Starting phenix.real_space_refine on Sat Sep 28 15:09:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/09_2024/6o1n_0593.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/09_2024/6o1n_0593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/09_2024/6o1n_0593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/09_2024/6o1n_0593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/09_2024/6o1n_0593.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/09_2024/6o1n_0593.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12660 2.51 5 N 3320 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Restraints were copied for chains: C, B, D Time building chain proxies: 10.63, per 1000 atoms: 0.54 Number of scatterers: 19608 At special positions: 0 Unit cell: (134.493, 132.375, 124.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3488 8.00 N 3320 7.00 C 12660 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: 4.50 Conformation dependent library (CDL) restraints added in 2.4 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 4 sheets defined 55.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 55 " --> pdb=" O GLN 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: 3.608A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.547A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 205' Processing helix chain 'A' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.883A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.645A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.929A pdb=" N GLN A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.633A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.275A pdb=" N MET A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.509A pdb=" N HIS A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.024A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.562A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.612A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.548A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 205' Processing helix chain 'B' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE B 211 " --> pdb=" O ASN B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.882A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.646A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.928A pdb=" N GLN B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.634A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.276A pdb=" N MET B 466 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.024A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.561A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.548A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 205' Processing helix chain 'C' and resid 208 through 211 removed outlier: 3.801A pdb=" N PHE C 211 " --> pdb=" O ASN C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.881A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.645A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.929A pdb=" N GLN C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.813A pdb=" N VAL C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.565A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.644A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.633A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 3.615A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.503A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 4.274A pdb=" N MET C 466 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.023A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.562A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.648A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.595A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.609A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.065A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.547A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 205' Processing helix chain 'D' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.883A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.646A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.928A pdb=" N GLN D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.634A pdb=" N MET D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 406 through 411 removed outlier: 4.140A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 4.276A pdb=" N MET D 466 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.023A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.561A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.832A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 274 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.831A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 274 " --> pdb=" O ASN B 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.831A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 274 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 264 through 268 removed outlier: 6.832A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 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: 5.18 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3164 1.31 - 1.44: 5472 1.44 - 1.56: 11197 1.56 - 1.68: 3 1.68 - 1.81: 228 Bond restraints: 20064 Sorted by residual: bond pdb=" N TYR D 623 " pdb=" CA TYR D 623 " ideal model delta sigma weight residual 1.462 1.557 -0.096 1.44e-02 4.82e+03 4.40e+01 bond pdb=" N TYR B 623 " pdb=" CA TYR B 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.39e+01 bond pdb=" N TYR C 623 " pdb=" CA TYR C 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.36e+01 bond pdb=" N TYR A 623 " pdb=" CA TYR A 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.36e+01 bond pdb=" N PRO C 614 " pdb=" CD PRO C 614 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 26409 3.25 - 6.49: 655 6.49 - 9.74: 140 9.74 - 12.98: 24 12.98 - 16.23: 20 Bond angle restraints: 27248 Sorted by residual: angle pdb=" N GLN C 370 " pdb=" CA GLN C 370 " pdb=" C GLN C 370 " ideal model delta sigma weight residual 110.30 126.53 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN A 370 " pdb=" CA GLN A 370 " pdb=" C GLN A 370 " ideal model delta sigma weight residual 110.30 126.53 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN B 370 " pdb=" CA GLN B 370 " pdb=" C GLN B 370 " ideal model delta sigma weight residual 110.30 126.51 -16.21 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN D 370 " pdb=" CA GLN D 370 " pdb=" C GLN D 370 " ideal model delta sigma weight residual 110.30 126.49 -16.19 1.50e+00 4.44e-01 1.16e+02 angle pdb=" N LEU C 229 " pdb=" CA LEU C 229 " pdb=" C LEU C 229 " ideal model delta sigma weight residual 110.24 94.65 15.59 1.47e+00 4.63e-01 1.12e+02 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 11047 15.19 - 30.37: 719 30.37 - 45.56: 126 45.56 - 60.74: 36 60.74 - 75.93: 8 Dihedral angle restraints: 11936 sinusoidal: 4780 harmonic: 7156 Sorted by residual: dihedral pdb=" C PHE B 611 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " pdb=" CB PHE B 611 " ideal model delta harmonic sigma weight residual -122.60 -102.25 -20.35 0 2.50e+00 1.60e-01 6.63e+01 dihedral pdb=" C PHE D 611 " pdb=" N PHE D 611 " pdb=" CA PHE D 611 " pdb=" CB PHE D 611 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" C PHE A 611 " pdb=" N PHE A 611 " pdb=" CA PHE A 611 " pdb=" CB PHE A 611 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 ... (remaining 11933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2639 0.090 - 0.181: 405 0.181 - 0.271: 32 0.271 - 0.361: 18 0.361 - 0.452: 6 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA PHE C 611 " pdb=" N PHE C 611 " pdb=" C PHE C 611 " pdb=" CB PHE C 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE D 611 " pdb=" N PHE D 611 " pdb=" C PHE D 611 " pdb=" CB PHE D 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA PHE B 611 " pdb=" N PHE B 611 " pdb=" C PHE B 611 " pdb=" CB PHE B 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 ... (remaining 3097 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 623 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C TYR B 623 " 0.085 2.00e-02 2.50e+03 pdb=" O TYR B 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY B 624 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 623 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C TYR A 623 " 0.085 2.00e-02 2.50e+03 pdb=" O TYR A 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY A 624 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 623 " -0.023 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C TYR C 623 " 0.084 2.00e-02 2.50e+03 pdb=" O TYR C 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY C 624 " -0.027 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 52 2.47 - 3.07: 11599 3.07 - 3.68: 27979 3.68 - 4.29: 40943 4.29 - 4.90: 66731 Nonbonded interactions: 147304 Sorted by model distance: nonbonded pdb=" O GLN B 230 " pdb=" O SER B 231 " model vdw 1.856 3.040 nonbonded pdb=" O GLN A 230 " pdb=" O SER A 231 " model vdw 1.857 3.040 nonbonded pdb=" O GLN C 230 " pdb=" O SER C 231 " model vdw 1.857 3.040 nonbonded pdb=" O GLN D 230 " pdb=" O SER D 231 " model vdw 1.857 3.040 nonbonded pdb=" O HIS D 228 " pdb=" C LEU D 229 " model vdw 2.009 3.270 ... (remaining 147299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 40.520 Find NCS groups from input model: 0.600 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.119 20064 Z= 0.685 Angle : 1.374 16.229 27248 Z= 0.811 Chirality : 0.072 0.452 3100 Planarity : 0.009 0.097 3460 Dihedral : 11.022 75.928 7312 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.39 % Favored : 93.11 % Rotamer: Outliers : 1.51 % Allowed : 1.51 % Favored : 96.98 % Cbeta Deviations : 0.52 % 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: -6.01 (0.12), residues: 2440 helix: -4.73 (0.05), residues: 1272 sheet: -3.48 (0.46), residues: 84 loop : -2.88 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 629 HIS 0.015 0.003 HIS B 238 PHE 0.044 0.004 PHE C 508 TYR 0.012 0.003 TYR A 349 ARG 0.008 0.001 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 552 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8340 (tp) cc_final: 0.8099 (tm) REVERT: A 80 GLU cc_start: 0.7434 (pm20) cc_final: 0.7097 (pm20) REVERT: A 91 ASN cc_start: 0.6288 (m-40) cc_final: 0.5709 (p0) REVERT: A 136 LEU cc_start: 0.7604 (mt) cc_final: 0.7254 (mp) REVERT: A 220 LEU cc_start: 0.7886 (mt) cc_final: 0.7397 (pp) REVERT: A 455 SER cc_start: 0.8724 (m) cc_final: 0.8461 (p) REVERT: A 580 ASP cc_start: 0.7161 (m-30) cc_final: 0.6910 (t70) REVERT: B 44 ILE cc_start: 0.7495 (mt) cc_final: 0.7259 (mt) REVERT: B 111 LEU cc_start: 0.8187 (mt) cc_final: 0.7908 (mt) REVERT: B 311 THR cc_start: 0.8466 (t) cc_final: 0.8171 (m) REVERT: B 368 LEU cc_start: 0.7935 (mp) cc_final: 0.7729 (pp) REVERT: B 381 GLN cc_start: 0.7538 (mt0) cc_final: 0.7300 (tm-30) REVERT: B 406 ASP cc_start: 0.8349 (t0) cc_final: 0.7897 (t0) REVERT: C 80 GLU cc_start: 0.8097 (pm20) cc_final: 0.7374 (pm20) REVERT: C 111 LEU cc_start: 0.8296 (mt) cc_final: 0.8015 (mt) REVERT: C 112 CYS cc_start: 0.7642 (t) cc_final: 0.7259 (t) REVERT: C 303 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7380 (mm-30) REVERT: D 115 PHE cc_start: 0.7779 (m-80) cc_final: 0.7570 (m-80) REVERT: D 215 MET cc_start: 0.8165 (tpp) cc_final: 0.7960 (tpp) REVERT: D 228 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5821 (m-70) REVERT: D 233 GLU cc_start: 0.6768 (tt0) cc_final: 0.5945 (tp30) REVERT: D 314 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7579 (ttpp) REVERT: D 381 GLN cc_start: 0.6866 (mt0) cc_final: 0.6493 (tm-30) REVERT: D 442 MET cc_start: 0.7923 (mmm) cc_final: 0.7720 (mmt) REVERT: D 447 MET cc_start: 0.8044 (mmm) cc_final: 0.7760 (mmt) outliers start: 32 outliers final: 15 residues processed: 567 average time/residue: 1.2609 time to fit residues: 805.3914 Evaluate side-chains 305 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 289 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 286 TRP Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 0.0040 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 51 GLN A 128 GLN A 157 HIS A 208 ASN A 217 ASN A 238 HIS A 252 ASN A 446 ASN A 519 ASN A 572 ASN A 596 GLN B 51 GLN B 128 GLN B 157 HIS B 238 HIS B 252 ASN B 446 ASN C 51 GLN C 128 GLN C 157 HIS C 238 HIS C 252 ASN C 446 ASN D 51 GLN D 214 GLN D 238 HIS D 446 ASN D 519 ASN D 572 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20064 Z= 0.207 Angle : 0.719 11.155 27248 Z= 0.367 Chirality : 0.043 0.236 3100 Planarity : 0.005 0.047 3460 Dihedral : 7.331 56.621 2705 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.22 % Rotamer: Outliers : 4.15 % Allowed : 11.93 % Favored : 83.92 % 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: -4.77 (0.14), residues: 2440 helix: -3.40 (0.10), residues: 1280 sheet: -3.31 (0.45), residues: 84 loop : -2.70 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 583 HIS 0.006 0.001 HIS A 157 PHE 0.020 0.001 PHE C 211 TYR 0.018 0.001 TYR D 621 ARG 0.010 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 352 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8266 (tp) cc_final: 0.8006 (tm) REVERT: A 80 GLU cc_start: 0.7440 (pm20) cc_final: 0.6904 (pm20) REVERT: A 91 ASN cc_start: 0.6543 (m-40) cc_final: 0.5693 (p0) REVERT: A 220 LEU cc_start: 0.8208 (mt) cc_final: 0.7377 (pp) REVERT: A 381 GLN cc_start: 0.5881 (tm-30) cc_final: 0.5379 (tm-30) REVERT: A 442 MET cc_start: 0.8054 (mmt) cc_final: 0.7789 (mmm) REVERT: A 455 SER cc_start: 0.8684 (m) cc_final: 0.8418 (p) REVERT: A 570 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7997 (mmm) REVERT: B 220 LEU cc_start: 0.8052 (mt) cc_final: 0.7684 (mt) REVERT: B 234 LEU cc_start: 0.7744 (mm) cc_final: 0.7449 (mm) REVERT: B 381 GLN cc_start: 0.7353 (mt0) cc_final: 0.6584 (tm-30) REVERT: B 406 ASP cc_start: 0.8254 (t0) cc_final: 0.7890 (t0) REVERT: B 482 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7319 (mm) REVERT: C 80 GLU cc_start: 0.8035 (pm20) cc_final: 0.7250 (pm20) REVERT: C 111 LEU cc_start: 0.8051 (mt) cc_final: 0.7722 (mt) REVERT: C 139 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6274 (ttm110) REVERT: C 250 GLU cc_start: 0.7598 (tp30) cc_final: 0.7397 (tp30) REVERT: C 367 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6832 (mt) REVERT: C 474 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7341 (ttp) REVERT: C 578 MET cc_start: 0.7974 (mmm) cc_final: 0.7747 (mtt) REVERT: D 115 PHE cc_start: 0.7696 (m-80) cc_final: 0.7374 (m-80) REVERT: D 123 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6267 (pt) REVERT: D 209 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6659 (mmpt) REVERT: D 215 MET cc_start: 0.8109 (tpp) cc_final: 0.7891 (mmm) REVERT: D 233 GLU cc_start: 0.6897 (tt0) cc_final: 0.6333 (tp30) REVERT: D 381 GLN cc_start: 0.6817 (mt0) cc_final: 0.6335 (tm-30) REVERT: D 515 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6844 (mm-30) outliers start: 88 outliers final: 22 residues processed: 402 average time/residue: 1.1323 time to fit residues: 518.7690 Evaluate side-chains 292 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 286 TRP Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 150 optimal weight: 0.0170 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS B 127 ASN B 128 GLN B 157 HIS B 252 ASN C 127 ASN C 128 GLN C 157 HIS C 252 ASN C 267 GLN C 483 GLN D 214 GLN D 257 GLN D 519 ASN D 572 ASN D 582 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20064 Z= 0.187 Angle : 0.668 12.851 27248 Z= 0.332 Chirality : 0.042 0.259 3100 Planarity : 0.004 0.044 3460 Dihedral : 6.299 56.082 2686 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 3.63 % Allowed : 15.24 % Favored : 81.13 % 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: -3.90 (0.15), residues: 2440 helix: -2.52 (0.12), residues: 1300 sheet: -2.92 (0.50), residues: 76 loop : -2.51 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 583 HIS 0.006 0.001 HIS A 157 PHE 0.026 0.001 PHE C 211 TYR 0.021 0.001 TYR D 467 ARG 0.008 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 301 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8366 (tp) cc_final: 0.8067 (tm) REVERT: A 43 ARG cc_start: 0.7383 (mmm-85) cc_final: 0.7166 (mmm-85) REVERT: A 57 ASP cc_start: 0.5681 (m-30) cc_final: 0.5259 (t0) REVERT: A 80 GLU cc_start: 0.7667 (pm20) cc_final: 0.7101 (pm20) REVERT: A 91 ASN cc_start: 0.6559 (m-40) cc_final: 0.5849 (p0) REVERT: A 126 MET cc_start: 0.6981 (tpt) cc_final: 0.6752 (ttp) REVERT: A 220 LEU cc_start: 0.7989 (mt) cc_final: 0.7348 (pp) REVERT: A 381 GLN cc_start: 0.6247 (tm-30) cc_final: 0.5683 (tm-30) REVERT: B 111 LEU cc_start: 0.8102 (tm) cc_final: 0.7824 (mt) REVERT: B 195 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6330 (tt) REVERT: B 216 TYR cc_start: 0.7313 (t80) cc_final: 0.6836 (t80) REVERT: B 220 LEU cc_start: 0.8014 (mt) cc_final: 0.7565 (mt) REVERT: B 234 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7450 (mm) REVERT: B 291 SER cc_start: 0.8060 (t) cc_final: 0.7831 (p) REVERT: B 381 GLN cc_start: 0.7369 (mt0) cc_final: 0.6576 (tm-30) REVERT: B 406 ASP cc_start: 0.8223 (t0) cc_final: 0.7830 (t0) REVERT: B 482 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7379 (mm) REVERT: B 485 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6379 (mtp) REVERT: C 80 GLU cc_start: 0.8122 (pm20) cc_final: 0.7302 (pm20) REVERT: C 104 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7192 (pp20) REVERT: C 111 LEU cc_start: 0.7918 (mt) cc_final: 0.7659 (mt) REVERT: C 139 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6364 (ttm110) REVERT: C 220 LEU cc_start: 0.8087 (mt) cc_final: 0.7377 (pp) REVERT: C 591 GLU cc_start: 0.7321 (tt0) cc_final: 0.7001 (tt0) REVERT: D 115 PHE cc_start: 0.7709 (m-80) cc_final: 0.7502 (m-80) REVERT: D 123 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6390 (pt) REVERT: D 209 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6611 (mmpt) REVERT: D 215 MET cc_start: 0.8311 (tpp) cc_final: 0.7803 (mmm) REVERT: D 233 GLU cc_start: 0.7228 (tt0) cc_final: 0.6336 (tp30) REVERT: D 246 LEU cc_start: 0.6966 (tp) cc_final: 0.6332 (tt) REVERT: D 322 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7883 (mmmt) REVERT: D 381 GLN cc_start: 0.6892 (mt0) cc_final: 0.6389 (tm-30) REVERT: D 515 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7696 (mm-30) outliers start: 77 outliers final: 23 residues processed: 352 average time/residue: 1.0606 time to fit residues: 430.5102 Evaluate side-chains 305 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 274 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 0.0020 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 0.2980 chunk 235 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 206 GLN A 310 GLN B 157 HIS B 206 GLN C 157 HIS C 206 GLN C 310 GLN D 127 ASN D 129 ASN D 519 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20064 Z= 0.150 Angle : 0.616 11.372 27248 Z= 0.303 Chirality : 0.040 0.199 3100 Planarity : 0.004 0.057 3460 Dihedral : 5.398 53.125 2680 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.10 % Allowed : 16.08 % Favored : 79.81 % 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: -3.26 (0.15), residues: 2440 helix: -1.86 (0.13), residues: 1312 sheet: -3.05 (0.48), residues: 76 loop : -2.37 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 583 HIS 0.003 0.000 HIS B 201 PHE 0.013 0.001 PHE B 72 TYR 0.016 0.001 TYR C 32 ARG 0.009 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 309 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8352 (tp) cc_final: 0.8056 (tm) REVERT: A 43 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.7061 (mmm-85) REVERT: A 57 ASP cc_start: 0.5595 (m-30) cc_final: 0.5208 (t0) REVERT: A 91 ASN cc_start: 0.6625 (m-40) cc_final: 0.5897 (p0) REVERT: A 99 MET cc_start: 0.5969 (mtp) cc_final: 0.5734 (mtm) REVERT: A 220 LEU cc_start: 0.7943 (mt) cc_final: 0.7323 (pp) REVERT: A 381 GLN cc_start: 0.6307 (tm-30) cc_final: 0.5371 (tm-30) REVERT: A 570 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7959 (mmm) REVERT: B 80 GLU cc_start: 0.8203 (pm20) cc_final: 0.7357 (pm20) REVERT: B 111 LEU cc_start: 0.7925 (tm) cc_final: 0.7601 (mt) REVERT: B 220 LEU cc_start: 0.7946 (mt) cc_final: 0.7486 (mt) REVERT: B 291 SER cc_start: 0.8014 (t) cc_final: 0.7770 (p) REVERT: B 381 GLN cc_start: 0.7234 (mt0) cc_final: 0.6459 (tm-30) REVERT: B 406 ASP cc_start: 0.8224 (t0) cc_final: 0.7843 (t0) REVERT: B 482 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7348 (mm) REVERT: B 577 MET cc_start: 0.7613 (ttp) cc_final: 0.7122 (ttm) REVERT: B 635 ASN cc_start: 0.7537 (m-40) cc_final: 0.7318 (m-40) REVERT: C 51 GLN cc_start: 0.6913 (tt0) cc_final: 0.6697 (tt0) REVERT: C 80 GLU cc_start: 0.8146 (pm20) cc_final: 0.7332 (pm20) REVERT: C 104 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: C 111 LEU cc_start: 0.7897 (mt) cc_final: 0.7681 (mt) REVERT: C 139 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6466 (ttm110) REVERT: C 220 LEU cc_start: 0.8071 (mt) cc_final: 0.7351 (pp) REVERT: C 371 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6675 (pmtt) REVERT: C 414 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7621 (ttp-110) REVERT: C 608 MET cc_start: 0.7286 (mtm) cc_final: 0.6965 (mtm) REVERT: D 123 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6337 (mp) REVERT: D 209 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6714 (mmmt) REVERT: D 214 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7956 (tp-100) REVERT: D 215 MET cc_start: 0.8325 (tpp) cc_final: 0.7904 (mmm) REVERT: D 233 GLU cc_start: 0.7016 (tt0) cc_final: 0.6215 (tp30) REVERT: D 250 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: D 283 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8249 (mp) REVERT: D 311 THR cc_start: 0.8553 (t) cc_final: 0.8185 (m) REVERT: D 322 LYS cc_start: 0.8352 (mmtp) cc_final: 0.7950 (mmmt) REVERT: D 381 GLN cc_start: 0.6974 (mt0) cc_final: 0.6331 (tm-30) REVERT: D 415 TYR cc_start: 0.6879 (t80) cc_final: 0.6674 (t80) REVERT: D 491 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6582 (ptp) REVERT: D 515 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: D 578 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7019 (mmt) REVERT: D 608 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6855 (mpp) REVERT: D 612 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7514 (mp) outliers start: 87 outliers final: 22 residues processed: 358 average time/residue: 1.0558 time to fit residues: 435.5751 Evaluate side-chains 319 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 282 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-dev-5461/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-dev-5461/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: 68.126 > 50: distance: 16 - 22: 7.713 distance: 22 - 23: 22.364 distance: 23 - 24: 39.467 distance: 23 - 26: 23.285 distance: 24 - 25: 47.980 distance: 24 - 28: 60.490 distance: 26 - 27: 11.486 distance: 28 - 29: 68.126 distance: 29 - 30: 20.955 distance: 30 - 31: 24.315 distance: 30 - 32: 25.916 distance: 32 - 33: 14.524 distance: 32 - 122: 17.944 distance: 33 - 34: 26.974 distance: 33 - 36: 23.342 distance: 34 - 35: 25.537 distance: 34 - 40: 19.508 distance: 35 - 119: 26.148 distance: 36 - 37: 20.541 distance: 36 - 38: 8.421 distance: 37 - 39: 15.915 distance: 40 - 41: 8.965 distance: 41 - 42: 3.826 distance: 41 - 44: 4.338 distance: 42 - 43: 17.055 distance: 42 - 46: 10.823 distance: 44 - 45: 7.237 distance: 46 - 47: 31.835 distance: 47 - 48: 26.566 distance: 48 - 49: 14.436 distance: 48 - 50: 17.591 distance: 50 - 51: 21.302 distance: 51 - 52: 10.097 distance: 51 - 54: 11.319 distance: 52 - 53: 11.807 distance: 52 - 62: 32.218 distance: 54 - 55: 10.090 distance: 55 - 56: 8.952 distance: 55 - 57: 12.699 distance: 56 - 58: 9.593 distance: 57 - 59: 9.866 distance: 58 - 60: 6.842 distance: 59 - 60: 4.340 distance: 60 - 61: 9.320 distance: 62 - 63: 14.651 distance: 63 - 64: 21.259 distance: 63 - 66: 14.588 distance: 64 - 65: 31.101 distance: 64 - 71: 18.739 distance: 66 - 67: 17.610 distance: 67 - 68: 8.509 distance: 68 - 69: 5.376 distance: 68 - 70: 3.790 distance: 71 - 72: 3.927 distance: 72 - 73: 21.002 distance: 72 - 75: 32.947 distance: 73 - 74: 22.398 distance: 73 - 83: 46.567 distance: 75 - 76: 18.973 distance: 76 - 77: 7.128 distance: 76 - 78: 3.519 distance: 77 - 79: 4.038 distance: 78 - 80: 4.585 distance: 79 - 81: 5.383 distance: 80 - 81: 5.404 distance: 81 - 82: 3.431 distance: 83 - 84: 36.847 distance: 84 - 85: 19.750 distance: 85 - 86: 30.805 distance: 85 - 87: 4.241 distance: 87 - 88: 5.844 distance: 88 - 91: 6.996 distance: 89 - 90: 3.912 distance: 89 - 95: 8.156 distance: 91 - 92: 6.554 distance: 92 - 93: 5.613