60 loop : -2.29 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.012 0.001 TYR B 570 PHE 0.025 0.001 PHE A 57 TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8995) covalent geometry : angle 0.74017 (12184) hydrogen bonds : bond 0.04318 ( 389) hydrogen bonds : angle 5.45777 ( 1122) Misc. bond : bond 0.00119 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9079 (t80) cc_final: 0.8675 (t80) REVERT: A 191 ILE cc_start: 0.9498 (tp) cc_final: 0.8996 (tt) REVERT: A 231 MET cc_start: 0.9122 (ttm) cc_final: 0.8724 (tpp) REVERT: A 256 LEU cc_start: 0.9500 (mm) cc_final: 0.9182 (mm) REVERT: A 258 LEU cc_start: 0.9522 (tt) cc_final: 0.9183 (tt) REVERT: A 262 LEU cc_start: 0.9236 (mm) cc_final: 0.8851 (mm) REVERT: A 299 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9166 (mm110) REVERT: A 326 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: A 460 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7218 (t80) REVERT: A 567 HIS cc_start: 0.7577 (t70) cc_final: 0.7269 (t-90) REVERT: B 77 GLN cc_start: 0.9160 (mt0) cc_final: 0.8716 (mt0) REVERT: B 145 PHE cc_start: 0.9215 (t80) cc_final: 0.8633 (t80) REVERT: B 191 ILE cc_start: 0.9519 (tp) cc_final: 0.9012 (tt) REVERT: B 219 SER cc_start: 0.8149 (t) cc_final: 0.7698 (p) REVERT: B 231 MET cc_start: 0.9193 (ttm) cc_final: 0.8840 (tpp) REVERT: B 243 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8782 (tm-30) REVERT: B 258 LEU cc_start: 0.9552 (tt) cc_final: 0.9162 (tt) REVERT: B 262 LEU cc_start: 0.9214 (mm) cc_final: 0.8934 (mm) REVERT: B 299 GLN cc_start: 0.9390 (mm-40) cc_final: 0.9142 (mm110) REVERT: B 326 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: B 433 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8867 (mt-10) REVERT: B 567 HIS cc_start: 0.7768 (t70) cc_final: 0.7339 (t-90) outliers start: 37 outliers final: 15 residues processed: 223 average time/residue: 0.0679 time to fit residues: 23.0635 Evaluate side-chains 204 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 0.0370 chunk 31 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.074917 restraints weight = 25702.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078010 restraints weight = 14252.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080133 restraints weight = 9614.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081648 restraints weight = 7302.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.082675 restraints weight = 6000.448| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8999 Z= 0.122 Angle : 0.724 8.928 12184 Z= 0.358 Chirality : 0.042 0.141 1469 Planarity : 0.004 0.049 1518 Dihedral : 8.557 84.321 1287 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.16 % Allowed : 25.16 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.25), residues: 1133 helix: -0.70 (0.21), residues: 607 sheet: -1.27 (0.66), residues: 55 loop : -2.28 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.009 0.001 TYR B 570 PHE 0.013 0.001 PHE A 57 TRP 0.008 0.001 TRP B 104 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8995) covalent geometry : angle 0.72437 (12184) hydrogen bonds : bond 0.03846 ( 389) hydrogen bonds : angle 5.07987 ( 1122) Misc. bond : bond 0.00126 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.9154 (ppp) cc_final: 0.8930 (ppp) REVERT: A 77 GLN cc_start: 0.9332 (mt0) cc_final: 0.8944 (mm-40) REVERT: A 145 PHE cc_start: 0.9076 (t80) cc_final: 0.8757 (t80) REVERT: A 188 MET cc_start: 0.9083 (mmm) cc_final: 0.8828 (tpp) REVERT: A 191 ILE cc_start: 0.9481 (tp) cc_final: 0.9134 (tt) REVERT: A 196 GLN cc_start: 0.9390 (mm110) cc_final: 0.8759 (mm110) REVERT: A 231 MET cc_start: 0.9123 (ttm) cc_final: 0.8731 (tpp) REVERT: A 256 LEU cc_start: 0.9475 (mm) cc_final: 0.9188 (mm) REVERT: A 258 LEU cc_start: 0.9558 (tt) cc_final: 0.9125 (tt) REVERT: A 262 LEU cc_start: 0.9200 (mm) cc_final: 0.8807 (mm) REVERT: A 299 GLN cc_start: 0.9506 (mm-40) cc_final: 0.9164 (mm110) REVERT: A 326 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: A 433 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8945 (mt-10) REVERT: A 460 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7303 (t80) REVERT: A 466 ASN cc_start: 0.8124 (t0) cc_final: 0.7827 (m-40) REVERT: A 525 MET cc_start: 0.8558 (mmm) cc_final: 0.8344 (mmm) REVERT: A 567 HIS cc_start: 0.7432 (t70) cc_final: 0.7110 (t-90) REVERT: B 77 GLN cc_start: 0.9148 (mt0) cc_final: 0.8670 (mt0) REVERT: B 145 PHE cc_start: 0.9187 (t80) cc_final: 0.8593 (t80) REVERT: B 191 ILE cc_start: 0.9454 (tp) cc_final: 0.9148 (tt) REVERT: B 196 GLN cc_start: 0.9430 (mm110) cc_final: 0.9009 (mm110) REVERT: B 219 SER cc_start: 0.8083 (t) cc_final: 0.7614 (p) REVERT: B 231 MET cc_start: 0.9182 (ttm) cc_final: 0.8809 (tpp) REVERT: B 258 LEU cc_start: 0.9517 (tt) cc_final: 0.9079 (tt) REVERT: B 262 LEU cc_start: 0.9195 (mm) cc_final: 0.8881 (mm) REVERT: B 299 GLN cc_start: 0.9427 (mm-40) cc_final: 0.9066 (mm110) REVERT: B 326 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: B 567 HIS cc_start: 0.7723 (t70) cc_final: 0.7311 (t70) outliers start: 40 outliers final: 21 residues processed: 222 average time/residue: 0.0700 time to fit residues: 23.6681 Evaluate side-chains 210 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 111 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 1 optimal weight: 0.0020 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 0.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080618 restraints weight = 26197.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083613 restraints weight = 14701.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085690 restraints weight = 9892.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087030 restraints weight = 7488.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.088062 restraints weight = 6178.199| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8999 Z= 0.124 Angle : 0.721 9.291 12184 Z= 0.356 Chirality : 0.043 0.211 1469 Planarity : 0.004 0.047 1518 Dihedral : 8.207 85.825 1287 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 4.57 % Allowed : 26.09 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.25), residues: 1133 helix: -0.50 (0.21), residues: 613 sheet: -0.90 (0.68), residues: 50 loop : -2.14 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.011 0.001 TYR B 350 PHE 0.011 0.001 PHE A 57 TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8995) covalent geometry : angle 0.72092 (12184) hydrogen bonds : bond 0.03629 ( 389) hydrogen bonds : angle 4.90124 ( 1122) Misc. bond : bond 0.00121 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9298 (mt0) cc_final: 0.8889 (mm-40) REVERT: A 145 PHE cc_start: 0.9040 (t80) cc_final: 0.8705 (t80) REVERT: A 188 MET cc_start: 0.8951 (mmm) cc_final: 0.8739 (tpp) REVERT: A 191 ILE cc_start: 0.9498 (tp) cc_final: 0.9123 (tt) REVERT: A 196 GLN cc_start: 0.9365 (mm110) cc_final: 0.8816 (mm-40) REVERT: A 231 MET cc_start: 0.9082 (ttm) cc_final: 0.8671 (tpp) REVERT: A 256 LEU cc_start: 0.9496 (mm) cc_final: 0.9232 (mm) REVERT: A 258 LEU cc_start: 0.9508 (tt) cc_final: 0.9015 (tt) REVERT: A 262 LEU cc_start: 0.9200 (mm) cc_final: 0.8871 (mm) REVERT: A 290 LEU cc_start: 0.9312 (tp) cc_final: 0.8748 (pp) REVERT: A 299 GLN cc_start: 0.9561 (mm-40) cc_final: 0.9213 (mm110) REVERT: A 326 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: A 433 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8631 (mp0) REVERT: A 466 ASN cc_start: 0.8009 (t0) cc_final: 0.7707 (t0) REVERT: A 567 HIS cc_start: 0.7444 (t70) cc_final: 0.7164 (t-90) REVERT: B 145 PHE cc_start: 0.9210 (t80) cc_final: 0.8575 (t80) REVERT: B 191 ILE cc_start: 0.9484 (tp) cc_final: 0.9094 (tt) REVERT: B 196 GLN cc_start: 0.9402 (mm110) cc_final: 0.8794 (mm-40) REVERT: B 219 SER cc_start: 0.7952 (t) cc_final: 0.7474 (p) REVERT: B 231 MET cc_start: 0.9154 (ttm) cc_final: 0.8728 (tpp) REVERT: B 247 GLN cc_start: 0.9318 (tp-100) cc_final: 0.9099 (tp40) REVERT: B 262 LEU cc_start: 0.9219 (mm) cc_final: 0.8885 (mm) REVERT: B 295 MET cc_start: 0.9123 (tmm) cc_final: 0.8760 (tmm) REVERT: B 299 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9150 (mm110) REVERT: B 326 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: B 433 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8651 (mp0) REVERT: B 485 GLN cc_start: 0.9745 (tp40) cc_final: 0.9518 (mm110) REVERT: B 567 HIS cc_start: 0.7772 (t70) cc_final: 0.7423 (t70) outliers start: 44 outliers final: 27 residues processed: 220 average time/residue: 0.0657 time to fit residues: 22.0279 Evaluate side-chains 215 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081373 restraints weight = 26606.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084353 restraints weight = 14739.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086402 restraints weight = 9862.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087734 restraints weight = 7415.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088728 restraints weight = 6111.853| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8999 Z= 0.129 Angle : 0.738 12.950 12184 Z= 0.361 Chirality : 0.043 0.202 1469 Planarity : 0.004 0.044 1518 Dihedral : 8.140 86.892 1287 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 3.85 % Allowed : 28.69 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.25), residues: 1133 helix: -0.35 (0.21), residues: 607 sheet: -0.84 (0.70), residues: 50 loop : -2.07 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 441 TYR 0.017 0.001 TYR A 408 PHE 0.008 0.001 PHE A 57 TRP 0.008 0.001 TRP B 413 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8995) covalent geometry : angle 0.73819 (12184) hydrogen bonds : bond 0.03556 ( 389) hydrogen bonds : angle 4.76428 ( 1122) Misc. bond : bond 0.00119 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9262 (mt0) cc_final: 0.8855 (mt0) REVERT: A 145 PHE cc_start: 0.9076 (t80) cc_final: 0.8745 (t80) REVERT: A 191 ILE cc_start: 0.9505 (tp) cc_final: 0.9138 (tt) REVERT: A 196 GLN cc_start: 0.9382 (mm110) cc_final: 0.8839 (mm-40) REVERT: A 231 MET cc_start: 0.9094 (ttm) cc_final: 0.8621 (tpp) REVERT: A 256 LEU cc_start: 0.9503 (mm) cc_final: 0.9241 (mm) REVERT: A 258 LEU cc_start: 0.9500 (tt) cc_final: 0.8981 (tt) REVERT: A 262 LEU cc_start: 0.9161 (mm) cc_final: 0.8831 (mm) REVERT: A 290 LEU cc_start: 0.9314 (tp) cc_final: 0.8708 (pp) REVERT: A 299 GLN cc_start: 0.9567 (mm-40) cc_final: 0.9211 (mm110) REVERT: A 326 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: A 433 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8850 (mt-10) REVERT: A 466 ASN cc_start: 0.7939 (t0) cc_final: 0.7644 (t0) REVERT: A 567 HIS cc_start: 0.7460 (t70) cc_final: 0.7198 (t-90) REVERT: B 145 PHE cc_start: 0.9205 (t80) cc_final: 0.8619 (t80) REVERT: B 191 ILE cc_start: 0.9502 (tp) cc_final: 0.9174 (tt) REVERT: B 196 GLN cc_start: 0.9397 (mm110) cc_final: 0.8781 (mm-40) REVERT: B 219 SER cc_start: 0.7975 (t) cc_final: 0.7492 (p) REVERT: B 231 MET cc_start: 0.9138 (ttm) cc_final: 0.8662 (tpp) REVERT: B 247 GLN cc_start: 0.9312 (tp-100) cc_final: 0.9009 (tp40) REVERT: B 258 LEU cc_start: 0.9469 (tt) cc_final: 0.8947 (tt) REVERT: B 262 LEU cc_start: 0.9184 (mm) cc_final: 0.8826 (mm) REVERT: B 295 MET cc_start: 0.9121 (tmm) cc_final: 0.8753 (tmm) REVERT: B 299 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9160 (mm110) REVERT: B 326 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: B 433 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8503 (mp0) REVERT: B 485 GLN cc_start: 0.9755 (tp40) cc_final: 0.9508 (mm110) REVERT: B 567 HIS cc_start: 0.7843 (t70) cc_final: 0.7500 (t70) outliers start: 37 outliers final: 26 residues processed: 216 average time/residue: 0.0701 time to fit residues: 22.8337 Evaluate side-chains 218 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.102235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.075702 restraints weight = 26009.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078888 restraints weight = 14338.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081029 restraints weight = 9661.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082449 restraints weight = 7371.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083509 restraints weight = 6133.680| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8999 Z= 0.127 Angle : 0.746 11.543 12184 Z= 0.363 Chirality : 0.044 0.237 1469 Planarity : 0.004 0.046 1518 Dihedral : 8.095 89.792 1287 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.33 % Allowed : 29.94 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.25), residues: 1133 helix: -0.28 (0.21), residues: 613 sheet: -0.81 (0.70), residues: 50 loop : -2.07 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.013 0.001 TYR B 350 PHE 0.014 0.001 PHE B 57 TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8995) covalent geometry : angle 0.74633 (12184) hydrogen bonds : bond 0.03507 ( 389) hydrogen bonds : angle 4.70625 ( 1122) Misc. bond : bond 0.00115 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9290 (mt0) cc_final: 0.8893 (mt0) REVERT: A 145 PHE cc_start: 0.8993 (t80) cc_final: 0.8638 (t80) REVERT: A 191 ILE cc_start: 0.9497 (tp) cc_final: 0.9094 (tt) REVERT: A 196 GLN cc_start: 0.9428 (mm110) cc_final: 0.8819 (mm-40) REVERT: A 256 LEU cc_start: 0.9454 (mm) cc_final: 0.9189 (mm) REVERT: A 258 LEU cc_start: 0.9522 (tt) cc_final: 0.9319 (tt) REVERT: A 290 LEU cc_start: 0.9316 (tp) cc_final: 0.8686 (pp) REVERT: A 299 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9149 (mm110) REVERT: A 326 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: A 433 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8875 (mt-10) REVERT: A 466 ASN cc_start: 0.7938 (t0) cc_final: 0.7678 (t0) REVERT: A 567 HIS cc_start: 0.7491 (t70) cc_final: 0.7188 (t-90) REVERT: B 145 PHE cc_start: 0.9166 (t80) cc_final: 0.8592 (t80) REVERT: B 191 ILE cc_start: 0.9493 (tp) cc_final: 0.9124 (tt) REVERT: B 196 GLN cc_start: 0.9430 (mm110) cc_final: 0.8745 (mm-40) REVERT: B 219 SER cc_start: 0.7982 (t) cc_final: 0.7546 (p) REVERT: B 231 MET cc_start: 0.9188 (ttm) cc_final: 0.8667 (tpp) REVERT: B 258 LEU cc_start: 0.9504 (tt) cc_final: 0.8924 (tt) REVERT: B 259 MET cc_start: 0.8596 (mmt) cc_final: 0.8304 (mmt) REVERT: B 262 LEU cc_start: 0.9172 (mm) cc_final: 0.8830 (mm) REVERT: B 295 MET cc_start: 0.9163 (tmm) cc_final: 0.8796 (tmm) REVERT: B 299 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9144 (mm110) REVERT: B 326 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: B 433 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8585 (mp0) REVERT: B 485 GLN cc_start: 0.9722 (tp40) cc_final: 0.9504 (mm110) REVERT: B 567 HIS cc_start: 0.7861 (t70) cc_final: 0.7589 (t70) outliers start: 32 outliers final: 24 residues processed: 215 average time/residue: 0.0689 time to fit residues: 22.0564 Evaluate side-chains 214 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 101 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.104105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077512 restraints weight = 25426.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080736 restraints weight = 14027.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082949 restraints weight = 9478.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.084341 restraints weight = 7215.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085392 restraints weight = 5988.233| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8999 Z= 0.118 Angle : 0.749 10.377 12184 Z= 0.359 Chirality : 0.043 0.211 1469 Planarity : 0.004 0.045 1518 Dihedral : 7.897 85.873 1287 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.85 % Allowed : 29.31 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.25), residues: 1133 helix: -0.20 (0.22), residues: 618 sheet: -0.73 (0.69), residues: 50 loop : -2.07 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 441 TYR 0.008 0.001 TYR B 570 PHE 0.010 0.001 PHE B 57 TRP 0.005 0.001 TRP B 413 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8995) covalent geometry : angle 0.74850 (12184) hydrogen bonds : bond 0.03348 ( 389) hydrogen bonds : angle 4.60193 ( 1122) Misc. bond : bond 0.00107 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9286 (mt0) cc_final: 0.8872 (mt0) REVERT: A 145 PHE cc_start: 0.9019 (t80) cc_final: 0.8700 (t80) REVERT: A 191 ILE cc_start: 0.9481 (tp) cc_final: 0.9071 (tt) REVERT: A 196 GLN cc_start: 0.9383 (mm110) cc_final: 0.8886 (mm-40) REVERT: A 210 LEU cc_start: 0.9585 (tp) cc_final: 0.9278 (tp) REVERT: A 247 GLN cc_start: 0.9318 (tp-100) cc_final: 0.9083 (tp40) REVERT: A 256 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9181 (mm) REVERT: A 258 LEU cc_start: 0.9507 (tt) cc_final: 0.9285 (tt) REVERT: A 290 LEU cc_start: 0.9332 (tp) cc_final: 0.8640 (pp) REVERT: A 295 MET cc_start: 0.9115 (tmm) cc_final: 0.8749 (tmm) REVERT: A 299 GLN cc_start: 0.9538 (mm-40) cc_final: 0.9240 (mm110) REVERT: A 326 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: A 433 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8857 (mt-10) REVERT: A 567 HIS cc_start: 0.7439 (t70) cc_final: 0.7134 (t-90) REVERT: B 145 PHE cc_start: 0.9211 (t80) cc_final: 0.8643 (t80) REVERT: B 191 ILE cc_start: 0.9462 (tp) cc_final: 0.9083 (tt) REVERT: B 196 GLN cc_start: 0.9388 (mm110) cc_final: 0.8556 (mm-40) REVERT: B 219 SER cc_start: 0.8040 (t) cc_final: 0.7589 (p) REVERT: B 231 MET cc_start: 0.9197 (ttm) cc_final: 0.8678 (tpp) REVERT: B 258 LEU cc_start: 0.9497 (tt) cc_final: 0.8924 (tt) REVERT: B 259 MET cc_start: 0.8612 (mmt) cc_final: 0.8338 (mmt) REVERT: B 262 LEU cc_start: 0.9130 (mm) cc_final: 0.8883 (mm) REVERT: B 290 LEU cc_start: 0.9316 (tp) cc_final: 0.8761 (pp) REVERT: B 295 MET cc_start: 0.9171 (tmm) cc_final: 0.8801 (tmm) REVERT: B 299 GLN cc_start: 0.9441 (mm-40) cc_final: 0.9145 (mm110) REVERT: B 326 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: B 433 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8566 (mp0) REVERT: B 471 GLU cc_start: 0.9134 (tt0) cc_final: 0.8642 (tp30) REVERT: B 528 ARG cc_start: 0.8446 (mpp80) cc_final: 0.8185 (mtt-85) REVERT: B 567 HIS cc_start: 0.7890 (t70) cc_final: 0.7529 (t70) outliers start: 37 outliers final: 27 residues processed: 224 average time/residue: 0.0723 time to fit residues: 23.8666 Evaluate side-chains 222 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 33 optimal weight: 9.9990 chunk 16 optimal weight: 0.0020 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 overall best weight: 0.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.103429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078660 restraints weight = 24669.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081785 restraints weight = 13786.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083934 restraints weight = 9332.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.085287 restraints weight = 7100.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.086340 restraints weight = 5894.706| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8999 Z= 0.123 Angle : 0.773 9.639 12184 Z= 0.370 Chirality : 0.044 0.253 1469 Planarity : 0.004 0.046 1518 Dihedral : 7.835 83.786 1287 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 3.95 % Allowed : 29.21 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.25), residues: 1133 helix: -0.15 (0.22), residues: 624 sheet: -0.76 (0.69), residues: 50 loop : -2.05 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 441 TYR 0.009 0.001 TYR B 350 PHE 0.012 0.001 PHE A 384 TRP 0.003 0.001 TRP A 413 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8995) covalent geometry : angle 0.77300 (12184) hydrogen bonds : bond 0.03279 ( 389) hydrogen bonds : angle 4.54810 ( 1122) Misc. bond : bond 0.00111 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9244 (mt0) cc_final: 0.8842 (mt0) REVERT: A 145 PHE cc_start: 0.9031 (t80) cc_final: 0.8716 (t80) REVERT: A 191 ILE cc_start: 0.9427 (tp) cc_final: 0.9002 (tt) REVERT: A 196 GLN cc_start: 0.9387 (mm110) cc_final: 0.8664 (mm-40) REVERT: A 210 LEU cc_start: 0.9590 (tp) cc_final: 0.9291 (tp) REVERT: A 247 GLN cc_start: 0.9292 (tp-100) cc_final: 0.9050 (tp40) REVERT: A 258 LEU cc_start: 0.9513 (tt) cc_final: 0.9117 (tt) REVERT: A 259 MET cc_start: 0.8405 (mmt) cc_final: 0.8043 (mmt) REVERT: A 290 LEU cc_start: 0.9341 (tp) cc_final: 0.8633 (pp) REVERT: A 295 MET cc_start: 0.9140 (tmm) cc_final: 0.8797 (tmm) REVERT: A 299 GLN cc_start: 0.9552 (mm-40) cc_final: 0.9262 (mm110) REVERT: A 319 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8997 (tp30) REVERT: A 326 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: A 433 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8819 (mt-10) REVERT: A 567 HIS cc_start: 0.7454 (t70) cc_final: 0.7169 (t-90) REVERT: B 145 PHE cc_start: 0.9220 (t80) cc_final: 0.8635 (t80) REVERT: B 191 ILE cc_start: 0.9449 (tp) cc_final: 0.9073 (tt) REVERT: B 196 GLN cc_start: 0.9388 (mm110) cc_final: 0.8586 (mm-40) REVERT: B 219 SER cc_start: 0.8286 (t) cc_final: 0.7807 (p) REVERT: B 258 LEU cc_start: 0.9498 (tt) cc_final: 0.8926 (tt) REVERT: B 259 MET cc_start: 0.8623 (mmt) cc_final: 0.8340 (mmt) REVERT: B 262 LEU cc_start: 0.9127 (mm) cc_final: 0.8866 (mm) REVERT: B 290 LEU cc_start: 0.9330 (tp) cc_final: 0.8732 (pp) REVERT: B 295 MET cc_start: 0.9170 (tmm) cc_final: 0.8628 (tmm) REVERT: B 299 GLN cc_start: 0.9446 (mm-40) cc_final: 0.8978 (mm-40) REVERT: B 326 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8207 (pp20) REVERT: B 433 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8566 (mp0) REVERT: B 471 GLU cc_start: 0.9121 (tt0) cc_final: 0.8668 (tp30) REVERT: B 567 HIS cc_start: 0.7889 (t70) cc_final: 0.7647 (t70) outliers start: 38 outliers final: 31 residues processed: 224 average time/residue: 0.0717 time to fit residues: 23.9677 Evaluate side-chains 228 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.104031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077455 restraints weight = 25522.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080624 restraints weight = 14054.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082891 restraints weight = 9496.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.084297 restraints weight = 7184.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085410 restraints weight = 5951.047| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8999 Z= 0.133 Angle : 0.796 13.146 12184 Z= 0.380 Chirality : 0.045 0.265 1469 Planarity : 0.004 0.046 1518 Dihedral : 7.835 82.264 1287 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.85 % Allowed : 29.63 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.25), residues: 1133 helix: -0.05 (0.22), residues: 618 sheet: -0.76 (0.69), residues: 50 loop : -2.07 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 441 TYR 0.017 0.001 TYR B 408 PHE 0.016 0.001 PHE A 384 TRP 0.005 0.001 TRP A 413 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8995) covalent geometry : angle 0.79563 (12184) hydrogen bonds : bond 0.03282 ( 389) hydrogen bonds : angle 4.55037 ( 1122) Misc. bond : bond 0.00121 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9239 (mt0) cc_final: 0.8840 (mt0) REVERT: A 145 PHE cc_start: 0.9039 (t80) cc_final: 0.8720 (t80) REVERT: A 191 ILE cc_start: 0.9453 (tp) cc_final: 0.9022 (tt) REVERT: A 196 GLN cc_start: 0.9396 (mm110) cc_final: 0.8618 (mm-40) REVERT: A 210 LEU cc_start: 0.9601 (tp) cc_final: 0.9313 (tp) REVERT: A 247 GLN cc_start: 0.9283 (tp-100) cc_final: 0.9055 (tp40) REVERT: A 258 LEU cc_start: 0.9511 (tt) cc_final: 0.9270 (tt) REVERT: A 290 LEU cc_start: 0.9341 (tp) cc_final: 0.8671 (pp) REVERT: A 295 MET cc_start: 0.9137 (tmm) cc_final: 0.8592 (tmm) REVERT: A 299 GLN cc_start: 0.9541 (mm-40) cc_final: 0.9117 (mm-40) REVERT: A 319 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9012 (tp30) REVERT: A 326 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8195 (pp20) REVERT: A 567 HIS cc_start: 0.7470 (t70) cc_final: 0.7178 (t-90) REVERT: B 145 PHE cc_start: 0.9220 (t80) cc_final: 0.8650 (t80) REVERT: B 191 ILE cc_start: 0.9438 (tp) cc_final: 0.9056 (tt) REVERT: B 196 GLN cc_start: 0.9409 (mm110) cc_final: 0.8591 (mm-40) REVERT: B 219 SER cc_start: 0.7556 (t) cc_final: 0.7061 (p) REVERT: B 258 LEU cc_start: 0.9514 (tt) cc_final: 0.8946 (tt) REVERT: B 259 MET cc_start: 0.8634 (mmt) cc_final: 0.8361 (mmt) REVERT: B 262 LEU cc_start: 0.9141 (mm) cc_final: 0.8889 (mm) REVERT: B 290 LEU cc_start: 0.9299 (tp) cc_final: 0.8726 (pp) REVERT: B 295 MET cc_start: 0.9191 (tmm) cc_final: 0.8659 (tmm) REVERT: B 299 GLN cc_start: 0.9456 (mm-40) cc_final: 0.9000 (mm-40) REVERT: B 326 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: B 433 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 471 GLU cc_start: 0.9138 (tt0) cc_final: 0.8639 (tp30) REVERT: B 567 HIS cc_start: 0.7944 (t70) cc_final: 0.7704 (t70) outliers start: 37 outliers final: 32 residues processed: 217 average time/residue: 0.0697 time to fit residues: 22.7834 Evaluate side-chains 229 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 chunk 84 optimal weight: 0.0060 chunk 5 optimal weight: 6.9990 overall best weight: 2.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074940 restraints weight = 25486.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078025 restraints weight = 14315.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080155 restraints weight = 9769.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081422 restraints weight = 7469.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.082498 restraints weight = 6261.466| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8999 Z= 0.171 Angle : 0.811 11.397 12184 Z= 0.394 Chirality : 0.045 0.245 1469 Planarity : 0.004 0.046 1518 Dihedral : 7.936 83.028 1287 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.64 % Allowed : 29.73 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.26), residues: 1133 helix: 0.10 (0.22), residues: 610 sheet: -0.84 (0.67), residues: 60 loop : -1.85 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 441 TYR 0.020 0.001 TYR B 350 PHE 0.015 0.001 PHE A 384 TRP 0.008 0.001 TRP B 413 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8995) covalent geometry : angle 0.81078 (12184) hydrogen bonds : bond 0.03385 ( 389) hydrogen bonds : angle 4.65033 ( 1122) Misc. bond : bond 0.00152 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1454.69 seconds wall clock time: 25 minutes 47.57 seconds (1547.57 seconds total)