Starting phenix.real_space_refine on Fri Jan 19 22:12:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/01_2024/6n7s_0362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/01_2024/6n7s_0362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/01_2024/6n7s_0362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/01_2024/6n7s_0362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/01_2024/6n7s_0362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/01_2024/6n7s_0362_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 7932 2.51 5 N 2253 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12783 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain breaks: 3 Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2121 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2003 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1995 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.16, per 1000 atoms: 0.56 Number of scatterers: 12783 At special positions: 0 Unit cell: (75.97, 129.47, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 25 15.00 Mg 4 11.99 O 2491 8.00 N 2253 7.00 C 7932 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 - 3.50 Amino acid : False - 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: 5.00 Conformation dependent library (CDL) restraints added in 2.5 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 11 sheets defined 25.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.515A pdb=" N HIS A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.942A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.297A pdb=" N GLU A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.076A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 278' Processing helix chain 'B' and resid 294 through 297 No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 320 through 328 removed outlier: 3.795A pdb=" N GLN B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.921A pdb=" N GLU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 405 through 414 removed outlier: 3.591A pdb=" N TYR B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.618A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'C' and resid 273 through 276 No H-bonds generated for 'chain 'C' and resid 273 through 276' Processing helix chain 'C' and resid 294 through 297 No H-bonds generated for 'chain 'C' and resid 294 through 297' Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.887A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 removed outlier: 4.194A pdb=" N TYR C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 446 through 456 removed outlier: 3.786A pdb=" N THR C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'C' and resid 491 through 493 No H-bonds generated for 'chain 'C' and resid 491 through 493' Processing helix chain 'D' and resid 273 through 276 No H-bonds generated for 'chain 'D' and resid 273 through 276' Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 348 through 357 removed outlier: 3.832A pdb=" N ASP D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 403 through 414 removed outlier: 3.733A pdb=" N ALA D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 removed outlier: 3.755A pdb=" N LYS D 448 " --> pdb=" O ASN D 444 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 273 through 276 No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.885A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 357 removed outlier: 4.866A pdb=" N ASP E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY E 355 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.552A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 removed outlier: 4.276A pdb=" N MET E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 446 through 456 removed outlier: 3.915A pdb=" N GLY E 451 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'F' and resid 268 through 271 removed outlier: 3.747A pdb=" N LEU F 271 " --> pdb=" O ALA F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 271' Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 318 through 322 Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.845A pdb=" N GLN F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 328' Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'F' and resid 378 through 383 Processing helix chain 'F' and resid 405 through 414 removed outlier: 4.955A pdb=" N ALA F 410 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR F 411 " --> pdb=" O LYS F 408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 413 " --> pdb=" O ALA F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 456 Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing sheet with id= A, first strand: chain 'A' and resid 308 through 311 removed outlier: 5.969A pdb=" N THR A 498 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 311 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 500 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 520 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 501 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE A 518 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A 503 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 516 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 516 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A 531 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 423 removed outlier: 6.394A pdb=" N VAL A 459 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 423 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 461 " --> pdb=" O LEU A 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 528 through 534 removed outlier: 7.400A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 515 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 310 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 461 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 528 through 534 removed outlier: 6.650A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 460 through 463 removed outlier: 3.721A pdb=" N VAL D 310 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR D 498 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR D 311 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE D 500 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 515 through 518 removed outlier: 6.123A pdb=" N ILE D 518 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE D 529 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.689A pdb=" N VAL E 420 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA E 340 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE E 422 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL E 459 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU E 423 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL E 461 " --> pdb=" O LEU E 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 498 through 503 removed outlier: 3.574A pdb=" N ILE E 499 " --> pdb=" O LYS E 520 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS E 520 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA E 501 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE E 518 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU E 503 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL E 516 " --> pdb=" O GLU E 503 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 531 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE E 518 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE E 529 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 308 through 311 removed outlier: 7.171A pdb=" N THR F 498 " --> pdb=" O MET F 309 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR F 311 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE F 500 " --> pdb=" O THR F 311 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 459 through 462 removed outlier: 6.650A pdb=" N LYS F 336 " --> pdb=" O ASP F 419 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE F 421 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY F 338 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU F 423 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA F 340 " --> pdb=" O LEU F 423 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 532 through 534 removed outlier: 3.750A pdb=" N TYR F 532 " --> pdb=" O SER F 545 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 546 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: 3.15 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2145 1.31 - 1.43: 3175 1.43 - 1.56: 7456 1.56 - 1.69: 46 1.69 - 1.82: 132 Bond restraints: 12954 Sorted by residual: bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.410 1.488 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.410 1.487 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 96.43 - 103.96: 156 103.96 - 111.49: 5347 111.49 - 119.02: 5311 119.02 - 126.55: 6496 126.55 - 134.08: 147 Bond angle restraints: 17457 Sorted by residual: angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 111.02 100.94 10.08 1.52e+00 4.33e-01 4.40e+01 angle pdb=" N PHE B 289 " pdb=" CA PHE B 289 " pdb=" C PHE B 289 " ideal model delta sigma weight residual 109.60 118.52 -8.92 1.53e+00 4.27e-01 3.40e+01 angle pdb=" N HIS C 357 " pdb=" CA HIS C 357 " pdb=" C HIS C 357 " ideal model delta sigma weight residual 111.28 117.55 -6.27 1.09e+00 8.42e-01 3.31e+01 angle pdb=" N ILE F 275 " pdb=" CA ILE F 275 " pdb=" C ILE F 275 " ideal model delta sigma weight residual 111.00 105.42 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N TYR B 411 " pdb=" CA TYR B 411 " pdb=" C TYR B 411 " ideal model delta sigma weight residual 111.82 117.59 -5.77 1.16e+00 7.43e-01 2.47e+01 ... (remaining 17452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 7594 35.33 - 70.67: 132 70.67 - 106.00: 14 106.00 - 141.33: 5 141.33 - 176.66: 3 Dihedral angle restraints: 7748 sinusoidal: 3275 harmonic: 4473 Sorted by residual: dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 118.35 -176.66 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP E 700 " pdb=" C1' TTP E 700 " pdb=" N1 TTP E 700 " pdb=" O4' TTP E 700 " ideal model delta sinusoidal sigma weight residual 301.68 134.74 166.94 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C2 TTP D 700 " pdb=" C1' TTP D 700 " pdb=" N1 TTP D 700 " pdb=" O4' TTP D 700 " ideal model delta sinusoidal sigma weight residual 301.68 150.44 151.24 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1333 0.059 - 0.117: 519 0.117 - 0.176: 106 0.176 - 0.234: 23 0.234 - 0.293: 9 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CA ASP B 352 " pdb=" N ASP B 352 " pdb=" C ASP B 352 " pdb=" CB ASP B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA HIS B 357 " pdb=" N HIS B 357 " pdb=" C HIS B 357 " pdb=" CB HIS B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' TTP C 700 " pdb=" C2' TTP C 700 " pdb=" C4' TTP C 700 " pdb=" O3' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1987 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 515 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU F 515 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU F 515 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL F 516 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 347 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C GLU E 347 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU E 347 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 348 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 322 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.89e+00 pdb=" C VAL C 322 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL C 322 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 323 " 0.015 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 26 2.43 - 3.05: 7287 3.05 - 3.66: 18365 3.66 - 4.28: 28017 4.28 - 4.90: 45286 Nonbonded interactions: 98981 Sorted by model distance: nonbonded pdb=" OE1 GLN C 343 " pdb="MG MG C 701 " model vdw 1.812 2.170 nonbonded pdb=" OE1 GLN E 343 " pdb="MG MG E 701 " model vdw 1.922 2.170 nonbonded pdb=" O1B TTP E 700 " pdb="MG MG E 701 " model vdw 1.987 2.170 nonbonded pdb=" O2G TTP D 700 " pdb="MG MG D 701 " model vdw 2.000 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.121 2.170 ... (remaining 98976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 506 or resid 510 through 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 4.100 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.070 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 12954 Z= 0.500 Angle : 1.198 12.171 17457 Z= 0.636 Chirality : 0.066 0.293 1990 Planarity : 0.005 0.054 2163 Dihedral : 14.865 176.665 4884 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.04 % Allowed : 4.37 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.16), residues: 1555 helix: -4.29 (0.12), residues: 485 sheet: -2.12 (0.30), residues: 276 loop : -3.22 (0.17), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 329 HIS 0.012 0.003 HIS D 465 PHE 0.027 0.003 PHE D 289 TYR 0.023 0.003 TYR C 535 ARG 0.013 0.001 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 338 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 GLU cc_start: 0.7967 (mp0) cc_final: 0.7542 (mp0) REVERT: A 484 THR cc_start: 0.8992 (p) cc_final: 0.8753 (p) REVERT: A 493 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4501 (ptt90) REVERT: A 515 LEU cc_start: 0.5832 (tt) cc_final: 0.4882 (mt) REVERT: A 533 MET cc_start: 0.6506 (mtm) cc_final: 0.5811 (mpp) REVERT: B 308 ILE cc_start: 0.8926 (mt) cc_final: 0.8501 (mp) REVERT: B 344 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5328 (mp0) REVERT: B 439 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5611 (mmp80) REVERT: B 533 MET cc_start: 0.4618 (mtm) cc_final: 0.4407 (mtp) REVERT: C 428 ILE cc_start: 0.7174 (pt) cc_final: 0.5741 (pt) REVERT: C 462 VAL cc_start: 0.7719 (t) cc_final: 0.6996 (t) REVERT: C 494 GLN cc_start: 0.7508 (mt0) cc_final: 0.7301 (mt0) REVERT: D 299 THR cc_start: 0.8128 (t) cc_final: 0.7738 (m) REVERT: D 341 MET cc_start: 0.2878 (mpm) cc_final: 0.2620 (mmp) REVERT: D 446 MET cc_start: 0.6842 (tpp) cc_final: 0.6636 (tpp) REVERT: E 444 ASN cc_start: 0.8332 (t0) cc_final: 0.8003 (t0) REVERT: E 468 ASN cc_start: 0.7076 (t0) cc_final: 0.6792 (t0) REVERT: F 335 LYS cc_start: 0.9244 (mttm) cc_final: 0.8938 (mtmt) REVERT: F 341 MET cc_start: 0.5101 (mpm) cc_final: 0.4622 (mpm) outliers start: 14 outliers final: 2 residues processed: 349 average time/residue: 0.3137 time to fit residues: 146.3689 Evaluate side-chains 185 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 66 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 425 HIS A 475 HIS A 512 ASN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 536 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 HIS D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 475 HIS E 475 HIS F 475 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 12954 Z= 0.166 Angle : 0.599 9.578 17457 Z= 0.305 Chirality : 0.043 0.186 1990 Planarity : 0.004 0.066 2163 Dihedral : 13.805 143.302 1896 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.18), residues: 1555 helix: -3.35 (0.17), residues: 485 sheet: -1.46 (0.31), residues: 283 loop : -2.76 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 541 HIS 0.006 0.001 HIS C 425 PHE 0.021 0.001 PHE B 523 TYR 0.009 0.001 TYR F 532 ARG 0.004 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.5819 (mmm) cc_final: 0.5504 (tpt) REVERT: A 348 GLU cc_start: 0.7827 (mp0) cc_final: 0.7512 (mp0) REVERT: A 503 GLU cc_start: 0.6401 (mt-10) cc_final: 0.5703 (tm-30) REVERT: A 515 LEU cc_start: 0.5818 (tt) cc_final: 0.4416 (mt) REVERT: B 289 PHE cc_start: 0.7137 (m-80) cc_final: 0.6875 (m-80) REVERT: B 452 PHE cc_start: 0.5961 (t80) cc_final: 0.5528 (t80) REVERT: B 526 ASP cc_start: 0.7592 (m-30) cc_final: 0.7392 (t0) REVERT: C 435 GLU cc_start: 0.3832 (mm-30) cc_final: 0.3184 (mt-10) REVERT: C 533 MET cc_start: 0.0145 (mtp) cc_final: -0.0325 (mtp) REVERT: D 299 THR cc_start: 0.8081 (t) cc_final: 0.7833 (m) REVERT: D 318 LYS cc_start: 0.4476 (mtmt) cc_final: 0.3661 (mttm) REVERT: D 418 CYS cc_start: 0.6582 (m) cc_final: 0.4891 (m) REVERT: E 316 MET cc_start: 0.7856 (mtp) cc_final: 0.7264 (ttp) REVERT: E 343 GLN cc_start: 0.6449 (tt0) cc_final: 0.6082 (tt0) REVERT: E 356 LEU cc_start: 0.7434 (tp) cc_final: 0.7066 (tp) REVERT: E 412 MET cc_start: 0.5527 (mtp) cc_final: 0.4804 (mtp) REVERT: E 444 ASN cc_start: 0.8248 (t0) cc_final: 0.8041 (t0) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.2774 time to fit residues: 93.8649 Evaluate side-chains 164 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 39 optimal weight: 0.0020 chunk 144 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN D 343 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 HIS E 425 HIS F 465 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12954 Z= 0.210 Angle : 0.632 9.380 17457 Z= 0.318 Chirality : 0.044 0.190 1990 Planarity : 0.004 0.063 2163 Dihedral : 13.375 131.194 1896 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.19), residues: 1555 helix: -2.79 (0.20), residues: 459 sheet: -1.53 (0.29), residues: 305 loop : -2.46 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 329 HIS 0.007 0.001 HIS C 425 PHE 0.012 0.002 PHE E 523 TYR 0.014 0.001 TYR A 535 ARG 0.006 0.001 ARG F 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ARG cc_start: 0.7051 (mpp-170) cc_final: 0.6031 (mtm110) REVERT: A 503 GLU cc_start: 0.6591 (mt-10) cc_final: 0.5580 (tm-30) REVERT: C 441 MET cc_start: 0.5734 (ttt) cc_final: 0.4811 (ttp) REVERT: D 316 MET cc_start: 0.7717 (ttm) cc_final: 0.7403 (ttt) REVERT: D 318 LYS cc_start: 0.5393 (mtmt) cc_final: 0.3807 (mttm) REVERT: D 477 GLU cc_start: 0.5151 (pp20) cc_final: 0.4530 (tm-30) REVERT: E 316 MET cc_start: 0.8046 (mtp) cc_final: 0.7308 (ttm) REVERT: E 406 LEU cc_start: 0.8963 (pt) cc_final: 0.8560 (mp) REVERT: E 412 MET cc_start: 0.6444 (mtp) cc_final: 0.6176 (mtp) REVERT: E 441 MET cc_start: 0.5661 (tpp) cc_final: 0.5371 (tpp) REVERT: E 446 MET cc_start: 0.1406 (mmm) cc_final: 0.0921 (mmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2869 time to fit residues: 80.2000 Evaluate side-chains 153 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 153 optimal weight: 0.0670 chunk 137 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 overall best weight: 1.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 HIS F 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12954 Z= 0.171 Angle : 0.576 9.341 17457 Z= 0.287 Chirality : 0.043 0.186 1990 Planarity : 0.004 0.064 2163 Dihedral : 13.121 136.967 1896 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.19), residues: 1555 helix: -2.32 (0.21), residues: 451 sheet: -1.25 (0.30), residues: 296 loop : -2.32 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 329 HIS 0.007 0.001 HIS C 425 PHE 0.010 0.001 PHE B 523 TYR 0.012 0.001 TYR A 547 ARG 0.006 0.001 ARG D 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.6698 (mpp) cc_final: 0.5766 (mpp) REVERT: A 503 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5616 (tm-30) REVERT: B 446 MET cc_start: 0.7319 (ttp) cc_final: 0.7072 (ttp) REVERT: C 309 MET cc_start: 0.6844 (mmt) cc_final: 0.6598 (mmt) REVERT: C 494 GLN cc_start: 0.6425 (mm110) cc_final: 0.6142 (mm110) REVERT: D 288 LEU cc_start: 0.8472 (mt) cc_final: 0.8265 (mp) REVERT: D 316 MET cc_start: 0.7600 (ttm) cc_final: 0.7362 (ttt) REVERT: D 318 LYS cc_start: 0.5575 (mtmt) cc_final: 0.5157 (mtpt) REVERT: D 477 GLU cc_start: 0.5320 (pp20) cc_final: 0.4981 (tm-30) REVERT: E 316 MET cc_start: 0.8022 (mtp) cc_final: 0.7424 (ttm) REVERT: E 412 MET cc_start: 0.6377 (mtp) cc_final: 0.5718 (mtp) REVERT: E 441 MET cc_start: 0.5759 (tpp) cc_final: 0.5395 (tpp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2712 time to fit residues: 76.7957 Evaluate side-chains 147 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 475 HIS ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS C 536 ASN D 328 GLN D 357 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 507 GLN E 536 ASN F 343 GLN F 358 ASN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12954 Z= 0.465 Angle : 0.980 10.080 17457 Z= 0.486 Chirality : 0.055 0.334 1990 Planarity : 0.007 0.067 2163 Dihedral : 14.593 137.381 1896 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.18), residues: 1555 helix: -2.57 (0.21), residues: 451 sheet: -1.79 (0.30), residues: 269 loop : -2.72 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 329 HIS 0.009 0.002 HIS C 278 PHE 0.028 0.003 PHE A 523 TYR 0.028 0.003 TYR A 411 ARG 0.019 0.001 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8014 (m-90) cc_final: 0.7778 (m-90) REVERT: A 333 MET cc_start: 0.6607 (mpp) cc_final: 0.6104 (mpp) REVERT: B 289 PHE cc_start: 0.7603 (m-10) cc_final: 0.7286 (m-10) REVERT: B 316 MET cc_start: 0.8542 (mmp) cc_final: 0.7558 (mmt) REVERT: B 370 ARG cc_start: 0.7577 (mmt180) cc_final: 0.5819 (mmm160) REVERT: C 441 MET cc_start: 0.5456 (ttt) cc_final: 0.4913 (ttp) REVERT: C 467 LYS cc_start: 0.7007 (pttp) cc_final: 0.6727 (pttp) REVERT: D 316 MET cc_start: 0.7882 (ttm) cc_final: 0.7681 (ttt) REVERT: D 477 GLU cc_start: 0.6171 (pp20) cc_final: 0.5599 (tm-30) REVERT: E 316 MET cc_start: 0.8525 (mtp) cc_final: 0.8283 (mtp) REVERT: E 365 SER cc_start: 0.3753 (t) cc_final: 0.3480 (m) REVERT: E 412 MET cc_start: 0.7181 (mtp) cc_final: 0.6712 (mtp) REVERT: E 441 MET cc_start: 0.5921 (tpp) cc_final: 0.5569 (tpp) REVERT: E 468 ASN cc_start: 0.7417 (t0) cc_final: 0.7033 (t0) REVERT: E 497 ASP cc_start: 0.6444 (m-30) cc_final: 0.6145 (t0) REVERT: F 309 MET cc_start: 0.4091 (mmm) cc_final: 0.3875 (mmt) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2793 time to fit residues: 69.6412 Evaluate side-chains 140 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9523 > 50: distance: 75 - 77: 8.431 distance: 77 - 78: 11.681 distance: 78 - 79: 6.155 distance: 78 - 81: 5.601 distance: 79 - 80: 12.544 distance: 79 - 89: 4.140 distance: 82 - 83: 4.746 distance: 83 - 85: 3.694 distance: 85 - 87: 3.239 distance: 86 - 87: 3.763 distance: 87 - 88: 3.762 distance: 89 - 90: 20.127 distance: 90 - 91: 30.772 distance: 90 - 93: 16.416 distance: 91 - 92: 25.846 distance: 91 - 97: 16.650 distance: 93 - 94: 10.035 distance: 94 - 95: 29.570 distance: 95 - 96: 30.046 distance: 97 - 98: 4.811 distance: 98 - 99: 18.785 distance: 98 - 101: 10.566 distance: 99 - 100: 35.034 distance: 99 - 106: 25.678 distance: 101 - 102: 9.161 distance: 102 - 103: 5.031 distance: 103 - 104: 8.689 distance: 103 - 105: 6.119 distance: 106 - 107: 16.817 distance: 107 - 108: 34.010 distance: 107 - 110: 21.091 distance: 108 - 109: 42.937 distance: 108 - 118: 44.365 distance: 110 - 111: 8.170 distance: 111 - 112: 5.876 distance: 111 - 113: 7.926 distance: 113 - 115: 6.624 distance: 114 - 116: 8.057 distance: 115 - 116: 6.762 distance: 118 - 119: 31.451 distance: 119 - 120: 37.357 distance: 119 - 122: 28.135 distance: 120 - 121: 46.612 distance: 120 - 126: 25.089 distance: 122 - 123: 9.541 distance: 123 - 125: 19.226 distance: 126 - 127: 40.211 distance: 127 - 128: 38.133 distance: 127 - 130: 43.683 distance: 128 - 129: 30.525 distance: 128 - 135: 28.989 distance: 130 - 131: 28.895 distance: 131 - 132: 16.635 distance: 132 - 133: 9.491 distance: 133 - 134: 11.402 distance: 135 - 136: 42.227 distance: 136 - 137: 39.489 distance: 136 - 139: 20.800 distance: 137 - 138: 51.387 distance: 137 - 144: 47.980 distance: 139 - 140: 24.541 distance: 140 - 141: 13.052 distance: 141 - 142: 17.795 distance: 141 - 143: 18.291 distance: 144 - 145: 35.087 distance: 145 - 146: 35.301 distance: 145 - 148: 21.705 distance: 146 - 147: 41.269 distance: 146 - 151: 42.720 distance: 148 - 149: 29.071 distance: 148 - 150: 22.994 distance: 151 - 152: 31.804 distance: 152 - 153: 14.039 distance: 153 - 154: 37.562 distance: 153 - 155: 20.807 distance: 155 - 156: 12.195 distance: 156 - 157: 42.022 distance: 156 - 159: 16.647 distance: 157 - 158: 40.581 distance: 157 - 169: 25.438 distance: 159 - 160: 8.300 distance: 160 - 161: 15.744 distance: 160 - 162: 20.456 distance: 161 - 163: 6.840 distance: 162 - 164: 30.998 distance: 162 - 165: 19.147 distance: 163 - 164: 23.487 distance: 164 - 166: 23.634 distance: 165 - 167: 7.375 distance: 166 - 168: 11.038 distance: 167 - 168: 5.052