Starting phenix.real_space_refine on Sun Aug 24 11:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b5v_7058/08_2025/6b5v_7058_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b5v_7058/08_2025/6b5v_7058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b5v_7058/08_2025/6b5v_7058_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b5v_7058/08_2025/6b5v_7058_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b5v_7058/08_2025/6b5v_7058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b5v_7058/08_2025/6b5v_7058.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 140 5.16 5 Cl 12 4.86 5 C 12276 2.51 5 N 3188 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18933 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, 'ECL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.89, per 1000 atoms: 0.26 Number of scatterers: 18933 At special positions: 0 Unit cell: (128.7, 128.7, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 12 17.00 S 140 16.00 O 3316 8.00 N 3188 7.00 C 12276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 841.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 4 sheets defined 57.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.633A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 47 removed outlier: 4.494A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.071A pdb=" N ALA A 53 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.814A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 81 through 87 removed outlier: 4.277A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 98 removed outlier: 4.471A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 98' Processing helix chain 'A' and resid 102 through 107 removed outlier: 4.337A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.820A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.771A pdb=" N ILE A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 removed outlier: 4.162A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 132 through 139' Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.113A pdb=" N ARG A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.778A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 184' Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.710A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 4.215A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE A 256 " --> pdb=" O ASN A 252 " (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 302 through 309 removed outlier: 3.757A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.858A pdb=" N CYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.547A pdb=" N TYR A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 397 removed outlier: 4.251A pdb=" N GLU A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.587A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 removed outlier: 3.706A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 removed outlier: 4.311A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.776A pdb=" N TYR A 467 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 468 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 464 through 471' Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.794A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 removed outlier: 4.582A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 495' Processing helix chain 'A' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.713A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 3.570A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.979A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 removed outlier: 3.917A pdb=" N VAL A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 37 through 47 removed outlier: 4.495A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.071A pdb=" N ALA B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.815A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 68' Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.276A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 4.472A pdb=" N LEU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 98' Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.338A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.819A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.772A pdb=" N ILE B 123 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 4.161A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 139' Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.113A pdb=" N ARG B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.778A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 184' Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.711A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 4.215A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE B 256 " --> pdb=" O ASN B 252 " (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 302 through 309 removed outlier: 3.756A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.858A pdb=" N CYS B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 347 removed outlier: 3.547A pdb=" N TYR B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 397 removed outlier: 4.251A pdb=" N GLU B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 404 through 411 removed outlier: 3.586A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 removed outlier: 3.706A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 4.312A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.775A pdb=" N TYR B 467 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 468 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 471' Processing helix chain 'B' and resid 477 through 487 removed outlier: 3.794A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 4.583A pdb=" N PHE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 495' Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.713A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 3.569A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 582 removed outlier: 3.979A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.917A pdb=" N VAL B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 37 through 47 removed outlier: 4.494A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.070A pdb=" N ALA D 53 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.814A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 68' Processing helix chain 'D' and resid 81 through 87 removed outlier: 4.276A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 4.471A pdb=" N LEU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.337A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.819A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.771A pdb=" N ILE D 123 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 4.162A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 139' Processing helix chain 'D' and resid 149 through 153 removed outlier: 4.112A pdb=" N ARG D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.778A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 184' Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.709A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 4.214A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE D 256 " --> pdb=" O ASN D 252 " (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 302 through 309 removed outlier: 3.757A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.857A pdb=" N CYS D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 347 removed outlier: 3.546A pdb=" N TYR D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS D 347 " --> pdb=" O PHE D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 397 removed outlier: 4.252A pdb=" N GLU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.586A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 removed outlier: 3.707A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 4.312A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.776A pdb=" N TYR D 467 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 468 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 464 through 471' Processing helix chain 'D' and resid 477 through 487 removed outlier: 3.793A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 495 removed outlier: 4.583A pdb=" N PHE D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 495' Processing helix chain 'D' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 537 removed outlier: 3.713A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 567 removed outlier: 3.570A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 582 removed outlier: 3.980A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 606 removed outlier: 3.916A pdb=" N VAL D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 37 through 47 removed outlier: 4.495A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.070A pdb=" N ALA C 53 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.815A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 68' Processing helix chain 'C' and resid 81 through 87 removed outlier: 4.276A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 removed outlier: 4.472A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 93 through 98' Processing helix chain 'C' and resid 102 through 107 removed outlier: 4.338A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.819A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.771A pdb=" N ILE C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 removed outlier: 4.161A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 139' Processing helix chain 'C' and resid 149 through 153 removed outlier: 4.113A pdb=" N ARG C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.777A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 184' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.710A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 4.215A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE C 256 " --> pdb=" O ASN C 252 " (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 302 through 309 removed outlier: 3.757A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.858A pdb=" N CYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 347 removed outlier: 3.547A pdb=" N TYR C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 397 removed outlier: 4.252A pdb=" N GLU C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.586A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 removed outlier: 3.707A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 436 " --> pdb=" O TYR C 432 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 removed outlier: 4.311A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.777A pdb=" N TYR C 467 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 468 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 464 through 471' Processing helix chain 'C' and resid 477 through 487 removed outlier: 3.794A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 495 removed outlier: 4.582A pdb=" N PHE C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 495' Processing helix chain 'C' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE C 501 " --> pdb=" O MET C 497 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 537 removed outlier: 3.712A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.570A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 removed outlier: 3.979A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.917A pdb=" N VAL C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.782A pdb=" N THR A 274 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 635 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.783A pdb=" N THR B 274 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 635 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.783A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 635 " --> pdb=" O THR D 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.782A pdb=" N THR C 274 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 635 " --> pdb=" O THR C 274 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5999 1.34 - 1.46: 4556 1.46 - 1.58: 8589 1.58 - 1.70: 4 1.70 - 1.82: 240 Bond restraints: 19388 Sorted by residual: bond pdb=" C11 ECL B1001 " pdb=" C9 ECL B1001 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C11 ECL C1001 " pdb=" C9 ECL C1001 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C13 ECL D1001 " pdb=" C2 ECL D1001 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C13 ECL A1001 " pdb=" C2 ECL A1001 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C11 ECL A1001 " pdb=" C9 ECL A1001 " ideal model delta sigma weight residual 1.384 1.525 -0.141 2.00e-02 2.50e+03 5.00e+01 ... (remaining 19383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 24601 2.09 - 4.19: 1268 4.19 - 6.28: 284 6.28 - 8.38: 119 8.38 - 10.47: 52 Bond angle restraints: 26324 Sorted by residual: angle pdb=" N ARG D 584 " pdb=" CA ARG D 584 " pdb=" C ARG D 584 " ideal model delta sigma weight residual 111.07 120.47 -9.40 1.07e+00 8.73e-01 7.71e+01 angle pdb=" N ARG B 584 " pdb=" CA ARG B 584 " pdb=" C ARG B 584 " ideal model delta sigma weight residual 111.07 120.45 -9.38 1.07e+00 8.73e-01 7.69e+01 angle pdb=" N ARG A 584 " pdb=" CA ARG A 584 " pdb=" C ARG A 584 " ideal model delta sigma weight residual 111.07 120.45 -9.38 1.07e+00 8.73e-01 7.69e+01 angle pdb=" N ARG C 584 " pdb=" CA ARG C 584 " pdb=" C ARG C 584 " ideal model delta sigma weight residual 111.07 120.44 -9.37 1.07e+00 8.73e-01 7.66e+01 angle pdb=" C MET A 608 " pdb=" N PRO A 609 " pdb=" CA PRO A 609 " ideal model delta sigma weight residual 119.78 126.56 -6.78 1.03e+00 9.43e-01 4.33e+01 ... (remaining 26319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 9965 14.38 - 28.76: 1035 28.76 - 43.15: 336 43.15 - 57.53: 96 57.53 - 71.91: 36 Dihedral angle restraints: 11468 sinusoidal: 4592 harmonic: 6876 Sorted by residual: dihedral pdb=" CA LEU B 88 " pdb=" C LEU B 88 " pdb=" N TYR B 89 " pdb=" CA TYR B 89 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU A 88 " pdb=" C LEU A 88 " pdb=" N TYR A 89 " pdb=" CA TYR A 89 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU D 88 " pdb=" C LEU D 88 " pdb=" N TYR D 89 " pdb=" CA TYR D 89 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 11465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1894 0.048 - 0.095: 765 0.095 - 0.143: 241 0.143 - 0.191: 68 0.191 - 0.238: 16 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA ARG A 584 " pdb=" N ARG A 584 " pdb=" C ARG A 584 " pdb=" CB ARG A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ARG B 584 " pdb=" N ARG B 584 " pdb=" C ARG B 584 " pdb=" CB ARG B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG C 584 " pdb=" N ARG C 584 " pdb=" C ARG C 584 " pdb=" CB ARG C 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2981 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 516 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO C 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 517 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 517 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 516 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 517 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 517 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 516 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " -0.035 5.00e-02 4.00e+02 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 6163 2.85 - 3.36: 17528 3.36 - 3.87: 29314 3.87 - 4.39: 32057 4.39 - 4.90: 51670 Nonbonded interactions: 136732 Sorted by model distance: nonbonded pdb=" O LYS C 54 " pdb=" OH TYR C 89 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 54 " pdb=" OH TYR A 89 " model vdw 2.333 3.040 nonbonded pdb=" O LYS B 54 " pdb=" OH TYR B 89 " model vdw 2.333 3.040 nonbonded pdb=" O LYS D 54 " pdb=" OH TYR D 89 " model vdw 2.334 3.040 nonbonded pdb=" O GLY B 422 " pdb=" OH TYR B 467 " model vdw 2.368 3.040 ... (remaining 136727 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 29 through 1001) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.970 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.142 19388 Z= 0.395 Angle : 1.235 10.471 26324 Z= 0.654 Chirality : 0.059 0.238 2984 Planarity : 0.008 0.064 3316 Dihedral : 14.290 71.912 7028 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.55 % Allowed : 14.35 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.79 (0.14), residues: 2340 helix: -4.04 (0.10), residues: 936 sheet: -0.18 (0.67), residues: 56 loop : -2.72 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG D 385 TYR 0.025 0.002 TYR B 278 PHE 0.029 0.002 PHE C 574 TRP 0.023 0.002 TRP B 629 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00769 (19388) covalent geometry : angle 1.23456 (26324) hydrogen bonds : bond 0.22062 ( 484) hydrogen bonds : angle 7.77524 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 599 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 126 MET cc_start: 0.9034 (ttp) cc_final: 0.8753 (ppp) REVERT: A 252 ASN cc_start: 0.9223 (t0) cc_final: 0.9005 (t0) REVERT: A 302 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7368 (ttt180) REVERT: A 386 LEU cc_start: 0.8988 (tm) cc_final: 0.8626 (mt) REVERT: A 403 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7775 (tp30) REVERT: A 491 MET cc_start: 0.7159 (ttm) cc_final: 0.6956 (tmm) REVERT: A 509 HIS cc_start: 0.9078 (t70) cc_final: 0.8740 (t70) REVERT: A 603 MET cc_start: 0.8640 (tmt) cc_final: 0.8227 (tmm) REVERT: A 616 SER cc_start: 0.9293 (p) cc_final: 0.9022 (t) REVERT: B 326 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7711 (mmm-85) REVERT: B 386 LEU cc_start: 0.9132 (tm) cc_final: 0.8798 (mt) REVERT: B 403 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7923 (tp30) REVERT: B 509 HIS cc_start: 0.9060 (t70) cc_final: 0.8727 (t70) REVERT: B 535 GLU cc_start: 0.8201 (pp20) cc_final: 0.7917 (pp20) REVERT: B 578 MET cc_start: 0.9098 (tmt) cc_final: 0.8822 (tmm) REVERT: B 632 ARG cc_start: 0.8755 (ttp-170) cc_final: 0.8324 (tmm-80) REVERT: D 42 GLU cc_start: 0.8834 (pm20) cc_final: 0.8599 (pm20) REVERT: D 59 ARG cc_start: 0.8033 (tmm160) cc_final: 0.7576 (ttp80) REVERT: D 252 ASN cc_start: 0.9293 (t0) cc_final: 0.9083 (t0) REVERT: D 302 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7314 (ttt180) REVERT: D 309 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8347 (tm-30) REVERT: D 326 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7772 (mmm-85) REVERT: D 386 LEU cc_start: 0.8813 (tm) cc_final: 0.8402 (mt) REVERT: D 403 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7772 (tp30) REVERT: D 442 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: D 497 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8429 (tpt) REVERT: D 509 HIS cc_start: 0.9108 (t70) cc_final: 0.8837 (t70) REVERT: D 520 LEU cc_start: 0.8202 (tp) cc_final: 0.7993 (tt) REVERT: D 535 GLU cc_start: 0.8237 (pp20) cc_final: 0.7946 (pp20) REVERT: D 562 PHE cc_start: 0.9263 (t80) cc_final: 0.9036 (t80) REVERT: D 603 MET cc_start: 0.8629 (tmt) cc_final: 0.8236 (tmm) REVERT: D 616 SER cc_start: 0.9232 (p) cc_final: 0.8788 (t) REVERT: C 42 GLU cc_start: 0.8833 (pm20) cc_final: 0.8588 (pm20) REVERT: C 59 ARG cc_start: 0.8060 (tmm160) cc_final: 0.7679 (ttp80) REVERT: C 260 MET cc_start: 0.8662 (mmp) cc_final: 0.8451 (mmp) REVERT: C 302 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7308 (ttt180) REVERT: C 386 LEU cc_start: 0.9108 (tm) cc_final: 0.8774 (mt) REVERT: C 403 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7814 (tp30) REVERT: C 497 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (ttm) REVERT: C 509 HIS cc_start: 0.9066 (t70) cc_final: 0.8744 (t70) REVERT: C 535 GLU cc_start: 0.8262 (pp20) cc_final: 0.8014 (pp20) REVERT: C 603 MET cc_start: 0.8637 (tmt) cc_final: 0.8236 (tmm) outliers start: 72 outliers final: 17 residues processed: 634 average time/residue: 0.1591 time to fit residues: 147.8974 Evaluate side-chains 452 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 432 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.0374 > 50: distance: 23 - 35: 3.466 distance: 37 - 40: 6.438 distance: 40 - 41: 9.914 distance: 41 - 42: 9.124 distance: 42 - 43: 6.612 distance: 42 - 49: 7.182 distance: 44 - 45: 15.101 distance: 45 - 46: 6.267 distance: 46 - 47: 19.425 distance: 46 - 48: 6.404 distance: 49 - 50: 33.326 distance: 49 - 55: 18.416 distance: 50 - 51: 8.334 distance: 50 - 53: 37.364 distance: 51 - 52: 9.970 distance: 51 - 56: 11.510 distance: 53 - 54: 20.585 distance: 54 - 55: 32.130 distance: 56 - 57: 18.867 distance: 57 - 58: 18.699 distance: 57 - 60: 14.068 distance: 58 - 59: 17.778 distance: 58 - 61: 14.645 distance: 61 - 62: 19.157 distance: 62 - 63: 15.772 distance: 62 - 65: 18.616 distance: 63 - 64: 27.227 distance: 63 - 69: 29.918 distance: 65 - 66: 36.002 distance: 66 - 67: 24.858 distance: 66 - 68: 13.524 distance: 69 - 70: 16.799 distance: 70 - 71: 32.606 distance: 70 - 73: 25.168 distance: 71 - 72: 19.238 distance: 71 - 75: 24.591 distance: 72 - 91: 34.870 distance: 73 - 74: 3.761 distance: 75 - 76: 4.763 distance: 76 - 77: 4.653 distance: 76 - 79: 7.854 distance: 77 - 78: 25.913 distance: 77 - 84: 4.456 distance: 79 - 80: 7.524 distance: 80 - 81: 5.147 distance: 81 - 82: 7.704 distance: 81 - 83: 7.337 distance: 84 - 85: 22.821 distance: 84 - 90: 30.925 distance: 85 - 86: 7.201 distance: 85 - 88: 9.051 distance: 86 - 87: 21.499 distance: 86 - 91: 17.205 distance: 88 - 89: 14.780 distance: 89 - 90: 15.254 distance: 91 - 92: 24.244 distance: 92 - 93: 15.785 distance: 92 - 95: 14.501 distance: 93 - 94: 17.254 distance: 93 - 102: 13.511 distance: 95 - 96: 10.312 distance: 96 - 97: 12.280 distance: 96 - 98: 9.100 distance: 97 - 99: 9.920 distance: 98 - 100: 8.110 distance: 99 - 101: 5.576 distance: 100 - 101: 9.002 distance: 102 - 103: 13.979 distance: 103 - 104: 24.533 distance: 103 - 106: 26.677 distance: 104 - 105: 21.376 distance: 104 - 109: 23.971 distance: 106 - 107: 22.975 distance: 106 - 108: 13.023 distance: 109 - 110: 9.269 distance: 110 - 111: 6.490 distance: 111 - 112: 11.008 distance: 111 - 113: 13.603