Starting phenix.real_space_refine on Thu Jul 2 22:34:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w98_21580/07_2026/6w98_21580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w98_21580/07_2026/6w98_21580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w98_21580/07_2026/6w98_21580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w98_21580/07_2026/6w98_21580.map" model { file = "/net/cci-nas-00/data/ceres_data/6w98_21580/07_2026/6w98_21580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w98_21580/07_2026/6w98_21580_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 22 5.16 5 C 6573 2.51 5 N 1810 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10317 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9653 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1312, 9643 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1202} Chain breaks: 6 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 1312, 9643 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1202} Chain breaks: 6 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 9872 Chain: "B" Number of atoms: 605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Conformer: "B" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} bond proxies already assigned to first conformer: 592 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'6OU': 1, 'PNS': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 residue: pdb=" N AASP B 56 " occ=0.60 ... (14 atoms not shown) pdb=" OD2BASP B 56 " occ=0.40 Time building chain proxies: 3.22, per 1000 atoms: 0.31 Number of scatterers: 10317 At special positions: 0 Unit cell: (143.168, 99.687, 95.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 22 16.00 P 2 15.00 O 1908 8.00 N 1810 7.00 C 6573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 703.6 milliseconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 14 sheets defined 39.1% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.553A pdb=" N ALA A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.517A pdb=" N PHE A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.629A pdb=" N ALA A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.616A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.834A pdb=" N THR A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.782A pdb=" N GLU A 148 " --> pdb=" O ILE A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 149 through 167 Proline residue: A 156 - end of helix removed outlier: 3.518A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.630A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 211 through 243 removed outlier: 3.996A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 5.928A pdb=" N TRP A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 288 through 308 removed outlier: 3.502A pdb=" N VAL A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.501A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 3.651A pdb=" N LYS A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 378 removed outlier: 3.661A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.542A pdb=" N HIS A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.567A pdb=" N ILE A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.838A pdb=" N TRP A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.810A pdb=" N ASN A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.093A pdb=" N ALA A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.576A pdb=" N ILE A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.556A pdb=" N ARG A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.695A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.527A pdb=" N ARG A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.703A pdb=" N SER A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR A 733 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 734 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 736 " --> pdb=" O THR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 940 removed outlier: 4.176A pdb=" N LEU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1268 through 1278 Processing helix chain 'A' and resid 1295 through 1310 removed outlier: 3.542A pdb=" N VAL A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1328 removed outlier: 3.735A pdb=" N MET A1315 " --> pdb=" O GLY A1311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A1327 " --> pdb=" O ALA A1323 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1353 removed outlier: 3.689A pdb=" N THR A1336 " --> pdb=" O LEU A1332 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A1339 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A1341 " --> pdb=" O ALA A1337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1385 removed outlier: 3.663A pdb=" N GLN A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A1377 " --> pdb=" O GLN A1373 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 35 through 51 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.784A pdb=" N TYR B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.697A pdb=" N ARG A 455 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 531 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 457 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG A 533 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 459 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY A 566 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 590 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN A 564 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 592 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579 removed outlier: 6.780A pdb=" N VAL A 578 " --> pdb=" O ARG A1061 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1181 through 1182 removed outlier: 3.663A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A1227 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 7.119A pdb=" N ARG A 614 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A 659 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA A 656 " --> pdb=" O GLY A 873 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASP A 875 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 658 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY A 877 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A1163 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG A 928 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 925 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A1135 " --> pdb=" O THR A1122 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A1122 " --> pdb=" O GLN A1135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 708 removed outlier: 3.756A pdb=" N ASN A 704 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A 910 " --> pdb=" O HIS A 858 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A1122 " --> pdb=" O GLN A1135 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A1135 " --> pdb=" O THR A1122 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 925 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714 removed outlier: 6.966A pdb=" N THR A 817 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.865A pdb=" N THR A 774 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 840 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 772 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 842 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 770 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 746 removed outlier: 4.688A pdb=" N LEU A 842 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 886 through 887 Processing sheet with id=AB2, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.178A pdb=" N SER A 986 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A1052 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 988 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1050 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS A 990 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1048 " --> pdb=" O LYS A 990 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASP A1046 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE A1044 " --> pdb=" O PRO A 994 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ALA A 996 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY A 998 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A1036 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN A1015 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TRP A1055 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 946 through 948 removed outlier: 3.934A pdb=" N ALA A 999 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 972 through 973 Processing sheet with id=AB5, first strand: chain 'A' and resid 1192 through 1197 438 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1695 1.30 - 1.43: 2619 1.43 - 1.56: 6208 1.56 - 1.69: 3 1.69 - 1.81: 35 Bond restraints: 10560 Sorted by residual: bond pdb=" C34 PNS A2004 " pdb=" N36 PNS A2004 " ideal model delta sigma weight residual 1.337 1.449 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C39 PNS A2004 " pdb=" N41 PNS A2004 " ideal model delta sigma weight residual 1.344 1.447 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C16 6OU A2003 " pdb=" O18 6OU A2003 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 6OU A2003 " pdb=" O30 6OU A2003 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O27 PNS A2004 " pdb=" P24 PNS A2004 " ideal model delta sigma weight residual 1.704 1.644 0.060 2.00e-02 2.50e+03 9.04e+00 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 14298 3.04 - 6.09: 187 6.09 - 9.13: 10 9.13 - 12.17: 4 12.17 - 15.22: 1 Bond angle restraints: 14500 Sorted by residual: angle pdb=" O22 6OU A2003 " pdb=" P23 6OU A2003 " pdb=" O26 6OU A2003 " ideal model delta sigma weight residual 93.95 109.17 -15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N GLY A 836 " pdb=" CA GLY A 836 " pdb=" C GLY A 836 " ideal model delta sigma weight residual 110.90 116.21 -5.31 1.53e+00 4.27e-01 1.20e+01 angle pdb=" O23 PNS A2004 " pdb=" P24 PNS A2004 " pdb=" O27 PNS A2004 " ideal model delta sigma weight residual 100.79 110.52 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" O24 6OU A2003 " pdb=" P23 6OU A2003 " pdb=" O25 6OU A2003 " ideal model delta sigma weight residual 118.72 109.03 9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C33 6OU A2003 " pdb=" C31 6OU A2003 " pdb=" O30 6OU A2003 " ideal model delta sigma weight residual 111.22 120.78 -9.56 3.00e+00 1.11e-01 1.01e+01 ... (remaining 14495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.44: 6086 27.44 - 54.88: 169 54.88 - 82.32: 18 82.32 - 109.75: 2 109.75 - 137.19: 3 Dihedral angle restraints: 6278 sinusoidal: 2328 harmonic: 3950 Sorted by residual: dihedral pdb=" CA PRO A1010 " pdb=" C PRO A1010 " pdb=" N ALA A1011 " pdb=" CA ALA A1011 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP A 977 " pdb=" C ASP A 977 " pdb=" N SER A 978 " pdb=" CA SER A 978 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PRO A 653 " pdb=" C PRO A 653 " pdb=" N GLY A 654 " pdb=" CA GLY A 654 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 6275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 791 0.030 - 0.060: 534 0.060 - 0.090: 237 0.090 - 0.120: 128 0.120 - 0.150: 32 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA THR A 661 " pdb=" N THR A 661 " pdb=" C THR A 661 " pdb=" CB THR A 661 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA PRO A 62 " pdb=" N PRO A 62 " pdb=" C PRO A 62 " pdb=" CB PRO A 62 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA VAL A1208 " pdb=" N VAL A1208 " pdb=" C VAL A1208 " pdb=" CB VAL A1208 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1719 not shown) Planarity restraints: 1875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 974 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 975 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 155 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 156 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 222 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 223 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.029 5.00e-02 4.00e+02 ... (remaining 1872 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 84 2.57 - 3.15: 8145 3.15 - 3.74: 15447 3.74 - 4.32: 21800 4.32 - 4.90: 37460 Nonbonded interactions: 82936 Sorted by model distance: nonbonded pdb=" O ALA A 735 " pdb=" OD1 ASP A 738 " model vdw 1.990 3.040 nonbonded pdb=" OD2 ASP A 965 " pdb=" OG1 THR A 970 " model vdw 2.077 3.040 nonbonded pdb=" O ALA A 735 " pdb="CA CA A2001 " model vdw 2.107 3.250 nonbonded pdb=" O ALA A1075 " pdb="CA CA A2002 " model vdw 2.159 3.250 nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.183 3.250 ... (remaining 82931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.100 Find NCS groups from input model: 0.050 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:5.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.560 10563 Z= 0.672 Angle : 0.874 15.215 14504 Z= 0.433 Chirality : 0.051 0.150 1722 Planarity : 0.007 0.056 1875 Dihedral : 13.583 137.191 3722 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.17), residues: 1379 helix: -4.11 (0.12), residues: 481 sheet: -1.60 (0.31), residues: 204 loop : -2.21 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 764 TYR 0.016 0.002 TYR A 439 PHE 0.018 0.002 PHE A 433 TRP 0.015 0.002 TRP A 232 HIS 0.010 0.002 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00994 / 0.39 (10560) covalent geometry : angle 0.87365 / 0.43 (14500) SS BOND : bond 0.00156 / 0.08 ( 2) SS BOND : angle 0.52563 / 0.26 ( 4) hydrogen bonds : bond 0.28687 / 18.97 ( 427) hydrogen bonds : angle 10.18680 / 7.20 ( 1209) Misc. bond : bond 0.56022 / 29.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ARG cc_start: 0.7993 (ttt90) cc_final: 0.7677 (tpm170) REVERT: A 689 PHE cc_start: 0.8948 (m-80) cc_final: 0.8740 (m-80) REVERT: A 953 VAL cc_start: 0.6943 (m) cc_final: 0.6629 (p) REVERT: A 959 SER cc_start: 0.7810 (p) cc_final: 0.7502 (m) REVERT: A 1014 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8321 (mtpm) REVERT: A 1210 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 4 GLU cc_start: 0.8513 (mp0) cc_final: 0.7864 (mm-30) REVERT: B 44 MET cc_start: 0.7042 (mtm) cc_final: 0.5922 (mtp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4868 time to fit residues: 89.7156 Evaluate side-chains 101 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 77 HIS A 360 HIS A 690 ASN A1068 GLN A1151 GLN B 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092055 restraints weight = 46318.823| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.02 r_work: 0.2857 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10563 Z= 0.146 Angle : 0.669 8.172 14504 Z= 0.340 Chirality : 0.045 0.277 1722 Planarity : 0.006 0.050 1875 Dihedral : 8.686 116.537 1519 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.24 % Allowed : 9.26 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.19), residues: 1379 helix: -1.88 (0.19), residues: 484 sheet: -1.04 (0.33), residues: 203 loop : -1.77 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 267 TYR 0.015 0.001 TYR B 71 PHE 0.008 0.001 PHE A 27 TRP 0.015 0.001 TRP A 214 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (10560) covalent geometry : angle 0.66932 / 0.34 (14500) SS BOND : bond 0.00169 / 0.08 ( 2) SS BOND : angle 0.25820 / 0.13 ( 4) hydrogen bonds : bond 0.04598 / 3.07 ( 427) hydrogen bonds : angle 5.68403 / 3.99 ( 1209) Misc. bond : bond 0.00136 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8944 (tpp-160) cc_final: 0.8438 (mmt90) REVERT: A 844 GLN cc_start: 0.8251 (tt0) cc_final: 0.7828 (tt0) REVERT: A 953 VAL cc_start: 0.7293 (m) cc_final: 0.6758 (p) REVERT: A 959 SER cc_start: 0.7569 (p) cc_final: 0.7187 (m) REVERT: A 1097 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8658 (mtmm) REVERT: A 1198 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7893 (pm20) outliers start: 13 outliers final: 5 residues processed: 134 average time/residue: 0.3827 time to fit residues: 56.3047 Evaluate side-chains 107 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 77 HIS A 551 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.089062 restraints weight = 35422.884| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.44 r_work: 0.2852 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10563 Z= 0.172 Angle : 0.634 7.898 14504 Z= 0.312 Chirality : 0.045 0.305 1722 Planarity : 0.005 0.047 1875 Dihedral : 7.934 92.010 1519 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.91 % Allowed : 10.40 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1379 helix: -0.47 (0.23), residues: 481 sheet: -0.75 (0.33), residues: 210 loop : -1.38 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 764 TYR 0.015 0.001 TYR A 439 PHE 0.010 0.001 PHE A 433 TRP 0.013 0.001 TRP A 214 HIS 0.008 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (10560) covalent geometry : angle 0.63437 / 0.31 (14500) SS BOND : bond 0.01135 / 0.54 ( 2) SS BOND : angle 0.29668 / 0.17 ( 4) hydrogen bonds : bond 0.04186 / 2.78 ( 427) hydrogen bonds : angle 5.08893 / 3.58 ( 1209) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 676 SER cc_start: 0.9430 (p) cc_final: 0.9175 (t) REVERT: A 844 GLN cc_start: 0.8217 (tt0) cc_final: 0.7795 (tt0) REVERT: A 953 VAL cc_start: 0.7740 (m) cc_final: 0.7102 (p) REVERT: A 959 SER cc_start: 0.7910 (p) cc_final: 0.7441 (m) REVERT: A 1054 ASP cc_start: 0.8137 (t70) cc_final: 0.7909 (t70) REVERT: A 1198 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 44 MET cc_start: 0.7280 (mmp) cc_final: 0.6922 (mtt) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 0.3610 time to fit residues: 46.1536 Evaluate side-chains 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1001 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain B residue 48 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.088006 restraints weight = 45549.451| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.95 r_work: 0.2813 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10563 Z= 0.170 Angle : 0.624 8.871 14504 Z= 0.304 Chirality : 0.045 0.321 1722 Planarity : 0.005 0.046 1875 Dihedral : 7.495 75.171 1519 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.48 % Allowed : 11.07 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1379 helix: 0.19 (0.24), residues: 481 sheet: -0.56 (0.34), residues: 211 loop : -1.18 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 267 TYR 0.013 0.001 TYR A 439 PHE 0.010 0.001 PHE A 433 TRP 0.013 0.001 TRP A 232 HIS 0.007 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (10560) covalent geometry : angle 0.62428 / 0.30 (14500) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 1.00887 / 0.50 ( 4) hydrogen bonds : bond 0.03692 / 2.44 ( 427) hydrogen bonds : angle 4.89069 / 3.44 ( 1209) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8061 (ttm170) REVERT: A 147 SER cc_start: 0.8402 (m) cc_final: 0.7970 (p) REVERT: A 676 SER cc_start: 0.9407 (p) cc_final: 0.9122 (t) REVERT: A 844 GLN cc_start: 0.8097 (tt0) cc_final: 0.7741 (tt0) REVERT: A 953 VAL cc_start: 0.7803 (m) cc_final: 0.7394 (p) REVERT: A 959 SER cc_start: 0.7927 (p) cc_final: 0.7488 (m) REVERT: A 1054 ASP cc_start: 0.8206 (t70) cc_final: 0.7964 (t70) REVERT: B 44 MET cc_start: 0.7214 (mmp) cc_final: 0.6795 (mtt) outliers start: 26 outliers final: 14 residues processed: 128 average time/residue: 0.3687 time to fit residues: 52.3484 Evaluate side-chains 118 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 598 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.088438 restraints weight = 33242.932| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.44 r_work: 0.2827 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10563 Z= 0.177 Angle : 0.630 8.365 14504 Z= 0.306 Chirality : 0.045 0.326 1722 Planarity : 0.005 0.057 1875 Dihedral : 6.930 77.191 1519 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.48 % Allowed : 12.31 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1379 helix: 0.50 (0.24), residues: 481 sheet: -0.46 (0.34), residues: 211 loop : -1.08 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 764 TYR 0.015 0.001 TYR A 439 PHE 0.009 0.001 PHE A 107 TRP 0.013 0.001 TRP A 232 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (10560) covalent geometry : angle 0.62969 / 0.31 (14500) SS BOND : bond 0.00056 / 0.03 ( 2) SS BOND : angle 1.46258 / 0.73 ( 4) hydrogen bonds : bond 0.03728 / 2.48 ( 427) hydrogen bonds : angle 4.83569 / 3.41 ( 1209) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8594 (tpp-160) cc_final: 0.7895 (ttm170) REVERT: A 147 SER cc_start: 0.8355 (m) cc_final: 0.7935 (p) REVERT: A 676 SER cc_start: 0.9370 (p) cc_final: 0.9151 (t) REVERT: A 844 GLN cc_start: 0.8077 (tt0) cc_final: 0.7688 (tt0) REVERT: A 953 VAL cc_start: 0.8086 (m) cc_final: 0.7587 (p) REVERT: A 959 SER cc_start: 0.7879 (p) cc_final: 0.7459 (m) REVERT: A 983 HIS cc_start: 0.6791 (t-170) cc_final: 0.6130 (p90) REVERT: A 1001 ARG cc_start: 0.6582 (ptp-170) cc_final: 0.6348 (ptm160) REVERT: A 1054 ASP cc_start: 0.8184 (t70) cc_final: 0.7942 (t70) REVERT: B 44 MET cc_start: 0.7264 (mmp) cc_final: 0.6785 (mtt) outliers start: 26 outliers final: 15 residues processed: 127 average time/residue: 0.3771 time to fit residues: 52.8862 Evaluate side-chains 123 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1375 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.088705 restraints weight = 42018.122| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.83 r_work: 0.2823 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10563 Z= 0.146 Angle : 0.602 8.920 14504 Z= 0.293 Chirality : 0.044 0.326 1722 Planarity : 0.005 0.050 1875 Dihedral : 6.656 79.493 1519 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.10 % Allowed : 12.69 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1379 helix: 0.82 (0.24), residues: 484 sheet: -0.40 (0.34), residues: 213 loop : -0.99 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 764 TYR 0.014 0.001 TYR A 439 PHE 0.008 0.001 PHE A 107 TRP 0.013 0.001 TRP A 232 HIS 0.007 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10560) covalent geometry : angle 0.60123 / 0.29 (14500) SS BOND : bond 0.00084 / 0.04 ( 2) SS BOND : angle 1.40550 / 0.70 ( 4) hydrogen bonds : bond 0.03438 / 2.29 ( 427) hydrogen bonds : angle 4.71446 / 3.32 ( 1209) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.7630 (mpt180) REVERT: A 137 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.7891 (ttm170) REVERT: A 147 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7887 (p) REVERT: A 844 GLN cc_start: 0.8092 (tt0) cc_final: 0.7681 (tt0) REVERT: A 953 VAL cc_start: 0.8179 (m) cc_final: 0.7709 (p) REVERT: A 954 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7653 (pp) REVERT: A 959 SER cc_start: 0.8041 (p) cc_final: 0.7541 (m) REVERT: A 983 HIS cc_start: 0.6572 (t-170) cc_final: 0.6214 (p90) REVERT: A 1001 ARG cc_start: 0.6628 (ptp-170) cc_final: 0.6420 (ptm160) REVERT: A 1097 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8366 (pmtt) REVERT: A 1341 TYR cc_start: 0.8220 (m-10) cc_final: 0.8020 (m-10) REVERT: B 44 MET cc_start: 0.7394 (mmp) cc_final: 0.6882 (mtt) outliers start: 22 outliers final: 11 residues processed: 129 average time/residue: 0.3613 time to fit residues: 51.4565 Evaluate side-chains 118 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 73 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 120 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.090136 restraints weight = 47993.671| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.02 r_work: 0.2840 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10563 Z= 0.113 Angle : 0.582 8.358 14504 Z= 0.282 Chirality : 0.043 0.334 1722 Planarity : 0.005 0.053 1875 Dihedral : 6.380 82.357 1519 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.72 % Allowed : 13.93 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.22), residues: 1379 helix: 1.09 (0.24), residues: 485 sheet: -0.28 (0.34), residues: 213 loop : -0.92 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 764 TYR 0.013 0.001 TYR A 439 PHE 0.007 0.001 PHE A 107 TRP 0.012 0.001 TRP A 232 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (10560) covalent geometry : angle 0.58162 / 0.28 (14500) SS BOND : bond 0.00019 / 0.01 ( 2) SS BOND : angle 1.13807 / 0.56 ( 4) hydrogen bonds : bond 0.03169 / 2.11 ( 427) hydrogen bonds : angle 4.56466 / 3.22 ( 1209) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8856 (mtm-85) cc_final: 0.7691 (mpt180) REVERT: A 137 ARG cc_start: 0.8499 (tpp-160) cc_final: 0.7788 (ttm170) REVERT: A 147 SER cc_start: 0.8178 (m) cc_final: 0.7836 (p) REVERT: A 844 GLN cc_start: 0.8216 (tt0) cc_final: 0.7808 (tt0) REVERT: A 953 VAL cc_start: 0.8164 (m) cc_final: 0.7774 (p) REVERT: A 954 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7653 (pp) REVERT: A 959 SER cc_start: 0.7898 (p) cc_final: 0.7438 (m) REVERT: A 983 HIS cc_start: 0.6572 (t-170) cc_final: 0.6230 (p90) REVERT: A 1054 ASP cc_start: 0.8155 (t70) cc_final: 0.7913 (t70) REVERT: A 1180 MET cc_start: 0.8912 (ptp) cc_final: 0.8555 (ptt) REVERT: A 1194 GLU cc_start: 0.8141 (tt0) cc_final: 0.7876 (mt-10) REVERT: B 44 MET cc_start: 0.7388 (mmp) cc_final: 0.6864 (mtt) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.3868 time to fit residues: 53.9526 Evaluate side-chains 119 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain B residue 48 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091166 restraints weight = 39097.696| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.60 r_work: 0.2856 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10563 Z= 0.128 Angle : 0.597 10.159 14504 Z= 0.289 Chirality : 0.044 0.330 1722 Planarity : 0.005 0.058 1875 Dihedral : 6.287 88.088 1519 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.72 % Allowed : 13.93 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1379 helix: 1.15 (0.24), residues: 491 sheet: -0.18 (0.35), residues: 213 loop : -0.86 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 764 TYR 0.014 0.001 TYR A 439 PHE 0.008 0.001 PHE A 107 TRP 0.013 0.001 TRP A 232 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10560) covalent geometry : angle 0.59720 / 0.29 (14500) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 1.11228 / 0.55 ( 4) hydrogen bonds : bond 0.03257 / 2.18 ( 427) hydrogen bonds : angle 4.53581 / 3.19 ( 1209) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.7632 (tpt170) REVERT: A 137 ARG cc_start: 0.8477 (tpp-160) cc_final: 0.7743 (ttm170) REVERT: A 147 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7826 (p) REVERT: A 844 GLN cc_start: 0.8198 (tt0) cc_final: 0.7497 (tt0) REVERT: A 953 VAL cc_start: 0.8210 (m) cc_final: 0.7839 (p) REVERT: A 954 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7654 (pp) REVERT: A 959 SER cc_start: 0.7883 (p) cc_final: 0.7447 (m) REVERT: A 983 HIS cc_start: 0.6581 (t-170) cc_final: 0.6217 (p90) REVERT: A 1054 ASP cc_start: 0.8149 (t70) cc_final: 0.7913 (t70) REVERT: A 1097 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8461 (pmtt) REVERT: A 1180 MET cc_start: 0.8903 (ptp) cc_final: 0.8544 (ptt) REVERT: A 1341 TYR cc_start: 0.8240 (m-10) cc_final: 0.8036 (m-10) REVERT: B 44 MET cc_start: 0.7527 (mmp) cc_final: 0.6933 (mtt) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 0.3717 time to fit residues: 47.9296 Evaluate side-chains 120 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain B residue 48 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6768 > 50: distance: 41 - 44: 32.656 distance: 44 - 45: 17.280 distance: 45 - 46: 54.372 distance: 45 - 48: 22.498 distance: 46 - 47: 37.046 distance: 46 - 53: 48.593 distance: 48 - 49: 30.743 distance: 49 - 50: 36.545 distance: 50 - 51: 7.232 distance: 50 - 52: 11.717 distance: 53 - 54: 38.100 distance: 54 - 55: 57.567 distance: 54 - 57: 68.380 distance: 55 - 56: 50.468 distance: 55 - 64: 25.033 distance: 57 - 58: 25.488 distance: 58 - 59: 11.515 distance: 58 - 60: 47.236 distance: 59 - 61: 34.527 distance: 61 - 63: 43.463 distance: 62 - 63: 55.622 distance: 64 - 65: 47.230 distance: 65 - 66: 39.437 distance: 66 - 67: 39.758 distance: 66 - 68: 5.860 distance: 68 - 69: 33.915 distance: 69 - 70: 16.328 distance: 70 - 71: 42.114 distance: 70 - 76: 42.950 distance: 72 - 73: 57.442 distance: 73 - 74: 38.993 distance: 73 - 75: 39.719 distance: 76 - 77: 57.442 distance: 76 - 82: 4.804 distance: 77 - 78: 55.551 distance: 77 - 80: 40.214 distance: 78 - 79: 53.968 distance: 78 - 83: 9.555 distance: 81 - 82: 33.479 distance: 83 - 84: 6.115 distance: 84 - 85: 57.944 distance: 84 - 87: 40.336 distance: 85 - 86: 40.160 distance: 85 - 90: 68.112 distance: 87 - 88: 56.482 distance: 87 - 89: 38.642 distance: 90 - 91: 39.612 distance: 91 - 92: 22.768 distance: 92 - 93: 23.608 distance: 92 - 94: 17.912 distance: 94 - 95: 13.591 distance: 95 - 96: 11.846 distance: 95 - 98: 9.748 distance: 96 - 97: 5.788 distance: 96 - 99: 46.226 distance: 100 - 101: 59.525 distance: 101 - 102: 43.513 distance: 101 - 103: 50.005 distance: 103 - 104: 49.840 distance: 104 - 105: 28.566 distance: 104 - 107: 40.805 distance: 105 - 106: 43.465 distance: 105 - 108: 18.351