Starting phenix.real_space_refine on Sat Aug 23 18:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh2_40031/08_2025/8gh2_40031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh2_40031/08_2025/8gh2_40031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh2_40031/08_2025/8gh2_40031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh2_40031/08_2025/8gh2_40031.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh2_40031/08_2025/8gh2_40031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh2_40031/08_2025/8gh2_40031.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8812 2.51 5 N 2465 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13941 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "C" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299} Chain: "D" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299} Chain: "F" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2352 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2029 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain breaks: 1 Time building chain proxies: 3.61, per 1000 atoms: 0.26 Number of scatterers: 13941 At special positions: 0 Unit cell: (102.34, 119.54, 155.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2583 8.00 N 2465 7.00 C 8812 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=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 817.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3404 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 55.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 95 through 116 removed outlier: 3.834A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix removed outlier: 3.622A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.014A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.996A pdb=" N ILE A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.549A pdb=" N LYS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.729A pdb=" N GLY A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 316 removed outlier: 3.645A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.970A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.646A pdb=" N THR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 116 removed outlier: 3.729A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix removed outlier: 4.129A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.827A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 203 through 226 removed outlier: 4.042A pdb=" N GLU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.992A pdb=" N LYS C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.668A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 97 through 116 removed outlier: 4.458A pdb=" N ASN B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.904A pdb=" N THR B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.001A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 232 through 252 removed outlier: 3.744A pdb=" N ALA B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 323 removed outlier: 4.216A pdb=" N GLU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N MET B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 38 through 46 removed outlier: 3.618A pdb=" N VAL D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.195A pdb=" N LEU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 76' Processing helix chain 'D' and resid 97 through 113 removed outlier: 4.392A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.590A pdb=" N ILE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.650A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 252 removed outlier: 3.783A pdb=" N GLY D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 removed outlier: 3.742A pdb=" N MET D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 346 removed outlier: 4.617A pdb=" N ARG F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR F 332 " --> pdb=" O TRP F 328 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 369 Processing helix chain 'F' and resid 376 through 387 removed outlier: 3.726A pdb=" N LEU F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.528A pdb=" N TRP F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU F 399 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY F 400 " --> pdb=" O TRP F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 421 removed outlier: 4.355A pdb=" N ILE F 414 " --> pdb=" O CYS F 410 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 440 removed outlier: 3.963A pdb=" N VAL F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 440 " --> pdb=" O SER F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 456 removed outlier: 3.711A pdb=" N ALA F 446 " --> pdb=" O ASN F 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 447 " --> pdb=" O VAL F 443 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F 448 " --> pdb=" O GLY F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 502 Processing helix chain 'F' and resid 510 through 524 removed outlier: 3.632A pdb=" N SER F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 539 removed outlier: 3.659A pdb=" N LYS F 532 " --> pdb=" O ASP F 528 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU F 539 " --> pdb=" O ARG F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 557 removed outlier: 4.024A pdb=" N TRP F 548 " --> pdb=" O ASP F 544 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR F 554 " --> pdb=" O LYS F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 575 removed outlier: 3.756A pdb=" N GLU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG F 570 " --> pdb=" O GLU F 566 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP F 573 " --> pdb=" O ASN F 569 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 592 Processing helix chain 'F' and resid 594 through 610 Processing helix chain 'F' and resid 620 through 623 removed outlier: 4.319A pdb=" N ALA F 623 " --> pdb=" O SER F 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 624 through 632 removed outlier: 3.704A pdb=" N LEU F 630 " --> pdb=" O GLY F 626 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 639 removed outlier: 4.014A pdb=" N MET F 638 " --> pdb=" O THR F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 648 removed outlier: 3.911A pdb=" N SER F 647 " --> pdb=" O VAL F 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 362 through 370 removed outlier: 3.813A pdb=" N LEU E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 387 removed outlier: 4.172A pdb=" N ALA E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 406 Processing helix chain 'E' and resid 410 through 423 removed outlier: 4.115A pdb=" N ILE E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS E 418 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 441 removed outlier: 3.825A pdb=" N VAL E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU E 440 " --> pdb=" O SER E 436 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS E 441 " --> pdb=" O HIS E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 456 removed outlier: 3.741A pdb=" N SER E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.594A pdb=" N SER E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 removed outlier: 3.560A pdb=" N ALA E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS E 532 " --> pdb=" O ASP E 528 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASN E 533 " --> pdb=" O GLU E 529 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU E 539 " --> pdb=" O ARG E 535 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 540 " --> pdb=" O ARG E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 558 removed outlier: 4.031A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU E 551 " --> pdb=" O MET E 547 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 566 Processing helix chain 'E' and resid 570 through 574 Processing helix chain 'E' and resid 578 through 593 Processing helix chain 'E' and resid 596 through 610 removed outlier: 3.856A pdb=" N LYS E 600 " --> pdb=" O PRO E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 625 Processing helix chain 'E' and resid 626 through 638 removed outlier: 3.653A pdb=" N LEU E 630 " --> pdb=" O GLY E 626 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 636 " --> pdb=" O ARG E 632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.571A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 263 removed outlier: 3.890A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 57 through 58 removed outlier: 6.636A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C 4 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR C 34 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 6 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN C 3 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL C 83 " --> pdb=" O ASN C 3 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 5 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 257 through 263 removed outlier: 4.253A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET C 275 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG C 286 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY C 280 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.263A pdb=" N ASP B 35 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 32 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 82 " --> pdb=" O CYS B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.781A pdb=" N VAL B 182 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 191 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 257 through 262 removed outlier: 5.544A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 283 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 54 through 56 removed outlier: 3.569A pdb=" N THR D 55 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL D 4 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 81 " --> pdb=" O ASN D 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'D' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 260 removed outlier: 3.634A pdb=" N ALA D 260 " --> pdb=" O MET D 275 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET D 275 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG D 286 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY D 280 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1830 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: 2.02 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3886 1.33 - 1.46: 2154 1.46 - 1.58: 8020 1.58 - 1.70: 1 1.70 - 1.82: 140 Bond restraints: 14201 Sorted by residual: bond pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 1.522 1.480 0.043 1.40e-02 5.10e+03 9.36e+00 bond pdb=" CA VAL D 179 " pdb=" C VAL D 179 " ideal model delta sigma weight residual 1.522 1.501 0.021 7.10e-03 1.98e+04 8.56e+00 bond pdb=" CA TYR D 259 " pdb=" C TYR D 259 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.08e-02 8.57e+03 8.47e+00 bond pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 1.458 1.425 0.033 1.17e-02 7.31e+03 8.04e+00 bond pdb=" CA TYR D 261 " pdb=" C TYR D 261 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.51e-02 4.39e+03 7.88e+00 ... (remaining 14196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 18814 2.21 - 4.43: 425 4.43 - 6.64: 63 6.64 - 8.85: 16 8.85 - 11.07: 4 Bond angle restraints: 19322 Sorted by residual: angle pdb=" N LEU D 158 " pdb=" CA LEU D 158 " pdb=" C LEU D 158 " ideal model delta sigma weight residual 111.75 104.40 7.35 1.28e+00 6.10e-01 3.30e+01 angle pdb=" C THR D 127 " pdb=" N ASN D 128 " pdb=" CA ASN D 128 " ideal model delta sigma weight residual 121.61 128.44 -6.83 1.39e+00 5.18e-01 2.41e+01 angle pdb=" N GLN D 196 " pdb=" CA GLN D 196 " pdb=" C GLN D 196 " ideal model delta sigma weight residual 112.41 106.34 6.07 1.30e+00 5.92e-01 2.18e+01 angle pdb=" C HIS C 172 " pdb=" CA HIS C 172 " pdb=" CB HIS C 172 " ideal model delta sigma weight residual 110.17 119.26 -9.09 1.97e+00 2.58e-01 2.13e+01 angle pdb=" C GLY A 38 " pdb=" N ALA A 39 " pdb=" CA ALA A 39 " ideal model delta sigma weight residual 121.80 132.87 -11.07 2.44e+00 1.68e-01 2.06e+01 ... (remaining 19317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7782 17.88 - 35.77: 700 35.77 - 53.65: 148 53.65 - 71.54: 31 71.54 - 89.42: 15 Dihedral angle restraints: 8676 sinusoidal: 3390 harmonic: 5286 Sorted by residual: dihedral pdb=" CA HIS C 172 " pdb=" C HIS C 172 " pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta harmonic sigma weight residual 180.00 -128.08 -51.92 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ASN F 354 " pdb=" C ASN F 354 " pdb=" N PRO F 355 " pdb=" CA PRO F 355 " ideal model delta harmonic sigma weight residual 180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG B 96 " pdb=" C ARG B 96 " pdb=" N ASP B 97 " pdb=" CA ASP B 97 " ideal model delta harmonic sigma weight residual -180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1717 0.045 - 0.091: 412 0.091 - 0.136: 128 0.136 - 0.181: 12 0.181 - 0.227: 4 Chirality restraints: 2273 Sorted by residual: chirality pdb=" CB ILE F 622 " pdb=" CA ILE F 622 " pdb=" CG1 ILE F 622 " pdb=" CG2 ILE F 622 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA HIS D 172 " pdb=" N HIS D 172 " pdb=" C HIS D 172 " pdb=" CB HIS D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS A 172 " pdb=" N HIS A 172 " pdb=" C HIS A 172 " pdb=" CB HIS A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2270 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 172 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 173 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 354 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO F 355 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 156 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER D 156 " 0.065 2.00e-02 2.50e+03 pdb=" O SER D 156 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D 157 " -0.022 2.00e-02 2.50e+03 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2305 2.76 - 3.30: 14370 3.30 - 3.83: 22394 3.83 - 4.37: 24736 4.37 - 4.90: 42172 Nonbonded interactions: 105977 Sorted by model distance: nonbonded pdb=" O GLU A 316 " pdb=" OG1 THR A 317 " model vdw 2.227 3.040 nonbonded pdb=" O VAL E 342 " pdb=" OG1 THR E 346 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN D 3 " pdb=" OG1 THR D 30 " model vdw 2.266 3.040 nonbonded pdb=" O ILE F 367 " pdb=" NE2 GLN F 371 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASP D 50 " pdb=" N ARG D 51 " model vdw 2.288 3.120 ... (remaining 105972 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 336 through 459 or resid 515 through 648)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.770 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.004 0.064 14201 Z= 0.244 Angle : 0.782 11.066 19322 Z= 0.435 Chirality : 0.044 0.227 2273 Planarity : 0.006 0.117 2522 Dihedral : 14.741 89.425 5272 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.93 % Allowed : 12.13 % Favored : 86.94 % Rotamer: Outliers : 2.14 % Allowed : 1.20 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.21), residues: 1830 helix: 0.27 (0.19), residues: 889 sheet: -1.60 (0.48), residues: 135 loop : -2.33 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 535 TYR 0.034 0.002 TYR E 358 PHE 0.012 0.001 PHE F 534 TRP 0.027 0.002 TRP E 648 HIS 0.010 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00375 (14201) covalent geometry : angle 0.78199 (19322) hydrogen bonds : bond 0.20246 ( 624) hydrogen bonds : angle 6.74656 ( 1830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 LEU cc_start: 0.7939 (tt) cc_final: 0.7315 (mp) REVERT: C 235 MET cc_start: 0.6879 (mtp) cc_final: 0.6651 (mtp) REVERT: C 261 TYR cc_start: 0.8782 (t80) cc_final: 0.8391 (t80) REVERT: D 46 LEU cc_start: 0.7948 (mm) cc_final: 0.7197 (pp) REVERT: E 382 PHE cc_start: 0.7361 (m-80) cc_final: 0.7121 (m-80) outliers start: 32 outliers final: 4 residues processed: 238 average time/residue: 0.1185 time to fit residues: 41.6622 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 169 ASN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN F 371 GLN F 549 ASN F 584 ASN E 614 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077054 restraints weight = 45924.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079145 restraints weight = 23289.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080509 restraints weight = 14591.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081409 restraints weight = 10602.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081983 restraints weight = 8562.067| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14201 Z= 0.148 Angle : 0.698 11.223 19322 Z= 0.346 Chirality : 0.044 0.219 2273 Planarity : 0.006 0.108 2522 Dihedral : 5.132 58.282 1992 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.15 % Favored : 88.31 % Rotamer: Outliers : 1.34 % Allowed : 9.89 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.21), residues: 1830 helix: 0.62 (0.18), residues: 929 sheet: -1.64 (0.48), residues: 135 loop : -2.30 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 320 TYR 0.018 0.002 TYR E 568 PHE 0.022 0.002 PHE E 382 TRP 0.020 0.002 TRP E 648 HIS 0.010 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00336 (14201) covalent geometry : angle 0.69790 (19322) hydrogen bonds : bond 0.04445 ( 624) hydrogen bonds : angle 4.70060 ( 1830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7250 (mmp-170) REVERT: C 172 HIS cc_start: 0.7620 (t70) cc_final: 0.7418 (t70) REVERT: C 207 LEU cc_start: 0.8005 (tt) cc_final: 0.7338 (mp) REVERT: C 235 MET cc_start: 0.7120 (mtp) cc_final: 0.6799 (mtp) REVERT: C 261 TYR cc_start: 0.8791 (t80) cc_final: 0.8534 (t80) REVERT: C 320 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7497 (ptt-90) REVERT: D 50 ASP cc_start: 0.8298 (p0) cc_final: 0.8056 (p0) REVERT: D 190 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6140 (mt) REVERT: F 369 MET cc_start: 0.6470 (ttt) cc_final: 0.6180 (ttt) REVERT: F 629 ASP cc_start: 0.8193 (m-30) cc_final: 0.7930 (m-30) REVERT: F 638 MET cc_start: 0.8803 (mmm) cc_final: 0.8525 (mpp) outliers start: 20 outliers final: 13 residues processed: 188 average time/residue: 0.1074 time to fit residues: 31.0743 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain D residue 178 TYR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain E residue 358 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 122 optimal weight: 8.9990 chunk 110 optimal weight: 0.0470 chunk 152 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074486 restraints weight = 46771.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076533 restraints weight = 24020.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077849 restraints weight = 15190.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078722 restraints weight = 11134.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079298 restraints weight = 9035.333| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14201 Z= 0.146 Angle : 0.672 11.262 19322 Z= 0.333 Chirality : 0.044 0.247 2273 Planarity : 0.005 0.109 2522 Dihedral : 5.064 56.265 1991 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.37 % Favored : 88.09 % Rotamer: Outliers : 2.27 % Allowed : 12.63 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.21), residues: 1830 helix: 0.76 (0.18), residues: 935 sheet: -1.67 (0.45), residues: 148 loop : -2.34 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 604 TYR 0.014 0.001 TYR F 568 PHE 0.025 0.002 PHE C 100 TRP 0.015 0.001 TRP E 648 HIS 0.007 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00342 (14201) covalent geometry : angle 0.67211 (19322) hydrogen bonds : bond 0.03896 ( 624) hydrogen bonds : angle 4.38484 ( 1830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6621 (tpt) cc_final: 0.6306 (tpp) REVERT: C 261 TYR cc_start: 0.8824 (t80) cc_final: 0.8582 (t80) REVERT: C 320 ARG cc_start: 0.7940 (ptt-90) cc_final: 0.7563 (ptt-90) REVERT: B 63 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6575 (mm) REVERT: D 50 ASP cc_start: 0.8435 (p0) cc_final: 0.8231 (p0) REVERT: D 190 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6156 (mm) REVERT: D 191 VAL cc_start: 0.8312 (t) cc_final: 0.8059 (t) REVERT: F 585 MET cc_start: 0.8997 (mmm) cc_final: 0.8784 (mmm) REVERT: F 629 ASP cc_start: 0.8169 (m-30) cc_final: 0.7708 (m-30) REVERT: E 548 TRP cc_start: 0.7049 (p90) cc_final: 0.5916 (p90) REVERT: E 597 LEU cc_start: 0.8991 (pt) cc_final: 0.8611 (mm) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.1070 time to fit residues: 28.9997 Evaluate side-chains 160 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain E residue 358 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 108 optimal weight: 0.4980 chunk 151 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN F 549 ASN F 584 ASN ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069589 restraints weight = 47418.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071500 restraints weight = 24323.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072757 restraints weight = 15489.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073581 restraints weight = 11392.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074126 restraints weight = 9276.705| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14201 Z= 0.245 Angle : 0.770 11.197 19322 Z= 0.389 Chirality : 0.047 0.280 2273 Planarity : 0.006 0.111 2522 Dihedral : 5.490 58.246 1991 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.17 % Favored : 86.28 % Rotamer: Outliers : 3.14 % Allowed : 14.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.20), residues: 1830 helix: 0.39 (0.17), residues: 941 sheet: -2.08 (0.43), residues: 151 loop : -2.48 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 536 TYR 0.019 0.002 TYR D 261 PHE 0.022 0.002 PHE A 27 TRP 0.018 0.002 TRP F 628 HIS 0.011 0.002 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00579 (14201) covalent geometry : angle 0.76966 (19322) hydrogen bonds : bond 0.04941 ( 624) hydrogen bonds : angle 4.78959 ( 1830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6679 (tpt) cc_final: 0.6423 (tpp) REVERT: C 172 HIS cc_start: 0.7720 (t70) cc_final: 0.7411 (t70) REVERT: C 320 ARG cc_start: 0.7979 (ptt-90) cc_final: 0.7594 (ptt-90) REVERT: D 1 MET cc_start: 0.7681 (tpt) cc_final: 0.7169 (tpp) REVERT: D 51 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7451 (tpt-90) REVERT: D 188 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.9000 (p) REVERT: F 375 MET cc_start: 0.8222 (ppp) cc_final: 0.7984 (ppp) REVERT: F 585 MET cc_start: 0.9143 (mmm) cc_final: 0.8797 (mmm) REVERT: F 629 ASP cc_start: 0.8310 (m-30) cc_final: 0.7778 (m-30) REVERT: E 382 PHE cc_start: 0.7820 (m-10) cc_final: 0.7509 (m-80) REVERT: E 425 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8523 (mmmt) REVERT: E 548 TRP cc_start: 0.7016 (p90) cc_final: 0.5898 (p90) outliers start: 47 outliers final: 32 residues processed: 174 average time/residue: 0.1134 time to fit residues: 30.1677 Evaluate side-chains 163 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 554 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 177 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 549 ASN F 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073101 restraints weight = 46267.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075129 restraints weight = 23290.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076436 restraints weight = 14616.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077304 restraints weight = 10631.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077866 restraints weight = 8577.183| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14201 Z= 0.123 Angle : 0.671 11.367 19322 Z= 0.331 Chirality : 0.044 0.269 2273 Planarity : 0.005 0.111 2522 Dihedral : 5.143 59.682 1991 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.66 % Favored : 88.80 % Rotamer: Outliers : 2.81 % Allowed : 16.98 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.21), residues: 1830 helix: 0.80 (0.18), residues: 937 sheet: -1.74 (0.43), residues: 166 loop : -2.28 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.017 0.002 TYR E 348 PHE 0.011 0.001 PHE C 318 TRP 0.014 0.001 TRP E 648 HIS 0.012 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00285 (14201) covalent geometry : angle 0.67119 (19322) hydrogen bonds : bond 0.03514 ( 624) hydrogen bonds : angle 4.23961 ( 1830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7394 (mmp-170) cc_final: 0.5924 (mmt180) REVERT: C 216 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8520 (t) REVERT: C 235 MET cc_start: 0.7266 (mtp) cc_final: 0.6900 (mtp) REVERT: C 320 ARG cc_start: 0.7933 (ptt-90) cc_final: 0.7502 (ptt-90) REVERT: B 63 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6870 (mm) REVERT: B 96 ARG cc_start: 0.8027 (ptm160) cc_final: 0.7799 (ptm160) REVERT: D 51 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6904 (tpt-90) REVERT: F 585 MET cc_start: 0.8975 (mmm) cc_final: 0.8677 (mmm) REVERT: F 629 ASP cc_start: 0.8229 (m-30) cc_final: 0.7876 (m-30) REVERT: E 356 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5393 (m-80) REVERT: E 382 PHE cc_start: 0.7700 (m-10) cc_final: 0.7481 (m-10) REVERT: E 425 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8510 (mmmt) REVERT: E 597 LEU cc_start: 0.9033 (pt) cc_final: 0.8623 (mm) outliers start: 42 outliers final: 25 residues processed: 181 average time/residue: 0.1075 time to fit residues: 29.7962 Evaluate side-chains 168 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 608 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 132 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN F 562 GLN F 584 ASN ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070949 restraints weight = 46702.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072915 restraints weight = 23923.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074198 restraints weight = 15177.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075052 restraints weight = 11096.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075551 restraints weight = 8997.433| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14201 Z= 0.177 Angle : 0.718 11.217 19322 Z= 0.357 Chirality : 0.046 0.287 2273 Planarity : 0.006 0.112 2522 Dihedral : 5.213 59.506 1991 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.80 % Favored : 87.65 % Rotamer: Outliers : 2.81 % Allowed : 17.51 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.21), residues: 1830 helix: 0.72 (0.18), residues: 942 sheet: -2.07 (0.43), residues: 147 loop : -2.37 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 536 TYR 0.018 0.002 TYR E 356 PHE 0.015 0.002 PHE A 27 TRP 0.014 0.001 TRP E 648 HIS 0.013 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00421 (14201) covalent geometry : angle 0.71827 (19322) hydrogen bonds : bond 0.04063 ( 624) hydrogen bonds : angle 4.44261 ( 1830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: B 96 ARG cc_start: 0.8047 (ptm160) cc_final: 0.7781 (ptm160) REVERT: D 51 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7257 (tpt-90) REVERT: D 159 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: F 375 MET cc_start: 0.8162 (ppp) cc_final: 0.7914 (ppp) REVERT: F 585 MET cc_start: 0.8919 (mmm) cc_final: 0.8638 (mmm) REVERT: F 629 ASP cc_start: 0.8267 (m-30) cc_final: 0.7742 (m-30) REVERT: E 382 PHE cc_start: 0.7787 (m-10) cc_final: 0.7501 (m-10) REVERT: E 425 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8504 (mmmt) outliers start: 42 outliers final: 31 residues processed: 171 average time/residue: 0.1112 time to fit residues: 28.7318 Evaluate side-chains 164 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 554 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 96 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 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 = 0.3623 r_free = 0.3623 target = 0.093068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071883 restraints weight = 46396.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073869 restraints weight = 23747.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075186 restraints weight = 15025.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076039 restraints weight = 10987.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076602 restraints weight = 8898.688| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14201 Z= 0.145 Angle : 0.701 14.614 19322 Z= 0.345 Chirality : 0.045 0.293 2273 Planarity : 0.006 0.112 2522 Dihedral : 5.175 59.686 1991 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.20 % Favored : 88.25 % Rotamer: Outliers : 2.41 % Allowed : 18.25 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.21), residues: 1830 helix: 0.82 (0.18), residues: 943 sheet: -1.94 (0.43), residues: 147 loop : -2.34 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.017 0.001 TYR E 356 PHE 0.012 0.001 PHE E 527 TRP 0.016 0.001 TRP E 648 HIS 0.016 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00347 (14201) covalent geometry : angle 0.70071 (19322) hydrogen bonds : bond 0.03666 ( 624) hydrogen bonds : angle 4.30578 ( 1830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: C 235 MET cc_start: 0.7313 (mtp) cc_final: 0.6929 (mtp) REVERT: D 51 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6957 (tpt-90) REVERT: D 159 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: F 375 MET cc_start: 0.8109 (ppp) cc_final: 0.7889 (ppp) REVERT: F 625 ARG cc_start: 0.5574 (tpt170) cc_final: 0.5087 (tpt170) REVERT: F 629 ASP cc_start: 0.8259 (m-30) cc_final: 0.7708 (m-30) REVERT: E 382 PHE cc_start: 0.7834 (m-10) cc_final: 0.7572 (m-80) REVERT: E 425 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8510 (mmmt) outliers start: 36 outliers final: 28 residues processed: 162 average time/residue: 0.1097 time to fit residues: 26.9624 Evaluate side-chains 165 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 441 HIS Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 172 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 52 optimal weight: 6.9990 chunk 143 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 108 optimal weight: 0.0470 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN F 584 ASN E 546 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.095807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074658 restraints weight = 46061.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076719 restraints weight = 23483.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078047 restraints weight = 14767.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078936 restraints weight = 10787.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079443 restraints weight = 8711.645| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14201 Z= 0.120 Angle : 0.695 14.492 19322 Z= 0.339 Chirality : 0.045 0.308 2273 Planarity : 0.005 0.112 2522 Dihedral : 4.987 59.627 1991 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.33 % Favored : 89.13 % Rotamer: Outliers : 2.27 % Allowed : 19.05 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.21), residues: 1830 helix: 1.03 (0.18), residues: 931 sheet: -1.67 (0.42), residues: 170 loop : -2.13 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.015 0.001 TYR E 358 PHE 0.012 0.001 PHE E 527 TRP 0.020 0.001 TRP E 648 HIS 0.017 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00272 (14201) covalent geometry : angle 0.69518 (19322) hydrogen bonds : bond 0.03057 ( 624) hydrogen bonds : angle 4.07662 ( 1830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7492 (mmp-170) cc_final: 0.5914 (mmt180) REVERT: C 235 MET cc_start: 0.7259 (mtp) cc_final: 0.7002 (mtp) REVERT: B 24 GLU cc_start: 0.8720 (tp30) cc_final: 0.8498 (tp30) REVERT: B 63 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6949 (mm) REVERT: D 51 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6423 (tpt-90) REVERT: D 159 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: F 585 MET cc_start: 0.8953 (mmm) cc_final: 0.8560 (mmm) REVERT: F 625 ARG cc_start: 0.5514 (tpt170) cc_final: 0.5294 (tpt170) REVERT: F 629 ASP cc_start: 0.8206 (m-30) cc_final: 0.7958 (m-30) REVERT: E 382 PHE cc_start: 0.7816 (m-10) cc_final: 0.7566 (m-10) REVERT: E 595 TYR cc_start: 0.6953 (m-80) cc_final: 0.6725 (m-80) REVERT: E 597 LEU cc_start: 0.9102 (pt) cc_final: 0.8723 (mm) outliers start: 34 outliers final: 26 residues processed: 177 average time/residue: 0.1099 time to fit residues: 29.5004 Evaluate side-chains 171 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 441 HIS Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 154 optimal weight: 5.9990 chunk 11 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073905 restraints weight = 46632.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075954 restraints weight = 23793.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077291 restraints weight = 15009.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.078169 restraints weight = 10926.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078739 restraints weight = 8813.124| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14201 Z= 0.124 Angle : 0.706 16.886 19322 Z= 0.342 Chirality : 0.045 0.314 2273 Planarity : 0.005 0.115 2522 Dihedral : 4.969 59.872 1991 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.49 % Favored : 89.02 % Rotamer: Outliers : 1.87 % Allowed : 19.72 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.21), residues: 1830 helix: 1.05 (0.18), residues: 936 sheet: -1.52 (0.43), residues: 161 loop : -2.19 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.016 0.001 TYR E 356 PHE 0.012 0.001 PHE E 527 TRP 0.010 0.001 TRP E 648 HIS 0.021 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00295 (14201) covalent geometry : angle 0.70592 (19322) hydrogen bonds : bond 0.03260 ( 624) hydrogen bonds : angle 4.10560 ( 1830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7236 (mtp) cc_final: 0.6942 (mtp) REVERT: C 261 TYR cc_start: 0.8822 (t80) cc_final: 0.8553 (t80) REVERT: B 24 GLU cc_start: 0.8744 (tp30) cc_final: 0.8436 (tp30) REVERT: B 63 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6886 (mm) REVERT: B 320 ARG cc_start: 0.7794 (mmp80) cc_final: 0.7448 (mmp80) REVERT: D 51 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6494 (tpt-90) REVERT: D 159 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: F 625 ARG cc_start: 0.5529 (tpt170) cc_final: 0.5189 (tpt170) REVERT: F 629 ASP cc_start: 0.8246 (m-30) cc_final: 0.7867 (m-30) REVERT: E 382 PHE cc_start: 0.7840 (m-10) cc_final: 0.7615 (m-10) REVERT: E 425 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8454 (mmmt) outliers start: 28 outliers final: 21 residues processed: 166 average time/residue: 0.1080 time to fit residues: 27.2413 Evaluate side-chains 167 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 181 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 131 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN F 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072463 restraints weight = 46653.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.074467 restraints weight = 23941.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075755 restraints weight = 15210.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076640 restraints weight = 11147.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077201 restraints weight = 9007.311| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14201 Z= 0.149 Angle : 0.715 15.660 19322 Z= 0.350 Chirality : 0.045 0.327 2273 Planarity : 0.006 0.119 2522 Dihedral : 5.032 58.749 1991 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.26 % Favored : 88.25 % Rotamer: Outliers : 1.94 % Allowed : 19.79 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.21), residues: 1830 helix: 0.99 (0.18), residues: 943 sheet: -1.77 (0.42), residues: 170 loop : -2.30 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.017 0.001 TYR E 356 PHE 0.013 0.001 PHE A 27 TRP 0.020 0.002 TRP E 648 HIS 0.022 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00356 (14201) covalent geometry : angle 0.71544 (19322) hydrogen bonds : bond 0.03591 ( 624) hydrogen bonds : angle 4.24685 ( 1830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7561 (mmp-170) cc_final: 0.6084 (mmt180) REVERT: C 235 MET cc_start: 0.7286 (mtp) cc_final: 0.6884 (mtp) REVERT: C 261 TYR cc_start: 0.8841 (t80) cc_final: 0.8529 (t80) REVERT: B 320 ARG cc_start: 0.7803 (mmp80) cc_final: 0.7528 (mmp80) REVERT: D 51 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6765 (tpt-90) REVERT: D 159 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: F 625 ARG cc_start: 0.5501 (tpt170) cc_final: 0.5185 (tpt170) REVERT: F 629 ASP cc_start: 0.8310 (m-30) cc_final: 0.7931 (m-30) REVERT: E 425 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8462 (mmmt) REVERT: E 595 TYR cc_start: 0.7440 (m-80) cc_final: 0.7226 (m-80) outliers start: 29 outliers final: 25 residues processed: 161 average time/residue: 0.1005 time to fit residues: 24.4292 Evaluate side-chains 164 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1245 > 50: distance: 34 - 39: 18.512 distance: 39 - 40: 33.128 distance: 39 - 45: 25.588 distance: 40 - 41: 18.683 distance: 40 - 43: 21.590 distance: 41 - 42: 14.994 distance: 41 - 46: 7.972 distance: 43 - 44: 13.604 distance: 44 - 45: 16.847 distance: 46 - 47: 3.677 distance: 47 - 48: 7.232 distance: 47 - 50: 11.336 distance: 48 - 49: 3.351 distance: 48 - 53: 23.281 distance: 50 - 51: 12.663 distance: 50 - 52: 36.094 distance: 53 - 54: 14.569 distance: 54 - 55: 15.451 distance: 54 - 57: 23.277 distance: 55 - 56: 20.325 distance: 55 - 60: 23.303 distance: 57 - 58: 20.301 distance: 57 - 59: 10.873 distance: 60 - 61: 13.719 distance: 61 - 62: 18.577 distance: 62 - 63: 8.708 distance: 62 - 64: 12.168 distance: 64 - 65: 15.439 distance: 65 - 66: 15.337 distance: 66 - 67: 24.251 distance: 66 - 68: 6.205 distance: 68 - 69: 8.320 distance: 69 - 70: 12.115 distance: 69 - 72: 4.440 distance: 70 - 71: 18.272 distance: 70 - 78: 23.273 distance: 72 - 73: 10.421 distance: 73 - 74: 4.962 distance: 73 - 75: 16.768 distance: 74 - 76: 11.593 distance: 75 - 77: 11.188 distance: 76 - 77: 9.421 distance: 78 - 79: 30.729 distance: 79 - 80: 31.671 distance: 79 - 82: 15.087 distance: 80 - 81: 20.418 distance: 80 - 84: 26.076 distance: 81 - 99: 28.378 distance: 82 - 83: 10.533 distance: 84 - 85: 18.532 distance: 85 - 86: 19.688 distance: 85 - 88: 10.681 distance: 86 - 87: 18.616 distance: 86 - 92: 19.606 distance: 87 - 106: 26.739 distance: 88 - 89: 18.135 distance: 89 - 90: 17.025 distance: 89 - 91: 18.818 distance: 92 - 93: 23.638 distance: 93 - 94: 15.117 distance: 93 - 96: 17.824 distance: 94 - 95: 7.665 distance: 94 - 99: 7.034 distance: 96 - 97: 19.435 distance: 96 - 98: 21.570 distance: 99 - 100: 10.820 distance: 100 - 101: 22.542 distance: 100 - 103: 28.405 distance: 101 - 102: 8.670 distance: 101 - 106: 10.596 distance: 103 - 104: 21.540 distance: 103 - 105: 14.473