Starting phenix.real_space_refine on Thu Mar 13 15:43:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r81_4749/03_2025/6r81_4749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r81_4749/03_2025/6r81_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_2025/6r81_4749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2025/6r81_4749.map" model { file = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2025/6r81_4749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r81_4749/03_2025/6r81_4749_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.00, per 1000 atoms: 0.68 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: 3.05 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.97 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: 2.33 Time building geometry restraints manager: 3.52 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 586 or resid 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: 0.010 Normalize map: mean=0, sd=1: 4.220 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.020 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- 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 : 0.011 0.154 8995 Z= 0.719 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.004 TRP B 413 HIS 0.012 0.003 HIS B 141 PHE 0.027 0.004 PHE A 57 TYR 0.023 0.003 TYR B 570 ARG 0.014 0.002 ARG A 414 *********************** 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 : 1.100 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: 0.9228 (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: 0.1896 time to fit residues: 59.9663 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 : 1.056 ------------------------------------------------------------------------------- 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 95 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.103705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078401 restraints weight = 26793.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.081353 restraints weight = 14802.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083411 restraints weight = 9945.722| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8995 Z= 0.245 Angle : 0.817 9.420 12184 Z= 0.424 Chirality : 0.046 0.135 1469 Planarity : 0.005 0.057 1518 Dihedral : 9.880 79.770 1301 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.74 % Favored : 91.09 % Rotamer: Outliers : 3.85 % Allowed : 20.48 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.23), residues: 1133 helix: -1.72 (0.19), residues: 616 sheet: -2.16 (0.66), residues: 50 loop : -2.65 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 413 HIS 0.010 0.002 HIS A 567 PHE 0.019 0.002 PHE A 74 TYR 0.018 0.002 TYR B 350 ARG 0.003 0.001 ARG A 432 *********************** 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 250 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.103 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: 0.9326 (mt0) cc_final: 0.9100 (mm-40) REVERT: A 145 PHE cc_start: 0.9157 (t80) cc_final: 0.8642 (t80) REVERT: A 231 MET cc_start: 0.9133 (ttm) cc_final: 0.8759 (tpp) REVERT: A 258 LEU cc_start: 0.9582 (tt) cc_final: 0.9251 (tt) REVERT: A 262 LEU cc_start: 0.9237 (mm) cc_final: 0.8882 (mm) REVERT: A 299 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9235 (mm110) REVERT: A 460 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 567 HIS cc_start: 0.7503 (t70) cc_final: 0.7188 (t-90) REVERT: B 77 GLN cc_start: 0.9139 (mt0) cc_final: 0.8715 (mt0) REVERT: B 145 PHE cc_start: 0.9270 (t80) cc_final: 0.8723 (t80) REVERT: B 231 MET cc_start: 0.9212 (ttm) cc_final: 0.8926 (tpp) REVERT: B 262 LEU cc_start: 0.9183 (mm) cc_final: 0.8906 (mm) REVERT: B 295 MET cc_start: 0.9310 (tpp) cc_final: 0.8947 (tmm) REVERT: B 299 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9047 (mm-40) REVERT: B 460 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 533 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8128 (pt) REVERT: B 567 HIS cc_start: 0.7339 (t70) cc_final: 0.7105 (t-90) REVERT: B 580 MET cc_start: 0.8331 (mtp) cc_final: 0.8057 (mtt) outliers start: 37 outliers final: 12 residues processed: 232 average time/residue: 0.1871 time to fit residues: 62.6471 Evaluate side-chains 196 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 PHE Chi-restraints excluded: chain A residue 300 ILE 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 533 ILE 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 60 optimal weight: 0.0870 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 0.0030 chunk 89 optimal weight: 10.0000 overall best weight: 1.7972 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.097748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.071954 restraints weight = 26071.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074925 restraints weight = 14399.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076964 restraints weight = 9699.840| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8995 Z= 0.214 Angle : 0.748 7.926 12184 Z= 0.383 Chirality : 0.044 0.190 1469 Planarity : 0.004 0.051 1518 Dihedral : 9.004 79.267 1287 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 4.57 % Allowed : 24.01 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1133 helix: -1.03 (0.20), residues: 618 sheet: -1.87 (0.63), residues: 60 loop : -2.35 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.007 0.001 HIS A 141 PHE 0.012 0.001 PHE B 348 TYR 0.013 0.001 TYR B 570 ARG 0.004 0.000 ARG B 389 *********************** 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 237 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.453 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 77 GLN cc_start: 0.9381 (mt0) cc_final: 0.9055 (mm-40) REVERT: A 145 PHE cc_start: 0.9074 (t80) cc_final: 0.8672 (t80) REVERT: A 188 MET cc_start: 0.8922 (tpp) cc_final: 0.8653 (mmm) REVERT: A 191 ILE cc_start: 0.9511 (tp) cc_final: 0.8963 (tt) REVERT: A 219 SER cc_start: 0.8260 (t) cc_final: 0.7812 (p) REVERT: A 231 MET cc_start: 0.9164 (ttm) cc_final: 0.8753 (tpp) REVERT: A 256 LEU cc_start: 0.9512 (mm) cc_final: 0.9204 (mm) REVERT: A 258 LEU cc_start: 0.9546 (tt) cc_final: 0.9170 (tt) REVERT: A 262 LEU cc_start: 0.9255 (mm) cc_final: 0.8874 (mm) REVERT: A 299 GLN cc_start: 0.9522 (mm-40) cc_final: 0.9125 (mm110) REVERT: A 326 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: A 441 ARG cc_start: 0.8406 (ptp90) cc_final: 0.8176 (ptp90) REVERT: A 466 ASN cc_start: 0.8086 (t0) cc_final: 0.7759 (t0) REVERT: A 567 HIS cc_start: 0.7625 (t70) cc_final: 0.7281 (t-90) REVERT: B 77 GLN cc_start: 0.9173 (mt0) cc_final: 0.8734 (mt0) REVERT: B 145 PHE cc_start: 0.9195 (t80) cc_final: 0.8631 (t80) REVERT: B 231 MET cc_start: 0.9245 (ttm) cc_final: 0.8858 (tpp) REVERT: B 262 LEU cc_start: 0.9235 (mm) cc_final: 0.8846 (mm) REVERT: B 299 GLN cc_start: 0.9398 (mm-40) cc_final: 0.9162 (mm110) REVERT: B 326 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: B 567 HIS cc_start: 0.7816 (t70) cc_final: 0.7360 (t-90) REVERT: B 580 MET cc_start: 0.8476 (mtp) cc_final: 0.8198 (mtt) outliers start: 44 outliers final: 23 residues processed: 222 average time/residue: 0.1623 time to fit residues: 54.1669 Evaluate side-chains 205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 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 431 ILE Chi-restraints excluded: chain A residue 435 ILE 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 254 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 388 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 0.0870 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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** ** 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 = 0.3621 r_free = 0.3621 target = 0.100206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074328 restraints weight = 25497.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077333 restraints weight = 14099.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079430 restraints weight = 9534.580| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8995 Z= 0.164 Angle : 0.717 8.610 12184 Z= 0.355 Chirality : 0.043 0.135 1469 Planarity : 0.004 0.050 1518 Dihedral : 8.555 83.991 1287 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.05 % Allowed : 24.95 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.25), residues: 1133 helix: -0.67 (0.21), residues: 613 sheet: -1.43 (0.65), residues: 60 loop : -2.22 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.006 0.001 HIS B 141 PHE 0.008 0.001 PHE A 460 TYR 0.009 0.001 TYR B 570 ARG 0.004 0.000 ARG A 414 *********************** 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 242 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.677 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: 0.9064 (t80) cc_final: 0.8738 (t80) REVERT: A 191 ILE cc_start: 0.9497 (tp) cc_final: 0.9096 (tt) REVERT: A 196 GLN cc_start: 0.9425 (mm110) cc_final: 0.8988 (mm110) REVERT: A 219 SER cc_start: 0.7983 (t) cc_final: 0.7456 (p) REVERT: A 231 MET cc_start: 0.9164 (ttm) cc_final: 0.8761 (tpp) REVERT: A 243 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8980 (tm-30) REVERT: A 256 LEU cc_start: 0.9510 (mm) cc_final: 0.9155 (mm) REVERT: A 258 LEU cc_start: 0.9531 (tt) cc_final: 0.9111 (tt) REVERT: A 262 LEU cc_start: 0.9234 (mm) cc_final: 0.8845 (mm) REVERT: A 288 LEU cc_start: 0.8897 (tt) cc_final: 0.8661 (pp) REVERT: A 295 MET cc_start: 0.9258 (tmm) cc_final: 0.8882 (tmm) REVERT: A 299 GLN cc_start: 0.9519 (mm-40) cc_final: 0.9172 (mm110) REVERT: A 326 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: A 466 ASN cc_start: 0.8092 (t0) cc_final: 0.7762 (m-40) REVERT: A 485 GLN cc_start: 0.9727 (tp40) cc_final: 0.9442 (mm110) REVERT: A 567 HIS cc_start: 0.7481 (t70) cc_final: 0.7154 (t-90) REVERT: B 77 GLN cc_start: 0.9158 (mt0) cc_final: 0.8682 (mt0) REVERT: B 145 PHE cc_start: 0.9177 (t80) cc_final: 0.8580 (t80) REVERT: B 191 ILE cc_start: 0.9505 (tp) cc_final: 0.9101 (tt) REVERT: B 196 GLN cc_start: 0.9450 (mm110) cc_final: 0.8990 (mm110) REVERT: B 219 SER cc_start: 0.7856 (t) cc_final: 0.7307 (p) REVERT: B 231 MET cc_start: 0.9204 (ttm) cc_final: 0.8804 (tpp) REVERT: B 243 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8976 (tm-30) REVERT: B 258 LEU cc_start: 0.9506 (tt) cc_final: 0.9075 (tt) REVERT: B 262 LEU cc_start: 0.9185 (mm) cc_final: 0.8896 (mm) REVERT: B 299 GLN cc_start: 0.9433 (mm-40) cc_final: 0.9064 (mm110) REVERT: B 326 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: B 433 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8902 (mt-10) REVERT: B 567 HIS cc_start: 0.7767 (t70) cc_final: 0.7334 (t70) REVERT: B 580 MET cc_start: 0.8435 (mtp) cc_final: 0.8206 (mtt) outliers start: 39 outliers final: 20 residues processed: 226 average time/residue: 0.2117 time to fit residues: 71.7479 Evaluate side-chains 210 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 326 GLU Chi-restraints excluded: chain A residue 334 ILE 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 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 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE 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 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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** ** 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 = 0.3745 r_free = 0.3745 target = 0.107191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.081485 restraints weight = 25695.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084429 restraints weight = 14451.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086469 restraints weight = 9790.454| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8995 Z= 0.155 Angle : 0.712 7.618 12184 Z= 0.351 Chirality : 0.043 0.201 1469 Planarity : 0.004 0.047 1518 Dihedral : 8.202 86.945 1287 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.26 % Allowed : 26.82 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 1133 helix: -0.43 (0.21), residues: 602 sheet: -0.82 (0.68), residues: 50 loop : -2.00 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS B 141 PHE 0.009 0.001 PHE A 202 TYR 0.012 0.001 TYR A 408 ARG 0.003 0.000 ARG B 389 *********************** 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 245 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.189 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 73 VAL cc_start: 0.9545 (p) cc_final: 0.9200 (m) REVERT: A 77 GLN cc_start: 0.9264 (mt0) cc_final: 0.8893 (mm-40) REVERT: A 101 GLU cc_start: 0.9113 (tp30) cc_final: 0.8879 (tp30) REVERT: A 145 PHE cc_start: 0.9047 (t80) cc_final: 0.8715 (t80) REVERT: A 191 ILE cc_start: 0.9524 (tp) cc_final: 0.9129 (tt) REVERT: A 196 GLN cc_start: 0.9344 (mm110) cc_final: 0.8821 (mm-40) REVERT: A 219 SER cc_start: 0.7746 (t) cc_final: 0.7390 (p) REVERT: A 231 MET cc_start: 0.9098 (ttm) cc_final: 0.8649 (tpp) REVERT: A 256 LEU cc_start: 0.9514 (mm) cc_final: 0.9242 (mm) REVERT: A 290 LEU cc_start: 0.9280 (tp) cc_final: 0.8744 (pp) REVERT: A 295 MET cc_start: 0.9260 (tmm) cc_final: 0.8865 (tmm) REVERT: A 299 GLN cc_start: 0.9537 (mm-40) cc_final: 0.9183 (mm110) REVERT: A 326 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: A 485 GLN cc_start: 0.9739 (tp40) cc_final: 0.9454 (mm110) REVERT: A 567 HIS cc_start: 0.7444 (t70) cc_final: 0.7178 (t-90) REVERT: B 145 PHE cc_start: 0.9225 (t80) cc_final: 0.8627 (t80) REVERT: B 191 ILE cc_start: 0.9526 (tp) cc_final: 0.9149 (tt) REVERT: B 196 GLN cc_start: 0.9391 (mm110) cc_final: 0.8823 (mm-40) REVERT: B 219 SER cc_start: 0.7861 (t) cc_final: 0.7359 (p) REVERT: B 231 MET cc_start: 0.9156 (ttm) cc_final: 0.8792 (tpp) REVERT: B 243 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8854 (tm-30) REVERT: B 247 GLN cc_start: 0.9315 (tp-100) cc_final: 0.9096 (tp40) REVERT: B 258 LEU cc_start: 0.9494 (tt) cc_final: 0.9017 (tt) REVERT: B 259 MET cc_start: 0.8540 (mmt) cc_final: 0.8319 (mmt) REVERT: B 262 LEU cc_start: 0.9203 (mm) cc_final: 0.8879 (mm) REVERT: B 295 MET cc_start: 0.9120 (tmm) cc_final: 0.8747 (tmm) REVERT: B 299 GLN cc_start: 0.9478 (mm-40) cc_final: 0.9159 (mm110) REVERT: B 326 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: B 471 GLU cc_start: 0.9074 (tt0) cc_final: 0.8800 (tp30) REVERT: B 485 GLN cc_start: 0.9744 (tp40) cc_final: 0.9509 (mm110) REVERT: B 567 HIS cc_start: 0.7831 (t70) cc_final: 0.7449 (t70) REVERT: B 580 MET cc_start: 0.8445 (mtp) cc_final: 0.8186 (mtt) outliers start: 41 outliers final: 23 residues processed: 226 average time/residue: 0.1685 time to fit residues: 56.5860 Evaluate side-chains 211 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL 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 363 VAL 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 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 363 VAL Chi-restraints excluded: chain B residue 388 GLU 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 7 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 0.0870 chunk 48 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.105049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078625 restraints weight = 25461.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081728 restraints weight = 14456.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083843 restraints weight = 9773.638| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8995 Z= 0.162 Angle : 0.750 12.590 12184 Z= 0.360 Chirality : 0.043 0.203 1469 Planarity : 0.004 0.048 1518 Dihedral : 8.043 89.848 1287 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.25), residues: 1133 helix: -0.35 (0.21), residues: 607 sheet: -0.69 (0.70), residues: 50 loop : -1.97 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.001 HIS A 141 PHE 0.007 0.001 PHE A 348 TYR 0.011 0.001 TYR B 350 ARG 0.005 0.000 ARG B 441 *********************** 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 236 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 1.022 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: 0.8889 (mt0) REVERT: A 145 PHE cc_start: 0.9065 (t80) cc_final: 0.8760 (t80) REVERT: A 191 ILE cc_start: 0.9516 (tp) cc_final: 0.9122 (tt) REVERT: A 196 GLN cc_start: 0.9356 (mm110) cc_final: 0.8885 (mm-40) REVERT: A 219 SER cc_start: 0.7881 (t) cc_final: 0.7369 (p) REVERT: A 231 MET cc_start: 0.9120 (ttm) cc_final: 0.8618 (tpp) REVERT: A 247 GLN cc_start: 0.9334 (tp-100) cc_final: 0.9100 (tp40) REVERT: A 256 LEU cc_start: 0.9488 (mm) cc_final: 0.9220 (mm) REVERT: A 290 LEU cc_start: 0.9238 (tp) cc_final: 0.8683 (pp) REVERT: A 295 MET cc_start: 0.9235 (tmm) cc_final: 0.8895 (tmm) REVERT: A 299 GLN cc_start: 0.9559 (mm-40) cc_final: 0.9217 (mm110) REVERT: A 326 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: A 567 HIS cc_start: 0.7513 (t70) cc_final: 0.7203 (t-90) REVERT: B 145 PHE cc_start: 0.9229 (t80) cc_final: 0.8650 (t80) REVERT: B 191 ILE cc_start: 0.9523 (tp) cc_final: 0.9168 (tt) REVERT: B 196 GLN cc_start: 0.9387 (mm110) cc_final: 0.8846 (mm-40) REVERT: B 219 SER cc_start: 0.7874 (t) cc_final: 0.7395 (p) REVERT: B 231 MET cc_start: 0.9186 (ttm) cc_final: 0.8724 (tpp) REVERT: B 247 GLN cc_start: 0.9287 (tp-100) cc_final: 0.8964 (tp40) REVERT: B 258 LEU cc_start: 0.9500 (tt) cc_final: 0.8961 (tt) REVERT: B 262 LEU cc_start: 0.9146 (mm) cc_final: 0.8841 (mm) REVERT: B 288 LEU cc_start: 0.8898 (tt) cc_final: 0.8656 (pp) REVERT: B 295 MET cc_start: 0.9121 (tmm) cc_final: 0.8740 (tmm) REVERT: B 299 GLN cc_start: 0.9478 (mm-40) cc_final: 0.9153 (mm110) REVERT: B 326 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: B 433 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8875 (mt-10) REVERT: B 471 GLU cc_start: 0.9068 (tt0) cc_final: 0.8756 (tp30) REVERT: B 567 HIS cc_start: 0.7872 (t70) cc_final: 0.7475 (t70) outliers start: 38 outliers final: 24 residues processed: 221 average time/residue: 0.1664 time to fit residues: 53.5906 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 : 0.963 ------------------------------------------------------------------------------- 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 206 LEU 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 430 THR 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 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 363 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 472 VAL 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 73 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.103568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077110 restraints weight = 25467.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080306 restraints weight = 14098.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082502 restraints weight = 9513.811| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8995 Z= 0.162 Angle : 0.735 9.920 12184 Z= 0.356 Chirality : 0.043 0.225 1469 Planarity : 0.004 0.044 1518 Dihedral : 7.907 85.445 1287 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.85 % Allowed : 28.48 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 1133 helix: -0.26 (0.21), residues: 614 sheet: -0.58 (0.70), residues: 50 loop : -2.01 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS B 141 PHE 0.017 0.001 PHE B 57 TYR 0.011 0.001 TYR B 350 ARG 0.004 0.000 ARG A 528 *********************** 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 233 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.090 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: 0.9306 (mt0) cc_final: 0.8898 (mt0) REVERT: A 145 PHE cc_start: 0.9057 (t80) cc_final: 0.8769 (t80) REVERT: A 191 ILE cc_start: 0.9467 (tp) cc_final: 0.9062 (tt) REVERT: A 196 GLN cc_start: 0.9357 (mm110) cc_final: 0.8880 (mm-40) REVERT: A 219 SER cc_start: 0.7840 (t) cc_final: 0.7346 (p) REVERT: A 247 GLN cc_start: 0.9334 (tp-100) cc_final: 0.9094 (tp40) REVERT: A 256 LEU cc_start: 0.9439 (mm) cc_final: 0.9175 (mm) REVERT: A 290 LEU cc_start: 0.9237 (tp) cc_final: 0.8616 (pp) REVERT: A 295 MET cc_start: 0.9212 (tmm) cc_final: 0.8876 (tmm) REVERT: A 299 GLN cc_start: 0.9550 (mm-40) cc_final: 0.9223 (mm110) REVERT: A 326 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8369 (tm-30) REVERT: A 567 HIS cc_start: 0.7506 (t70) cc_final: 0.7212 (t-90) REVERT: B 145 PHE cc_start: 0.9213 (t80) cc_final: 0.8674 (t80) REVERT: B 191 ILE cc_start: 0.9519 (tp) cc_final: 0.9150 (tt) REVERT: B 196 GLN cc_start: 0.9410 (mm110) cc_final: 0.8828 (mm-40) REVERT: B 219 SER cc_start: 0.7788 (t) cc_final: 0.7276 (p) REVERT: B 231 MET cc_start: 0.9216 (ttm) cc_final: 0.8689 (tpp) REVERT: B 258 LEU cc_start: 0.9477 (tt) cc_final: 0.8943 (tt) REVERT: B 262 LEU cc_start: 0.9184 (mm) cc_final: 0.8886 (mm) REVERT: B 290 LEU cc_start: 0.9278 (tp) cc_final: 0.8736 (pp) REVERT: B 295 MET cc_start: 0.9143 (tmm) cc_final: 0.8764 (tmm) REVERT: B 299 GLN cc_start: 0.9504 (mm-40) cc_final: 0.9202 (mm110) REVERT: B 326 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: B 433 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8910 (mt-10) REVERT: B 471 GLU cc_start: 0.9096 (tt0) cc_final: 0.8599 (tp30) REVERT: B 567 HIS cc_start: 0.7889 (t70) cc_final: 0.7484 (t70) outliers start: 37 outliers final: 28 residues processed: 218 average time/residue: 0.1512 time to fit residues: 49.6791 Evaluate side-chains 219 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 255 SER 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 430 THR 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 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 363 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 110 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.103634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079033 restraints weight = 24797.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082181 restraints weight = 13733.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084383 restraints weight = 9235.444| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8995 Z= 0.161 Angle : 0.752 12.731 12184 Z= 0.358 Chirality : 0.043 0.203 1469 Planarity : 0.004 0.045 1518 Dihedral : 7.761 81.601 1287 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.53 % Allowed : 29.63 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.25), residues: 1133 helix: -0.15 (0.22), residues: 612 sheet: -0.40 (0.70), residues: 50 loop : -2.02 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.003 0.001 HIS B 141 PHE 0.011 0.001 PHE B 286 TYR 0.011 0.001 TYR A 408 ARG 0.002 0.000 ARG A 528 *********************** 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 235 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9283 (mt0) cc_final: 0.8859 (mt0) REVERT: A 145 PHE cc_start: 0.9019 (t80) cc_final: 0.8733 (t80) REVERT: A 162 MET cc_start: 0.7435 (tpp) cc_final: 0.6907 (tpp) REVERT: A 191 ILE cc_start: 0.9449 (tp) cc_final: 0.9044 (tt) REVERT: A 196 GLN cc_start: 0.9300 (mm110) cc_final: 0.8872 (mm-40) REVERT: A 210 LEU cc_start: 0.9609 (tp) cc_final: 0.9341 (tp) REVERT: A 219 SER cc_start: 0.7792 (t) cc_final: 0.7241 (p) REVERT: A 247 GLN cc_start: 0.9306 (tp-100) cc_final: 0.9068 (tp40) REVERT: A 290 LEU cc_start: 0.9255 (tp) cc_final: 0.8621 (pp) REVERT: A 295 MET cc_start: 0.9211 (tmm) cc_final: 0.8894 (tmm) REVERT: A 299 GLN cc_start: 0.9537 (mm-40) cc_final: 0.9212 (mm110) REVERT: A 319 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9029 (tp30) REVERT: A 326 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: A 441 ARG cc_start: 0.8244 (ptp90) cc_final: 0.8008 (ptp90) REVERT: A 567 HIS cc_start: 0.7466 (t70) cc_final: 0.7144 (t-90) REVERT: B 145 PHE cc_start: 0.9220 (t80) cc_final: 0.8672 (t80) REVERT: B 191 ILE cc_start: 0.9458 (tp) cc_final: 0.9081 (tt) REVERT: B 196 GLN cc_start: 0.9390 (mm110) cc_final: 0.8626 (mm-40) REVERT: B 219 SER cc_start: 0.7705 (t) cc_final: 0.7195 (p) REVERT: B 258 LEU cc_start: 0.9484 (tt) cc_final: 0.8943 (tt) REVERT: B 262 LEU cc_start: 0.9122 (mm) cc_final: 0.8836 (mm) REVERT: B 290 LEU cc_start: 0.9277 (tp) cc_final: 0.8704 (pp) REVERT: B 295 MET cc_start: 0.9142 (tmm) cc_final: 0.8780 (tmm) REVERT: B 299 GLN cc_start: 0.9501 (mm-40) cc_final: 0.9197 (mm110) REVERT: B 326 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 471 GLU cc_start: 0.9074 (tt0) cc_final: 0.8617 (tp30) REVERT: B 567 HIS cc_start: 0.7913 (t70) cc_final: 0.7558 (t70) outliers start: 34 outliers final: 29 residues processed: 217 average time/residue: 0.1742 time to fit residues: 56.6333 Evaluate side-chains 223 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 255 SER 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 334 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET 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 A residue 580 MET 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 346 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 427 MET 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 17 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 0.0060 chunk 73 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.103500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.076914 restraints weight = 25626.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080082 restraints weight = 14209.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082246 restraints weight = 9615.956| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8995 Z= 0.194 Angle : 0.768 10.971 12184 Z= 0.371 Chirality : 0.044 0.248 1469 Planarity : 0.004 0.046 1518 Dihedral : 7.745 80.628 1287 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.85 % Allowed : 30.04 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1133 helix: -0.04 (0.22), residues: 618 sheet: -0.44 (0.71), residues: 50 loop : -2.03 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 413 HIS 0.003 0.001 HIS B 141 PHE 0.008 0.001 PHE A 348 TYR 0.014 0.001 TYR B 350 ARG 0.004 0.000 ARG B 432 *********************** 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 234 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 1.011 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: 0.9269 (mt0) cc_final: 0.8861 (mt0) REVERT: A 145 PHE cc_start: 0.9016 (t80) cc_final: 0.8739 (t80) REVERT: A 162 MET cc_start: 0.7616 (tpp) cc_final: 0.7173 (tpp) REVERT: A 191 ILE cc_start: 0.9448 (tp) cc_final: 0.9025 (tt) REVERT: A 196 GLN cc_start: 0.9409 (mm110) cc_final: 0.8878 (mm-40) REVERT: A 210 LEU cc_start: 0.9611 (tp) cc_final: 0.9348 (tp) REVERT: A 219 SER cc_start: 0.7893 (t) cc_final: 0.7383 (p) REVERT: A 247 GLN cc_start: 0.9296 (tp-100) cc_final: 0.8961 (tp40) REVERT: A 290 LEU cc_start: 0.9289 (tp) cc_final: 0.8651 (pp) REVERT: A 295 MET cc_start: 0.9208 (tmm) cc_final: 0.8874 (tmm) REVERT: A 299 GLN cc_start: 0.9549 (mm-40) cc_final: 0.9232 (mm110) REVERT: A 319 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9046 (tp30) REVERT: A 326 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8113 (pp20) REVERT: A 567 HIS cc_start: 0.7528 (t70) cc_final: 0.7235 (t-90) REVERT: B 122 GLU cc_start: 0.8464 (tt0) cc_final: 0.7353 (tp30) REVERT: B 145 PHE cc_start: 0.9241 (t80) cc_final: 0.8706 (t80) REVERT: B 191 ILE cc_start: 0.9458 (tp) cc_final: 0.9060 (tt) REVERT: B 196 GLN cc_start: 0.9437 (mm110) cc_final: 0.8584 (mm-40) REVERT: B 219 SER cc_start: 0.7779 (t) cc_final: 0.7302 (p) REVERT: B 258 LEU cc_start: 0.9494 (tt) cc_final: 0.8918 (tt) REVERT: B 259 MET cc_start: 0.8621 (mmt) cc_final: 0.8306 (mmt) REVERT: B 262 LEU cc_start: 0.9140 (mm) cc_final: 0.8873 (mm) REVERT: B 290 LEU cc_start: 0.9315 (tp) cc_final: 0.8677 (pp) REVERT: B 295 MET cc_start: 0.9166 (tmm) cc_final: 0.8825 (tmm) REVERT: B 299 GLN cc_start: 0.9513 (mm-40) cc_final: 0.9215 (mm110) REVERT: B 326 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8205 (pp20) REVERT: B 471 GLU cc_start: 0.9125 (tt0) cc_final: 0.8736 (tp30) REVERT: B 567 HIS cc_start: 0.7933 (t70) cc_final: 0.7682 (t70) outliers start: 37 outliers final: 34 residues processed: 219 average time/residue: 0.1724 time to fit residues: 57.2789 Evaluate side-chains 227 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 255 SER 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 334 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET 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 A residue 580 MET 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 206 LEU Chi-restraints excluded: chain B residue 207 ASN 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 363 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 529 THR Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3726 > 50: distance: 18 - 36: 19.645 distance: 23 - 41: 23.785 distance: 32 - 36: 20.273 distance: 36 - 37: 11.749 distance: 37 - 38: 7.149 distance: 37 - 40: 7.478 distance: 38 - 39: 21.447 distance: 38 - 41: 9.347 distance: 41 - 42: 24.802 distance: 42 - 43: 22.993 distance: 43 - 44: 31.894 distance: 43 - 45: 23.324 distance: 45 - 46: 13.023 distance: 46 - 47: 12.582 distance: 46 - 49: 11.893 distance: 47 - 48: 15.903 distance: 47 - 53: 21.964 distance: 48 - 76: 23.557 distance: 49 - 50: 23.487 distance: 50 - 51: 22.971 distance: 50 - 52: 8.605 distance: 53 - 54: 5.538 distance: 54 - 55: 18.887 distance: 54 - 57: 9.711 distance: 55 - 56: 12.724 distance: 55 - 59: 10.748 distance: 56 - 81: 23.115 distance: 57 - 58: 41.310 distance: 59 - 60: 14.008 distance: 60 - 61: 30.394 distance: 60 - 63: 23.230 distance: 61 - 62: 17.154 distance: 61 - 64: 18.026 distance: 62 - 88: 39.086 distance: 64 - 65: 7.696 distance: 65 - 66: 7.446 distance: 65 - 68: 15.447 distance: 66 - 67: 13.325 distance: 66 - 76: 13.965 distance: 67 - 100: 41.924 distance: 68 - 69: 12.800 distance: 69 - 70: 6.521 distance: 69 - 71: 24.513 distance: 70 - 72: 18.274 distance: 71 - 73: 19.403 distance: 72 - 74: 25.729 distance: 73 - 74: 8.417 distance: 74 - 75: 16.601 distance: 77 - 78: 10.136 distance: 77 - 80: 13.785 distance: 78 - 79: 25.532 distance: 78 - 81: 17.162 distance: 79 - 105: 29.573 distance: 81 - 82: 16.002 distance: 82 - 83: 16.781 distance: 82 - 85: 11.246 distance: 83 - 84: 25.664 distance: 83 - 88: 21.385 distance: 84 - 112: 36.583 distance: 85 - 86: 26.358 distance: 85 - 87: 25.627 distance: 88 - 89: 3.612 distance: 89 - 90: 27.703 distance: 89 - 92: 28.253 distance: 90 - 91: 20.632 distance: 90 - 100: 18.795 distance: 91 - 118: 29.846 distance: 92 - 93: 18.410 distance: 93 - 94: 21.028 distance: 93 - 95: 25.699 distance: 94 - 96: 9.806 distance: 96 - 98: 20.213 distance: 97 - 98: 22.080 distance: 98 - 99: 9.933 distance: 100 - 101: 15.149 distance: 101 - 102: 15.239 distance: 101 - 104: 14.679 distance: 102 - 103: 5.761 distance: 102 - 105: 23.077 distance: 103 - 125: 23.443