Starting phenix.real_space_refine on Wed Jun 18 10:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e2g_8962/06_2025/6e2g_8962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e2g_8962/06_2025/6e2g_8962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e2g_8962/06_2025/6e2g_8962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e2g_8962/06_2025/6e2g_8962.map" model { file = "/net/cci-nas-00/data/ceres_data/6e2g_8962/06_2025/6e2g_8962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e2g_8962/06_2025/6e2g_8962.cif" } resolution = 3.6 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= 0.006 sd= 0.078 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 149 5.16 5 C 13616 2.51 5 N 3553 2.21 5 O 3784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21108 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4885 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 25, 'TRANS': 585} Chain: "B" Number of atoms: 4979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4979 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain: "C" Number of atoms: 5172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5172 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 25, 'TRANS': 618} Chain breaks: 1 Chain: "D" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4901 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.59, per 1000 atoms: 0.60 Number of scatterers: 21108 At special positions: 0 Unit cell: (133.56, 130.38, 131.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 149 16.00 O 3784 8.00 N 3553 7.00 C 13616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 2.8 seconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4946 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 8 sheets defined 58.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 4.470A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.753A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.545A pdb=" N TYR A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.653A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.738A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.094A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.595A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.871A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.565A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.823A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.564A pdb=" N VAL A 234 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.533A pdb=" N MET A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 4.238A pdb=" N VAL A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.597A pdb=" N ARG A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.693A pdb=" N TRP A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 347 removed outlier: 3.544A pdb=" N PHE A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.779A pdb=" N GLY A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.004A pdb=" N ILE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.922A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.691A pdb=" N PHE A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.731A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.647A pdb=" N VAL A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.548A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.555A pdb=" N THR A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 removed outlier: 4.078A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 4.279A pdb=" N ALA A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 removed outlier: 3.605A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.719A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.978A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.873A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.203A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.240A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.824A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.763A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.533A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.992A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.819A pdb=" N GLY B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.770A pdb=" N VAL B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.905A pdb=" N ALA B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 305 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 4.030A pdb=" N TRP B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.555A pdb=" N TYR B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 403 removed outlier: 3.774A pdb=" N VAL B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.578A pdb=" N ARG B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 442 removed outlier: 3.634A pdb=" N ILE B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.594A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.748A pdb=" N GLY B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.813A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.184A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.584A pdb=" N LEU B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.859A pdb=" N SER B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 556 " --> pdb=" O PHE B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.113A pdb=" N ALA B 575 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.557A pdb=" N ARG B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.832A pdb=" N ILE B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.701A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.807A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.518A pdb=" N LEU C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.520A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.673A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.818A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.590A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.584A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.608A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.504A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 204' Processing helix chain 'C' and resid 211 through 223 removed outlier: 4.151A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.792A pdb=" N GLY C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.556A pdb=" N GLN C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.894A pdb=" N VAL C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 4.290A pdb=" N GLN C 305 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 307 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 removed outlier: 3.734A pdb=" N TRP C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 347 removed outlier: 3.631A pdb=" N TYR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 407 removed outlier: 3.568A pdb=" N LEU C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.877A pdb=" N PHE C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 426 through 442 removed outlier: 4.164A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 438 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.517A pdb=" N VAL C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 3.592A pdb=" N TYR C 466 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 489 removed outlier: 3.801A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.914A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 524 through 534 removed outlier: 4.381A pdb=" N PHE C 530 " --> pdb=" O PRO C 526 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 566 removed outlier: 3.978A pdb=" N SER C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 556 " --> pdb=" O PHE C 552 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 582 removed outlier: 4.126A pdb=" N ALA C 575 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP C 582 " --> pdb=" O GLY C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.535A pdb=" N LEU C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 651 removed outlier: 3.654A pdb=" N ALA C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 removed outlier: 3.658A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.684A pdb=" N SER D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.649A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.647A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.516A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.530A pdb=" N ALA D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.517A pdb=" N ALA D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.548A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.832A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.763A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.745A pdb=" N GLY D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.550A pdb=" N GLN D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.759A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.888A pdb=" N ARG D 304 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 305 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 307 " --> pdb=" O ARG D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.802A pdb=" N LEU D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.721A pdb=" N TYR D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 407 removed outlier: 3.524A pdb=" N VAL D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 422 through 425 removed outlier: 3.559A pdb=" N HIS D 425 " --> pdb=" O GLY D 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 422 through 425' Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.635A pdb=" N THR D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 437 " --> pdb=" O PHE D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 removed outlier: 4.107A pdb=" N MET D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 474 through 486 removed outlier: 3.805A pdb=" N THR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 480 " --> pdb=" O PRO D 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 511 removed outlier: 4.016A pdb=" N VAL D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 511 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 537 removed outlier: 4.064A pdb=" N PHE D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 534 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 567 removed outlier: 4.155A pdb=" N SER D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 556 " --> pdb=" O PHE D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 4.483A pdb=" N ALA D 575 " --> pdb=" O ASN D 571 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 582 " --> pdb=" O GLY D 578 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 605 removed outlier: 3.948A pdb=" N ARG D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.621A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.918A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.581A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.731A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.875A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.527A pdb=" N ARG E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.608A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.727A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 269 removed outlier: 7.295A pdb=" N SER A 274 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A 268 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 269 removed outlier: 6.916A pdb=" N SER B 274 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 268 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 269 removed outlier: 5.065A pdb=" N ILE C 265 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 276 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 267 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 269 removed outlier: 6.956A pdb=" N SER D 274 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR D 268 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 273 " --> pdb=" O ASP D 634 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 630 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 351 through 353 795 hydrogen bonds defined for protein. 2268 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: 7.03 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6165 1.33 - 1.45: 3815 1.45 - 1.57: 11336 1.57 - 1.69: 0 1.69 - 1.81: 254 Bond restraints: 21570 Sorted by residual: bond pdb=" C LYS A 606 " pdb=" N LEU A 607 " ideal model delta sigma weight residual 1.331 1.230 0.101 2.83e-02 1.25e+03 1.28e+01 bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.83e-02 1.25e+03 9.31e+00 bond pdb=" C ILE A 403 " pdb=" N PRO A 404 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.39e+00 bond pdb=" CB ARG D 469 " pdb=" CG ARG D 469 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.72e+00 bond pdb=" C VAL D 451 " pdb=" N PRO D 452 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.20e-02 6.94e+03 4.44e+00 ... (remaining 21565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 28522 3.27 - 6.54: 638 6.54 - 9.82: 75 9.82 - 13.09: 19 13.09 - 16.36: 8 Bond angle restraints: 29262 Sorted by residual: angle pdb=" C ASP B 637 " pdb=" N LEU B 638 " pdb=" CA LEU B 638 " ideal model delta sigma weight residual 121.54 134.79 -13.25 1.91e+00 2.74e-01 4.81e+01 angle pdb=" C LYS C 209 " pdb=" N THR C 210 " pdb=" CA THR C 210 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" N PHE D 211 " pdb=" CA PHE D 211 " pdb=" C PHE D 211 " ideal model delta sigma weight residual 114.75 108.24 6.51 1.26e+00 6.30e-01 2.67e+01 angle pdb=" N THR B 310 " pdb=" CA THR B 310 " pdb=" C THR B 310 " ideal model delta sigma weight residual 109.81 121.13 -11.32 2.21e+00 2.05e-01 2.62e+01 ... (remaining 29257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 11986 17.49 - 34.99: 719 34.99 - 52.48: 141 52.48 - 69.97: 11 69.97 - 87.47: 12 Dihedral angle restraints: 12869 sinusoidal: 5192 harmonic: 7677 Sorted by residual: dihedral pdb=" CA GLY B 286 " pdb=" C GLY B 286 " pdb=" N ASP B 287 " pdb=" CA ASP B 287 " ideal model delta harmonic sigma weight residual 180.00 -131.18 -48.82 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA ARG C 362 " pdb=" C ARG C 362 " pdb=" N ASP C 363 " pdb=" CA ASP C 363 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CA LYS C 209 " pdb=" C LYS C 209 " pdb=" N THR C 210 " pdb=" CA THR C 210 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 ... (remaining 12866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2713 0.079 - 0.157: 539 0.157 - 0.235: 58 0.235 - 0.314: 10 0.314 - 0.392: 1 Chirality restraints: 3321 Sorted by residual: chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA THR B 310 " pdb=" N THR B 310 " pdb=" C THR B 310 " pdb=" CB THR B 310 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 355 " pdb=" CA ILE A 355 " pdb=" CG1 ILE A 355 " pdb=" CG2 ILE A 355 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3318 not shown) Planarity restraints: 3721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 286 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLY B 286 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY B 286 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 287 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 612 " -0.021 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP C 612 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 612 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 612 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 612 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 612 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 612 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 612 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 612 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 612 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 403 " 0.048 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO D 404 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " 0.040 5.00e-02 4.00e+02 ... (remaining 3718 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5219 2.78 - 3.31: 19522 3.31 - 3.84: 33101 3.84 - 4.37: 38798 4.37 - 4.90: 64150 Nonbonded interactions: 160790 Sorted by model distance: nonbonded pdb=" OG SER D 505 " pdb=" OH TYR D 525 " model vdw 2.249 3.040 nonbonded pdb=" O VAL B 151 " pdb=" ND2 ASN B 158 " model vdw 2.270 3.120 nonbonded pdb=" NH1 ARG B 469 " pdb=" OE1 GLN B 595 " model vdw 2.283 3.120 nonbonded pdb=" O VAL A 440 " pdb=" OG1 THR A 444 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP A 34 " pdb=" NH1 ARG D 631 " model vdw 2.298 3.120 ... (remaining 160785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 637) selection = (chain 'B' and resid 27 through 637) selection = (chain 'C' and resid 27 through 637) selection = (chain 'D' and resid 27 through 637) } 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: 1.000 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 46.750 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.010 0.106 21570 Z= 0.426 Angle : 1.212 16.361 29262 Z= 0.629 Chirality : 0.064 0.392 3321 Planarity : 0.007 0.071 3721 Dihedral : 11.958 87.467 7923 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.38 % Favored : 87.20 % Rotamer: Outliers : 1.05 % Allowed : 7.42 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -5.78 (0.12), residues: 2625 helix: -4.05 (0.07), residues: 1393 sheet: -1.74 (0.61), residues: 80 loop : -3.60 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 612 HIS 0.013 0.002 HIS B 157 PHE 0.026 0.004 PHE B 552 TYR 0.028 0.003 TYR D 523 ARG 0.015 0.001 ARG D 631 Details of bonding type rmsd hydrogen bonds : bond 0.32427 ( 795) hydrogen bonds : angle 9.54556 ( 2268) covalent geometry : bond 0.00973 (21570) covalent geometry : angle 1.21228 (29262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 497 time to evaluate : 2.266 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: A 99 MET cc_start: 0.8572 (mtm) cc_final: 0.8134 (mtm) REVERT: A 219 LEU cc_start: 0.9388 (mm) cc_final: 0.8976 (mp) REVERT: A 278 ASP cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: A 289 GLN cc_start: 0.8727 (mt0) cc_final: 0.8377 (pm20) REVERT: A 344 MET cc_start: 0.8057 (mtt) cc_final: 0.7651 (mmp) REVERT: A 455 PHE cc_start: 0.8619 (m-10) cc_final: 0.8080 (m-80) REVERT: A 484 MET cc_start: 0.7996 (mmt) cc_final: 0.7665 (mmt) REVERT: A 494 TRP cc_start: 0.8442 (m100) cc_final: 0.8094 (m100) REVERT: A 590 GLU cc_start: 0.8101 (tp30) cc_final: 0.7511 (tp30) REVERT: B 301 ARG cc_start: 0.8697 (ttt-90) cc_final: 0.8428 (tpt90) REVERT: B 434 MET cc_start: 0.8979 (mmt) cc_final: 0.8122 (mmm) REVERT: B 484 MET cc_start: 0.8600 (mmt) cc_final: 0.8169 (mmt) REVERT: B 547 ASP cc_start: 0.8488 (m-30) cc_final: 0.8203 (t0) REVERT: B 572 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8823 (tm) REVERT: B 602 MET cc_start: 0.8261 (tmm) cc_final: 0.7941 (tmm) REVERT: B 641 GLN cc_start: 0.8701 (tt0) cc_final: 0.8181 (tm-30) REVERT: C 110 MET cc_start: 0.9287 (mtt) cc_final: 0.9005 (mtp) REVERT: C 113 GLU cc_start: 0.9133 (tp30) cc_final: 0.8907 (tm-30) REVERT: C 237 ASN cc_start: 0.8894 (t160) cc_final: 0.8638 (m110) REVERT: C 281 GLU cc_start: 0.8170 (tp30) cc_final: 0.7959 (tm-30) REVERT: C 283 ASP cc_start: 0.7737 (t0) cc_final: 0.6906 (t0) REVERT: C 300 LYS cc_start: 0.9027 (mtpm) cc_final: 0.8815 (ttmt) REVERT: C 301 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7815 (tpt90) REVERT: C 441 MET cc_start: 0.8828 (mmt) cc_final: 0.8544 (mmm) REVERT: C 473 MET cc_start: 0.8696 (ttt) cc_final: 0.7632 (ptp) REVERT: C 576 MET cc_start: 0.9221 (tpt) cc_final: 0.8758 (tpp) REVERT: C 595 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8456 (mm-40) REVERT: D 65 LEU cc_start: 0.9325 (mt) cc_final: 0.9095 (mt) REVERT: D 78 MET cc_start: 0.8740 (mpt) cc_final: 0.8026 (mpt) REVERT: D 176 GLU cc_start: 0.8588 (pt0) cc_final: 0.8375 (pp20) REVERT: D 233 LEU cc_start: 0.8796 (mm) cc_final: 0.8450 (mp) REVERT: D 293 GLU cc_start: 0.8929 (tp30) cc_final: 0.8541 (tp30) REVERT: D 301 ARG cc_start: 0.8987 (tpp-160) cc_final: 0.8724 (tpp80) REVERT: D 322 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8337 (tpt170) REVERT: D 389 LEU cc_start: 0.9471 (mm) cc_final: 0.9157 (mm) REVERT: E 14 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8532 (mm-30) REVERT: E 34 THR cc_start: 0.7952 (p) cc_final: 0.7714 (t) REVERT: E 39 LEU cc_start: 0.8842 (tt) cc_final: 0.8579 (tt) REVERT: E 77 LYS cc_start: 0.6736 (mmpt) cc_final: 0.5907 (mmtt) REVERT: E 144 MET cc_start: 0.8332 (mmm) cc_final: 0.8037 (mmt) outliers start: 24 outliers final: 7 residues processed: 516 average time/residue: 0.3557 time to fit residues: 274.2509 Evaluate side-chains 301 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 293 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 110 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN A 217 ASN A 237 ASN A 251 ASN A 364 ASN A 571 ASN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS B 237 ASN B 251 ASN B 256 GLN B 364 ASN B 368 GLN B 581 HIS B 586 HIS C 37 ASN C 118 GLN C 237 ASN C 251 ASN C 256 GLN C 309 GLN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 641 GLN D 74 GLN D 237 ASN D 251 ASN D 445 ASN D 482 GLN D 571 ASN D 581 HIS E 8 GLN E 41 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.112349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091195 restraints weight = 49244.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094260 restraints weight = 22618.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096252 restraints weight = 13709.913| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21570 Z= 0.150 Angle : 0.773 16.713 29262 Z= 0.390 Chirality : 0.044 0.203 3321 Planarity : 0.005 0.052 3721 Dihedral : 6.895 53.639 2893 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.06 % Favored : 89.79 % Rotamer: Outliers : 3.20 % Allowed : 12.38 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.95 (0.14), residues: 2625 helix: -2.18 (0.11), residues: 1437 sheet: -1.61 (0.58), residues: 83 loop : -3.24 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 612 HIS 0.010 0.001 HIS C 586 PHE 0.022 0.002 PHE E 65 TYR 0.015 0.001 TYR C 216 ARG 0.007 0.001 ARG D 469 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 795) hydrogen bonds : angle 4.98310 ( 2268) covalent geometry : bond 0.00332 (21570) covalent geometry : angle 0.77290 (29262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8408 (mtt) cc_final: 0.8191 (mmt) REVERT: A 269 TYR cc_start: 0.7893 (t80) cc_final: 0.7445 (t80) REVERT: A 275 THR cc_start: 0.9030 (m) cc_final: 0.8715 (p) REVERT: A 278 ASP cc_start: 0.8118 (t0) cc_final: 0.7254 (t0) REVERT: A 289 GLN cc_start: 0.8500 (mt0) cc_final: 0.8289 (pm20) REVERT: A 344 MET cc_start: 0.8143 (mtt) cc_final: 0.7658 (mmt) REVERT: A 388 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8045 (tt0) REVERT: A 473 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8296 (ppp) REVERT: A 500 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8860 (tt) REVERT: A 576 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8081 (ttt) REVERT: B 96 MET cc_start: 0.8439 (tmm) cc_final: 0.8160 (tmm) REVERT: B 110 MET cc_start: 0.9045 (mtp) cc_final: 0.8684 (mtp) REVERT: B 314 GLU cc_start: 0.7681 (mp0) cc_final: 0.7460 (mp0) REVERT: B 479 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8933 (mp) REVERT: B 490 MET cc_start: 0.7931 (mmm) cc_final: 0.7683 (mmm) REVERT: B 547 ASP cc_start: 0.8244 (m-30) cc_final: 0.7793 (t0) REVERT: B 590 GLU cc_start: 0.8705 (tp30) cc_final: 0.8289 (tp30) REVERT: B 595 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8313 (mm-40) REVERT: B 602 MET cc_start: 0.8297 (tmm) cc_final: 0.8010 (tmm) REVERT: B 611 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 641 GLN cc_start: 0.8624 (tt0) cc_final: 0.8268 (tp40) REVERT: C 215 MET cc_start: 0.8484 (tpp) cc_final: 0.8260 (tpp) REVERT: C 237 ASN cc_start: 0.8847 (t0) cc_final: 0.8594 (m110) REVERT: C 254 MET cc_start: 0.8973 (mmm) cc_final: 0.8652 (mmt) REVERT: C 283 ASP cc_start: 0.7562 (t0) cc_final: 0.6705 (t0) REVERT: C 288 ASP cc_start: 0.8344 (m-30) cc_final: 0.8008 (t0) REVERT: C 304 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8349 (mtp-110) REVERT: C 473 MET cc_start: 0.8743 (ttt) cc_final: 0.7640 (ptp) REVERT: C 576 MET cc_start: 0.8993 (tpt) cc_final: 0.8701 (tpp) REVERT: C 586 HIS cc_start: 0.7686 (t70) cc_final: 0.7277 (t-170) REVERT: C 589 ASP cc_start: 0.8472 (m-30) cc_final: 0.8202 (p0) REVERT: D 65 LEU cc_start: 0.9236 (mt) cc_final: 0.9034 (mt) REVERT: D 78 MET cc_start: 0.8687 (mpt) cc_final: 0.7968 (mpt) REVERT: D 99 MET cc_start: 0.9039 (mtm) cc_final: 0.8561 (mtm) REVERT: D 308 ASP cc_start: 0.8240 (m-30) cc_final: 0.7939 (m-30) REVERT: D 315 LEU cc_start: 0.9139 (mp) cc_final: 0.8829 (mp) REVERT: D 322 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8421 (tpt170) REVERT: D 482 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7785 (mm-40) REVERT: D 553 MET cc_start: 0.8043 (tpp) cc_final: 0.7750 (tpp) REVERT: D 571 ASN cc_start: 0.8912 (m-40) cc_final: 0.8607 (m110) REVERT: E 13 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8822 (tppt) REVERT: E 34 THR cc_start: 0.7912 (p) cc_final: 0.7661 (t) REVERT: E 49 GLN cc_start: 0.7500 (pm20) cc_final: 0.7264 (pm20) REVERT: E 51 MET cc_start: 0.8894 (ttm) cc_final: 0.8178 (ttm) REVERT: E 144 MET cc_start: 0.8243 (mmm) cc_final: 0.7840 (mmm) outliers start: 73 outliers final: 33 residues processed: 421 average time/residue: 0.3130 time to fit residues: 206.7174 Evaluate side-chains 324 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 139 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 229 optimal weight: 5.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 HIS ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 586 HIS C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN E 8 GLN E 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093077 restraints weight = 52882.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096091 restraints weight = 24755.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098060 restraints weight = 15157.565| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21570 Z= 0.144 Angle : 0.724 16.453 29262 Z= 0.360 Chirality : 0.043 0.199 3321 Planarity : 0.004 0.044 3721 Dihedral : 6.181 48.891 2888 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.36 % Favored : 89.52 % Rotamer: Outliers : 3.29 % Allowed : 14.75 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.15), residues: 2625 helix: -1.16 (0.13), residues: 1451 sheet: -1.41 (0.57), residues: 83 loop : -3.13 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 612 HIS 0.004 0.001 HIS A 157 PHE 0.015 0.001 PHE B 530 TYR 0.017 0.001 TYR B 338 ARG 0.008 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 795) hydrogen bonds : angle 4.48440 ( 2268) covalent geometry : bond 0.00322 (21570) covalent geometry : angle 0.72370 (29262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 317 time to evaluate : 2.508 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 269 TYR cc_start: 0.8028 (t80) cc_final: 0.7572 (t80) REVERT: A 275 THR cc_start: 0.9014 (m) cc_final: 0.8734 (p) REVERT: A 344 MET cc_start: 0.7981 (mtt) cc_final: 0.7654 (mmt) REVERT: A 453 MET cc_start: 0.8356 (ttm) cc_final: 0.8090 (ttm) REVERT: A 473 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8467 (ppp) REVERT: A 500 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 576 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8583 (ttm) REVERT: A 633 GLU cc_start: 0.8499 (pm20) cc_final: 0.7935 (pt0) REVERT: B 96 MET cc_start: 0.8436 (tmm) cc_final: 0.8127 (tmm) REVERT: B 110 MET cc_start: 0.8931 (mtp) cc_final: 0.8575 (mtp) REVERT: B 259 MET cc_start: 0.8951 (tpp) cc_final: 0.8442 (tpp) REVERT: B 275 THR cc_start: 0.8815 (m) cc_final: 0.8383 (p) REVERT: B 399 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9037 (mm) REVERT: B 547 ASP cc_start: 0.8237 (m-30) cc_final: 0.7963 (t0) REVERT: B 590 GLU cc_start: 0.8696 (tp30) cc_final: 0.8248 (tp30) REVERT: B 602 MET cc_start: 0.8222 (tmm) cc_final: 0.7914 (tmm) REVERT: B 634 ASP cc_start: 0.8357 (m-30) cc_final: 0.7739 (p0) REVERT: B 641 GLN cc_start: 0.8552 (tt0) cc_final: 0.8255 (tp40) REVERT: C 237 ASN cc_start: 0.8779 (t0) cc_final: 0.8579 (m110) REVERT: C 283 ASP cc_start: 0.7515 (t0) cc_final: 0.6832 (t0) REVERT: C 289 GLN cc_start: 0.8939 (mt0) cc_final: 0.8689 (mt0) REVERT: C 473 MET cc_start: 0.8725 (ttt) cc_final: 0.7692 (ptp) REVERT: C 480 MET cc_start: 0.8646 (tpt) cc_final: 0.8436 (tpp) REVERT: C 495 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9045 (mm) REVERT: C 586 HIS cc_start: 0.7572 (t70) cc_final: 0.7325 (t-170) REVERT: C 589 ASP cc_start: 0.8463 (m-30) cc_final: 0.8249 (p0) REVERT: D 78 MET cc_start: 0.8627 (mpt) cc_final: 0.8094 (mpp) REVERT: D 308 ASP cc_start: 0.8322 (m-30) cc_final: 0.8004 (m-30) REVERT: D 322 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8435 (tpt170) REVERT: D 569 MET cc_start: 0.9232 (mmm) cc_final: 0.9026 (mmm) REVERT: E 8 GLN cc_start: 0.8121 (mt0) cc_final: 0.7895 (mt0) REVERT: E 13 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8931 (ttpt) REVERT: E 36 MET cc_start: 0.8380 (tpp) cc_final: 0.7740 (tpp) REVERT: E 49 GLN cc_start: 0.7479 (pm20) cc_final: 0.7235 (pm20) REVERT: E 84 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7904 (tm-30) REVERT: E 109 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8593 (mmt) REVERT: E 144 MET cc_start: 0.8254 (mmm) cc_final: 0.7954 (mmm) outliers start: 75 outliers final: 43 residues processed: 367 average time/residue: 0.2981 time to fit residues: 175.2800 Evaluate side-chains 322 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5734 > 50: distance: 42 - 57: 27.432 distance: 48 - 69: 17.193 distance: 53 - 57: 23.820 distance: 54 - 80: 8.624 distance: 57 - 58: 43.616 distance: 58 - 59: 13.858 distance: 58 - 61: 34.601 distance: 59 - 60: 26.207 distance: 59 - 69: 26.111 distance: 60 - 85: 8.359 distance: 61 - 62: 43.709 distance: 62 - 63: 29.451 distance: 62 - 64: 26.481 distance: 63 - 65: 25.832 distance: 64 - 66: 18.188 distance: 65 - 67: 13.074 distance: 66 - 67: 10.068 distance: 67 - 68: 13.237 distance: 69 - 70: 19.647 distance: 70 - 71: 7.549 distance: 70 - 73: 44.257 distance: 71 - 72: 14.157 distance: 71 - 80: 24.038 distance: 73 - 74: 18.853 distance: 74 - 75: 9.735 distance: 74 - 76: 10.677 distance: 75 - 77: 26.808 distance: 76 - 78: 21.568 distance: 77 - 79: 20.164 distance: 78 - 79: 25.755 distance: 80 - 81: 28.586 distance: 81 - 82: 31.643 distance: 81 - 84: 28.668 distance: 82 - 83: 20.868 distance: 82 - 85: 24.336 distance: 85 - 86: 25.574 distance: 86 - 87: 29.823 distance: 86 - 89: 31.064 distance: 87 - 88: 47.544 distance: 87 - 96: 38.011 distance: 89 - 90: 10.700 distance: 90 - 91: 9.316 distance: 91 - 92: 26.737 distance: 92 - 93: 43.324 distance: 93 - 94: 32.920 distance: 93 - 95: 35.361 distance: 96 - 97: 13.902 distance: 97 - 98: 25.092 distance: 98 - 99: 11.954 distance: 98 - 100: 19.860 distance: 100 - 101: 36.783 distance: 101 - 102: 30.648 distance: 101 - 104: 35.813 distance: 102 - 103: 34.916 distance: 102 - 111: 42.160 distance: 104 - 105: 19.530 distance: 105 - 106: 4.583 distance: 105 - 107: 8.111 distance: 106 - 108: 10.469 distance: 107 - 109: 12.154 distance: 108 - 110: 9.736 distance: 109 - 110: 5.719 distance: 111 - 112: 27.587 distance: 112 - 113: 36.274 distance: 112 - 115: 27.197 distance: 113 - 114: 56.712 distance: 113 - 120: 20.772 distance: 115 - 116: 21.851 distance: 116 - 117: 11.077 distance: 117 - 118: 18.768 distance: 117 - 119: 18.123 distance: 120 - 121: 12.226 distance: 121 - 122: 46.156 distance: 121 - 124: 15.325 distance: 122 - 123: 29.591 distance: 122 - 128: 24.848 distance: 124 - 125: 22.777 distance: 125 - 126: 20.487 distance: 126 - 127: 10.315 distance: 128 - 129: 56.716 distance: 129 - 130: 35.369 distance: 129 - 132: 28.845 distance: 130 - 131: 34.463 distance: 130 - 136: 36.344 distance: 132 - 133: 21.683 distance: 133 - 134: 14.133 distance: 133 - 135: 16.737 distance: 136 - 137: 45.267 distance: 137 - 138: 32.739 distance: 138 - 139: 23.226 distance: 138 - 140: 24.505