Starting phenix.real_space_refine on Sun Aug 24 12:53:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4f_22667/08_2025/7k4f_22667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4f_22667/08_2025/7k4f_22667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k4f_22667/08_2025/7k4f_22667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4f_22667/08_2025/7k4f_22667_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k4f_22667/08_2025/7k4f_22667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4f_22667/08_2025/7k4f_22667.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.091 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 160 5.16 5 C 12855 2.51 5 N 3359 2.21 5 O 3485 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s 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: 19875 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "B" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "C" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "D" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' CA': 1, '5GK': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.21 Number of scatterers: 19875 At special positions: 0 Unit cell: (146.012, 146.012, 124.912, 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 S 160 16.00 F 15 9.00 O 3485 8.00 N 3359 7.00 C 12855 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: 1.42 Conformation dependent library (CDL) restraints added in 903.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 63.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.868A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.540A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.612A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.671A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.169A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.045A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.535A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.694A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.761A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.613A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 224 No H-bonds generated for 'chain 'A' and resid 223 through 224' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.597A pdb=" N LEU A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.703A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.688A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.879A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.534A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 4.102A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 402 removed outlier: 4.118A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.528A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.713A pdb=" N ARG A 414 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 415 " --> pdb=" O VAL A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 415' Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.721A pdb=" N GLY A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 4.436A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.852A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.759A pdb=" N TYR A 467 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.863A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 510 removed outlier: 4.046A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 5.090A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 removed outlier: 3.719A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.813A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 3.845A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.868A pdb=" N GLN B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.540A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.612A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.671A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.170A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.046A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.535A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.694A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.761A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.612A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 224 No H-bonds generated for 'chain 'B' and resid 223 through 224' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.596A pdb=" N LEU B 229 " --> pdb=" O GLY B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.703A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.688A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.880A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.535A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 4.102A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 402 removed outlier: 4.117A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.527A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.713A pdb=" N ARG B 414 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B 415 " --> pdb=" O VAL B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 411 through 415' Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.720A pdb=" N GLY B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 4.435A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.852A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.759A pdb=" N TYR B 467 " --> pdb=" O ASN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.863A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 510 removed outlier: 4.046A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 5.089A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.719A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 removed outlier: 3.814A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 608 removed outlier: 3.844A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 44 removed outlier: 3.868A pdb=" N GLN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.540A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.612A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.671A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.169A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 4.045A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.535A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.694A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.761A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.612A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 224 No H-bonds generated for 'chain 'C' and resid 223 through 224' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.596A pdb=" N LEU C 229 " --> pdb=" O GLY C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.703A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.689A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.880A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.535A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 4.101A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 402 removed outlier: 4.119A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.527A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.712A pdb=" N ARG C 414 " --> pdb=" O GLY C 411 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C 415 " --> pdb=" O VAL C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 415' Processing helix chain 'C' and resid 418 through 423 removed outlier: 3.720A pdb=" N GLY C 422 " --> pdb=" O GLN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 4.436A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.852A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.760A pdb=" N TYR C 467 " --> pdb=" O ASN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.863A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 510 removed outlier: 4.046A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 5.091A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 565 removed outlier: 3.718A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 584 removed outlier: 3.813A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 3.845A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 44 removed outlier: 3.868A pdb=" N GLN D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.540A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.612A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.672A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.169A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.045A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.535A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.695A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.761A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.613A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 224 No H-bonds generated for 'chain 'D' and resid 223 through 224' Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.597A pdb=" N LEU D 229 " --> pdb=" O GLY D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.702A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.688A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.879A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.535A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 4.101A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 402 removed outlier: 4.119A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.527A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.712A pdb=" N ARG D 414 " --> pdb=" O GLY D 411 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE D 415 " --> pdb=" O VAL D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 411 through 415' Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.721A pdb=" N GLY D 422 " --> pdb=" O GLN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 4.436A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.851A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.760A pdb=" N TYR D 467 " --> pdb=" O ASN D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 487 removed outlier: 3.863A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 510 removed outlier: 4.046A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 5.091A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 565 removed outlier: 3.719A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 584 removed outlier: 3.813A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 3.844A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 5.320A pdb=" N THR A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU A 277 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 275 " --> pdb=" O TRP A 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 270 removed outlier: 5.320A pdb=" N THR B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 277 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 275 " --> pdb=" O TRP B 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 270 removed outlier: 5.320A pdb=" N THR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU C 277 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 275 " --> pdb=" O TRP C 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 265 through 270 removed outlier: 5.321A pdb=" N THR D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU D 277 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 275 " --> pdb=" O TRP D 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2220 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: 2.24 Time building geometry restraints manager: 1.94 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: 6162 1.34 - 1.45: 3606 1.45 - 1.57: 10291 1.57 - 1.69: 10 1.69 - 1.81: 272 Bond restraints: 20341 Sorted by residual: bond pdb=" C01 5GK A 702 " pdb=" O01 5GK A 702 " ideal model delta sigma weight residual 1.230 1.403 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C01 5GK D 701 " pdb=" O01 5GK D 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" C01 5GK C 701 " pdb=" O01 5GK C 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C01 5GK A 701 " pdb=" O01 5GK A 701 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C01 5GK B 701 " pdb=" O01 5GK B 701 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 20336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 26742 3.49 - 6.98: 692 6.98 - 10.46: 150 10.46 - 13.95: 15 13.95 - 17.44: 8 Bond angle restraints: 27607 Sorted by residual: angle pdb=" C ARG C 224 " pdb=" N HIS C 225 " pdb=" CA HIS C 225 " ideal model delta sigma weight residual 121.54 132.34 -10.80 1.91e+00 2.74e-01 3.20e+01 angle pdb=" C ARG B 224 " pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 121.54 132.29 -10.75 1.91e+00 2.74e-01 3.17e+01 angle pdb=" C ARG A 224 " pdb=" N HIS A 225 " pdb=" CA HIS A 225 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C ARG D 224 " pdb=" N HIS D 225 " pdb=" CA HIS D 225 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 ... (remaining 27602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 11248 16.73 - 33.47: 775 33.47 - 50.20: 208 50.20 - 66.94: 19 66.94 - 83.67: 9 Dihedral angle restraints: 12259 sinusoidal: 5075 harmonic: 7184 Sorted by residual: dihedral pdb=" CA SER D 361 " pdb=" C SER D 361 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " ideal model delta harmonic sigma weight residual -180.00 -121.57 -58.43 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA SER A 361 " pdb=" C SER A 361 " pdb=" N PRO A 362 " pdb=" CA PRO A 362 " ideal model delta harmonic sigma weight residual -180.00 -121.61 -58.39 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA SER C 361 " pdb=" C SER C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta harmonic sigma weight residual -180.00 -121.65 -58.35 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 12256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2587 0.081 - 0.162: 460 0.162 - 0.243: 57 0.243 - 0.324: 13 0.324 - 0.405: 1 Chirality restraints: 3118 Sorted by residual: chirality pdb=" C14 5GK A 702 " pdb=" C13 5GK A 702 " pdb=" C15 5GK A 702 " pdb=" C22 5GK A 702 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C14 5GK A 701 " pdb=" C13 5GK A 701 " pdb=" C15 5GK A 701 " pdb=" C22 5GK A 701 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU C 574 " pdb=" CB LEU C 574 " pdb=" CD1 LEU C 574 " pdb=" CD2 LEU C 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3115 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 526 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO B 527 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 526 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO D 527 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 526 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO A 527 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.045 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4250 2.76 - 3.30: 18538 3.30 - 3.83: 31158 3.83 - 4.37: 35537 4.37 - 4.90: 58279 Nonbonded interactions: 147762 Sorted by model distance: nonbonded pdb=" OG SER D 506 " pdb=" OH TYR D 526 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 506 " pdb=" OH TYR B 526 " model vdw 2.232 3.040 nonbonded pdb=" OG SER C 506 " pdb=" OH TYR C 526 " model vdw 2.232 3.040 nonbonded pdb=" O ASP B 590 " pdb=" NH1 ARG B 594 " model vdw 2.305 3.120 ... (remaining 147757 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 26 through 701) 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: 1.260 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.012 0.173 20341 Z= 0.535 Angle : 1.381 17.439 27607 Z= 0.683 Chirality : 0.065 0.405 3118 Planarity : 0.008 0.079 3474 Dihedral : 12.592 83.670 7619 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 1.50 % Allowed : 9.76 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -5.98 (0.12), residues: 2448 helix: -4.20 (0.07), residues: 1324 sheet: -3.72 (0.52), residues: 40 loop : -3.55 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 615 TYR 0.021 0.003 TYR B 328 PHE 0.027 0.003 PHE C 523 TRP 0.020 0.003 TRP A 629 HIS 0.013 0.003 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.01166 (20341) covalent geometry : angle 1.38150 (27607) hydrogen bonds : bond 0.31640 ( 772) hydrogen bonds : angle 10.28336 ( 2220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 788 time to evaluate : 0.662 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: A 68 GLU cc_start: 0.8083 (tt0) cc_final: 0.7865 (mm-30) REVERT: A 92 LEU cc_start: 0.9243 (tt) cc_final: 0.8863 (tt) REVERT: A 96 MET cc_start: 0.8731 (mtp) cc_final: 0.8169 (mtm) REVERT: A 113 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8301 (tm-30) REVERT: A 150 THR cc_start: 0.9275 (p) cc_final: 0.8700 (p) REVERT: A 167 LEU cc_start: 0.8857 (pt) cc_final: 0.8582 (tp) REVERT: A 177 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8492 (tm-30) REVERT: A 208 ASN cc_start: 0.8223 (t0) cc_final: 0.7873 (t0) REVERT: A 306 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8848 (tm-30) REVERT: A 322 LYS cc_start: 0.9120 (tttt) cc_final: 0.8887 (ttmm) REVERT: A 331 MET cc_start: 0.7571 (mmp) cc_final: 0.7345 (tmm) REVERT: A 489 ASP cc_start: 0.8184 (m-30) cc_final: 0.7933 (m-30) REVERT: A 495 TRP cc_start: 0.8798 (m100) cc_final: 0.8539 (m100) REVERT: A 525 ASP cc_start: 0.8478 (t0) cc_final: 0.8262 (t70) REVERT: A 527 PRO cc_start: 0.9418 (Cg_exo) cc_final: 0.9173 (Cg_endo) REVERT: A 547 TYR cc_start: 0.9231 (m-10) cc_final: 0.8949 (m-10) REVERT: A 577 MET cc_start: 0.8873 (ptm) cc_final: 0.8459 (ptm) REVERT: A 622 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8052 (tp30) REVERT: B 92 LEU cc_start: 0.9159 (tt) cc_final: 0.8867 (tt) REVERT: B 96 MET cc_start: 0.8798 (mtp) cc_final: 0.8336 (mtm) REVERT: B 113 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8566 (tm-30) REVERT: B 128 GLN cc_start: 0.8091 (pt0) cc_final: 0.7784 (tm-30) REVERT: B 150 THR cc_start: 0.9188 (p) cc_final: 0.8809 (t) REVERT: B 177 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8544 (tm-30) REVERT: B 178 ILE cc_start: 0.9386 (mm) cc_final: 0.9171 (mm) REVERT: B 188 ASP cc_start: 0.8234 (t0) cc_final: 0.7842 (t0) REVERT: B 208 ASN cc_start: 0.8245 (t0) cc_final: 0.7859 (t0) REVERT: B 214 GLN cc_start: 0.9160 (tt0) cc_final: 0.8936 (tm-30) REVERT: B 294 GLU cc_start: 0.8365 (tt0) cc_final: 0.8154 (tt0) REVERT: B 300 LYS cc_start: 0.8319 (mttt) cc_final: 0.8066 (mttt) REVERT: B 322 LYS cc_start: 0.9126 (tttt) cc_final: 0.8852 (ttmm) REVERT: B 491 MET cc_start: 0.8249 (tpt) cc_final: 0.7994 (tpp) REVERT: B 527 PRO cc_start: 0.9344 (Cg_exo) cc_final: 0.9082 (Cg_endo) REVERT: B 622 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8139 (tp30) REVERT: C 113 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8416 (tm-30) REVERT: C 128 GLN cc_start: 0.8099 (pt0) cc_final: 0.7801 (tm-30) REVERT: C 150 THR cc_start: 0.9216 (p) cc_final: 0.8637 (p) REVERT: C 177 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8607 (tm-30) REVERT: C 178 ILE cc_start: 0.9415 (mm) cc_final: 0.9196 (mm) REVERT: C 188 ASP cc_start: 0.8181 (t0) cc_final: 0.7729 (t0) REVERT: C 208 ASN cc_start: 0.8332 (t0) cc_final: 0.7926 (t0) REVERT: C 214 GLN cc_start: 0.9174 (tt0) cc_final: 0.8954 (tm-30) REVERT: C 294 GLU cc_start: 0.8408 (tt0) cc_final: 0.8198 (tt0) REVERT: C 300 LYS cc_start: 0.8301 (mttt) cc_final: 0.8083 (mttt) REVERT: C 306 GLN cc_start: 0.9225 (tm-30) cc_final: 0.9010 (tm-30) REVERT: C 315 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9130 (mm-30) REVERT: C 321 TRP cc_start: 0.8769 (t60) cc_final: 0.8386 (t-100) REVERT: C 322 LYS cc_start: 0.9156 (tttt) cc_final: 0.8861 (ttmm) REVERT: C 367 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8758 (tt) REVERT: C 489 ASP cc_start: 0.8097 (m-30) cc_final: 0.7715 (m-30) REVERT: C 527 PRO cc_start: 0.9394 (Cg_exo) cc_final: 0.9158 (Cg_endo) REVERT: C 528 MET cc_start: 0.9074 (tpt) cc_final: 0.8832 (tpp) REVERT: C 577 MET cc_start: 0.8897 (ptm) cc_final: 0.8180 (ptm) REVERT: C 622 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8015 (tp30) REVERT: D 96 MET cc_start: 0.8919 (mtp) cc_final: 0.8322 (mtp) REVERT: D 113 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8397 (tp30) REVERT: D 177 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8591 (tm-30) REVERT: D 208 ASN cc_start: 0.8618 (t0) cc_final: 0.8332 (t0) REVERT: D 259 LEU cc_start: 0.9248 (mt) cc_final: 0.8999 (mt) REVERT: D 264 LYS cc_start: 0.8320 (pttt) cc_final: 0.8099 (pttm) REVERT: D 294 GLU cc_start: 0.8639 (tt0) cc_final: 0.8383 (tt0) REVERT: D 306 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 322 LYS cc_start: 0.9190 (tttt) cc_final: 0.8790 (ttmm) REVERT: D 345 MET cc_start: 0.8098 (tpp) cc_final: 0.7705 (mmt) REVERT: D 367 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8156 (tt) REVERT: D 377 TYR cc_start: 0.7055 (m-10) cc_final: 0.6816 (m-10) REVERT: D 382 ASP cc_start: 0.8366 (m-30) cc_final: 0.7923 (m-30) REVERT: D 473 GLN cc_start: 0.8696 (tp40) cc_final: 0.7790 (pm20) REVERT: D 525 ASP cc_start: 0.8344 (t0) cc_final: 0.8133 (t0) REVERT: D 528 MET cc_start: 0.9061 (tpt) cc_final: 0.8772 (tpp) REVERT: D 622 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 627 ASP cc_start: 0.8915 (m-30) cc_final: 0.8675 (m-30) outliers start: 32 outliers final: 6 residues processed: 805 average time/residue: 0.1274 time to fit residues: 155.8088 Evaluate side-chains 461 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 453 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN A 239 GLN A 252 ASN A 365 ASN A 464 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 230 GLN B 239 GLN B 252 ASN B 365 ASN B 464 ASN B 546 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 230 GLN C 239 GLN C 252 ASN C 261 GLN C 365 ASN C 546 ASN D 74 GLN D 201 HIS D 239 GLN D 252 ASN D 267 GLN D 365 ASN D 546 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105494 restraints weight = 36921.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108762 restraints weight = 17886.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110954 restraints weight = 10997.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112349 restraints weight = 7885.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113348 restraints weight = 6364.797| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20341 Z= 0.177 Angle : 0.849 10.743 27607 Z= 0.415 Chirality : 0.044 0.196 3118 Planarity : 0.006 0.067 3474 Dihedral : 7.465 49.085 2887 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.09 % Favored : 91.54 % Rotamer: Outliers : 5.16 % Allowed : 15.20 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -4.07 (0.14), residues: 2448 helix: -2.20 (0.11), residues: 1356 sheet: -1.51 (0.59), residues: 56 loop : -3.42 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 414 TYR 0.013 0.002 TYR D 67 PHE 0.015 0.002 PHE B 553 TRP 0.026 0.002 TRP C 613 HIS 0.007 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00401 (20341) covalent geometry : angle 0.84877 (27607) hydrogen bonds : bond 0.04900 ( 772) hydrogen bonds : angle 5.29895 ( 2220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 547 time to evaluate : 0.869 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: A 150 THR cc_start: 0.9294 (p) cc_final: 0.8644 (p) REVERT: A 177 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8503 (tm-30) REVERT: A 195 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8959 (tm) REVERT: A 302 ARG cc_start: 0.7543 (tpm170) cc_final: 0.6596 (tpm170) REVERT: A 305 ARG cc_start: 0.8907 (ttm110) cc_final: 0.8208 (ttp80) REVERT: A 306 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 322 LYS cc_start: 0.9281 (tttt) cc_final: 0.8994 (ttmm) REVERT: A 347 CYS cc_start: 0.8908 (t) cc_final: 0.8620 (t) REVERT: A 442 MET cc_start: 0.8950 (ttm) cc_final: 0.8661 (ttm) REVERT: A 536 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8951 (tt) REVERT: A 547 TYR cc_start: 0.8995 (m-10) cc_final: 0.8696 (m-10) REVERT: A 577 MET cc_start: 0.8622 (ptm) cc_final: 0.8160 (ptm) REVERT: A 605 GLU cc_start: 0.8470 (tt0) cc_final: 0.8259 (tt0) REVERT: A 622 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8012 (tp30) REVERT: B 150 THR cc_start: 0.9262 (p) cc_final: 0.8706 (p) REVERT: B 176 GLU cc_start: 0.8684 (pm20) cc_final: 0.8052 (pm20) REVERT: B 195 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9091 (tm) REVERT: B 270 TYR cc_start: 0.8963 (t80) cc_final: 0.8759 (t80) REVERT: B 279 ASP cc_start: 0.8062 (t70) cc_final: 0.7588 (t70) REVERT: B 300 LYS cc_start: 0.8304 (mttt) cc_final: 0.8098 (mttt) REVERT: B 306 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8865 (tm-30) REVERT: B 322 LYS cc_start: 0.9294 (tttt) cc_final: 0.8944 (ttmm) REVERT: B 345 MET cc_start: 0.8520 (tpp) cc_final: 0.8299 (mmt) REVERT: B 347 CYS cc_start: 0.8964 (t) cc_final: 0.8684 (t) REVERT: B 363 ARG cc_start: 0.7975 (mmt180) cc_final: 0.7437 (mmp80) REVERT: B 442 MET cc_start: 0.8909 (ttm) cc_final: 0.8636 (ttm) REVERT: B 536 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 622 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8078 (tp30) REVERT: C 113 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8327 (tm-30) REVERT: C 150 THR cc_start: 0.9264 (p) cc_final: 0.8721 (p) REVERT: C 177 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8468 (tm-30) REVERT: C 195 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9131 (tm) REVERT: C 270 TYR cc_start: 0.8879 (t80) cc_final: 0.8520 (t80) REVERT: C 279 ASP cc_start: 0.8091 (t70) cc_final: 0.7651 (t70) REVERT: C 306 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8929 (tm-30) REVERT: C 321 TRP cc_start: 0.8893 (t60) cc_final: 0.8549 (t-100) REVERT: C 322 LYS cc_start: 0.9285 (tttt) cc_final: 0.8984 (ttmm) REVERT: C 347 CYS cc_start: 0.8996 (t) cc_final: 0.8565 (t) REVERT: C 442 MET cc_start: 0.8862 (ttm) cc_final: 0.8606 (ttm) REVERT: C 536 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9028 (tt) REVERT: C 577 MET cc_start: 0.8715 (ptm) cc_final: 0.8404 (ptm) REVERT: C 618 ILE cc_start: 0.8892 (mp) cc_final: 0.8685 (pt) REVERT: C 622 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7928 (tp30) REVERT: D 54 LYS cc_start: 0.8403 (tptm) cc_final: 0.8154 (tptp) REVERT: D 208 ASN cc_start: 0.8251 (t0) cc_final: 0.7899 (t0) REVERT: D 279 ASP cc_start: 0.8561 (t0) cc_final: 0.8354 (t70) REVERT: D 306 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8538 (tm-30) REVERT: D 322 LYS cc_start: 0.9186 (tttt) cc_final: 0.8835 (ttmm) REVERT: D 367 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8132 (tt) REVERT: D 434 PHE cc_start: 0.8530 (t80) cc_final: 0.7961 (t80) REVERT: D 473 GLN cc_start: 0.8626 (tp40) cc_final: 0.7904 (pm20) REVERT: D 495 TRP cc_start: 0.8840 (m100) cc_final: 0.8561 (m100) REVERT: D 522 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.7827 (t-90) REVERT: D 536 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8901 (tt) REVERT: D 578 MET cc_start: 0.8934 (ttm) cc_final: 0.8699 (mtm) REVERT: D 622 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7680 (tp30) outliers start: 110 outliers final: 46 residues processed: 614 average time/residue: 0.1413 time to fit residues: 136.1807 Evaluate side-chains 507 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 452 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 211 optimal weight: 0.0050 chunk 200 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099191 restraints weight = 37236.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102378 restraints weight = 18489.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104537 restraints weight = 11537.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105986 restraints weight = 8350.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106912 restraints weight = 6727.098| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20341 Z= 0.210 Angle : 0.860 12.135 27607 Z= 0.410 Chirality : 0.045 0.197 3118 Planarity : 0.005 0.051 3474 Dihedral : 6.708 47.271 2879 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.93 % Favored : 89.83 % Rotamer: Outliers : 6.99 % Allowed : 18.29 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.92 (0.16), residues: 2448 helix: -1.02 (0.13), residues: 1364 sheet: -2.28 (0.50), residues: 76 loop : -3.21 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 323 TYR 0.012 0.002 TYR A 67 PHE 0.015 0.002 PHE B 425 TRP 0.018 0.002 TRP A 613 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00484 (20341) covalent geometry : angle 0.86032 (27607) hydrogen bonds : bond 0.04396 ( 772) hydrogen bonds : angle 4.92495 ( 2220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 466 time to evaluate : 0.742 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: A 176 GLU cc_start: 0.8699 (pm20) cc_final: 0.7997 (pm20) REVERT: A 239 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.8284 (tm-30) REVERT: A 279 ASP cc_start: 0.8240 (t0) cc_final: 0.8037 (t0) REVERT: A 302 ARG cc_start: 0.7469 (tpm170) cc_final: 0.6470 (tpm170) REVERT: A 305 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8262 (ttp80) REVERT: A 306 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8812 (tm-30) REVERT: A 322 LYS cc_start: 0.9334 (tttt) cc_final: 0.9054 (ttmm) REVERT: A 442 MET cc_start: 0.8826 (ttm) cc_final: 0.8576 (ttm) REVERT: A 536 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8943 (tt) REVERT: A 583 TRP cc_start: 0.8991 (p-90) cc_final: 0.8729 (p-90) REVERT: A 605 GLU cc_start: 0.8460 (tt0) cc_final: 0.8022 (tt0) REVERT: A 622 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7951 (tp30) REVERT: B 71 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7855 (pmmt) REVERT: B 176 GLU cc_start: 0.8577 (pm20) cc_final: 0.8185 (pm20) REVERT: B 177 GLU cc_start: 0.8889 (mp0) cc_final: 0.8562 (mp0) REVERT: B 195 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9188 (tm) REVERT: B 279 ASP cc_start: 0.8111 (t70) cc_final: 0.7643 (t0) REVERT: B 305 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8312 (ttp80) REVERT: B 306 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8984 (tm-30) REVERT: B 322 LYS cc_start: 0.9328 (tttt) cc_final: 0.9011 (ttmm) REVERT: B 363 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7482 (mmp80) REVERT: B 442 MET cc_start: 0.8845 (ttm) cc_final: 0.8595 (ttm) REVERT: B 621 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8233 (ttm170) REVERT: B 622 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7956 (tp30) REVERT: C 150 THR cc_start: 0.9292 (p) cc_final: 0.8772 (p) REVERT: C 176 GLU cc_start: 0.8682 (pm20) cc_final: 0.7965 (pm20) REVERT: C 178 ILE cc_start: 0.9400 (mm) cc_final: 0.9200 (tt) REVERT: C 195 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9201 (tm) REVERT: C 279 ASP cc_start: 0.8207 (t70) cc_final: 0.7770 (t0) REVERT: C 321 TRP cc_start: 0.8938 (t60) cc_final: 0.8587 (t-100) REVERT: C 322 LYS cc_start: 0.9285 (tttt) cc_final: 0.8984 (ttmm) REVERT: C 326 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7603 (ttm110) REVERT: C 367 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8435 (tt) REVERT: C 442 MET cc_start: 0.8847 (ttm) cc_final: 0.8592 (ttm) REVERT: C 522 HIS cc_start: 0.9086 (OUTLIER) cc_final: 0.7767 (t-90) REVERT: C 523 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8487 (p90) REVERT: C 605 GLU cc_start: 0.8315 (tt0) cc_final: 0.8105 (tt0) REVERT: C 622 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7998 (tp30) REVERT: D 164 GLU cc_start: 0.7949 (mp0) cc_final: 0.7674 (mp0) REVERT: D 167 LEU cc_start: 0.8930 (pt) cc_final: 0.8617 (tp) REVERT: D 208 ASN cc_start: 0.8119 (t0) cc_final: 0.7801 (t0) REVERT: D 239 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8965 (tm-30) REVERT: D 279 ASP cc_start: 0.8530 (t0) cc_final: 0.8041 (t0) REVERT: D 306 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8548 (tm-30) REVERT: D 322 LYS cc_start: 0.9270 (tttt) cc_final: 0.8950 (ttmm) REVERT: D 363 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7623 (mmp80) REVERT: D 367 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8337 (tt) REVERT: D 442 MET cc_start: 0.8864 (ttm) cc_final: 0.8453 (ttm) REVERT: D 495 TRP cc_start: 0.8863 (m100) cc_final: 0.8477 (m100) REVERT: D 522 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8143 (t-90) REVERT: D 536 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8934 (tt) REVERT: D 547 TYR cc_start: 0.9060 (m-10) cc_final: 0.8831 (m-10) REVERT: D 577 MET cc_start: 0.9324 (ttp) cc_final: 0.8915 (ttp) REVERT: D 622 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7692 (tp30) outliers start: 149 outliers final: 83 residues processed: 562 average time/residue: 0.1407 time to fit residues: 124.7187 Evaluate side-chains 515 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 419 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 621 ARG Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 199 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 261 GLN D 40 GLN D 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103690 restraints weight = 36895.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107027 restraints weight = 18039.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109251 restraints weight = 11111.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110778 restraints weight = 7967.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111741 restraints weight = 6340.015| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20341 Z= 0.128 Angle : 0.790 13.642 27607 Z= 0.370 Chirality : 0.043 0.212 3118 Planarity : 0.004 0.043 3474 Dihedral : 6.277 46.874 2877 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.80 % Favored : 91.91 % Rotamer: Outliers : 5.21 % Allowed : 21.44 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.34 (0.16), residues: 2448 helix: -0.45 (0.14), residues: 1356 sheet: -2.22 (0.51), residues: 76 loop : -3.10 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 323 TYR 0.018 0.001 TYR A 216 PHE 0.026 0.001 PHE D 553 TRP 0.024 0.001 TRP B 613 HIS 0.005 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00287 (20341) covalent geometry : angle 0.79022 (27607) hydrogen bonds : bond 0.03549 ( 772) hydrogen bonds : angle 4.52989 ( 2220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 478 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8433 (pm20) cc_final: 0.8228 (pm20) REVERT: A 177 GLU cc_start: 0.8501 (mp0) cc_final: 0.8278 (mp0) REVERT: A 227 ASP cc_start: 0.6179 (m-30) cc_final: 0.5906 (t70) REVERT: A 302 ARG cc_start: 0.7422 (tpm170) cc_final: 0.7159 (tpm170) REVERT: A 306 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 322 LYS cc_start: 0.9320 (tttt) cc_final: 0.8989 (ttmm) REVERT: A 440 MET cc_start: 0.8723 (ptm) cc_final: 0.8450 (tmm) REVERT: A 442 MET cc_start: 0.8807 (ttm) cc_final: 0.8552 (ttm) REVERT: A 605 GLU cc_start: 0.8444 (tt0) cc_final: 0.7919 (tt0) REVERT: A 622 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7945 (tp30) REVERT: B 113 GLU cc_start: 0.8783 (tp30) cc_final: 0.8568 (tp30) REVERT: B 177 GLU cc_start: 0.8715 (mp0) cc_final: 0.8448 (tm-30) REVERT: B 195 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9135 (tm) REVERT: B 239 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.9087 (tm-30) REVERT: B 279 ASP cc_start: 0.8067 (t70) cc_final: 0.7564 (t0) REVERT: B 302 ARG cc_start: 0.7507 (tpm170) cc_final: 0.6320 (tpm170) REVERT: B 305 ARG cc_start: 0.8853 (ttm110) cc_final: 0.8040 (ttp80) REVERT: B 306 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8870 (tm-30) REVERT: B 322 LYS cc_start: 0.9335 (tttt) cc_final: 0.8976 (ttmm) REVERT: B 363 ARG cc_start: 0.7942 (mmt180) cc_final: 0.7443 (mmp80) REVERT: B 440 MET cc_start: 0.8755 (ptm) cc_final: 0.8454 (tmm) REVERT: B 442 MET cc_start: 0.8822 (ttm) cc_final: 0.8567 (ttm) REVERT: B 536 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9072 (tt) REVERT: B 622 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7960 (tp30) REVERT: C 193 ASP cc_start: 0.7924 (m-30) cc_final: 0.7595 (m-30) REVERT: C 195 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9124 (tm) REVERT: C 239 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.9046 (tm-30) REVERT: C 279 ASP cc_start: 0.8150 (t70) cc_final: 0.7671 (t0) REVERT: C 302 ARG cc_start: 0.7356 (tpm170) cc_final: 0.6670 (tpm170) REVERT: C 305 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8443 (ttp80) REVERT: C 306 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8594 (tm-30) REVERT: C 321 TRP cc_start: 0.8906 (t60) cc_final: 0.8510 (t-100) REVERT: C 322 LYS cc_start: 0.9273 (tttt) cc_final: 0.8945 (ttmm) REVERT: C 326 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7275 (ttp80) REVERT: C 367 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8343 (tt) REVERT: C 442 MET cc_start: 0.8822 (ttm) cc_final: 0.8576 (ttm) REVERT: C 518 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: C 536 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9099 (tt) REVERT: C 622 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8004 (tp30) REVERT: D 71 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7272 (pmmt) REVERT: D 279 ASP cc_start: 0.8436 (t0) cc_final: 0.7977 (t0) REVERT: D 303 GLU cc_start: 0.8436 (mp0) cc_final: 0.8216 (pm20) REVERT: D 306 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8480 (tm-30) REVERT: D 322 LYS cc_start: 0.9277 (tttt) cc_final: 0.8936 (ttmm) REVERT: D 357 ASN cc_start: 0.7313 (p0) cc_final: 0.7094 (p0) REVERT: D 522 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: D 523 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7995 (p90) REVERT: D 605 GLU cc_start: 0.8002 (tt0) cc_final: 0.7525 (tt0) REVERT: D 622 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7724 (tp30) outliers start: 111 outliers final: 60 residues processed: 557 average time/residue: 0.1479 time to fit residues: 127.8363 Evaluate side-chains 502 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 431 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 68.0918 > 50: distance: 56 - 60: 20.178 distance: 60 - 61: 31.680 distance: 61 - 62: 25.656 distance: 61 - 64: 41.288 distance: 62 - 63: 56.168 distance: 62 - 68: 33.346 distance: 64 - 65: 23.201 distance: 65 - 66: 34.268 distance: 65 - 67: 23.151 distance: 68 - 69: 4.718 distance: 69 - 70: 15.492 distance: 70 - 71: 40.262 distance: 70 - 72: 25.352 distance: 73 - 74: 40.365 distance: 74 - 75: 52.205 distance: 74 - 80: 40.908 distance: 76 - 77: 50.832 distance: 77 - 78: 44.836 distance: 77 - 79: 39.429 distance: 80 - 81: 19.079 distance: 81 - 82: 32.708 distance: 81 - 84: 33.824 distance: 82 - 83: 36.810 distance: 82 - 87: 25.713 distance: 84 - 85: 43.535 distance: 84 - 86: 64.331 distance: 87 - 88: 33.832 distance: 88 - 89: 34.022 distance: 88 - 91: 27.763 distance: 89 - 90: 27.139 distance: 89 - 94: 32.340 distance: 91 - 92: 57.467 distance: 91 - 93: 37.526 distance: 94 - 95: 43.825 distance: 95 - 96: 36.594 distance: 95 - 98: 4.877 distance: 96 - 97: 35.893 distance: 96 - 102: 26.944 distance: 97 - 128: 38.495 distance: 98 - 99: 4.012 distance: 99 - 100: 3.274 distance: 99 - 101: 18.369 distance: 102 - 103: 19.801 distance: 103 - 104: 49.228 distance: 103 - 106: 15.560 distance: 104 - 105: 39.261 distance: 104 - 112: 17.293 distance: 106 - 107: 32.432 distance: 107 - 108: 49.854 distance: 107 - 109: 44.637 distance: 108 - 110: 48.180 distance: 109 - 111: 45.696 distance: 110 - 111: 43.674 distance: 112 - 113: 30.181 distance: 113 - 114: 27.641 distance: 113 - 116: 26.837 distance: 114 - 115: 48.854 distance: 114 - 120: 32.281 distance: 116 - 117: 14.094 distance: 116 - 118: 34.737 distance: 117 - 119: 39.176 distance: 120 - 121: 43.827 distance: 121 - 122: 45.536 distance: 121 - 124: 55.377 distance: 122 - 123: 25.182 distance: 122 - 128: 12.911 distance: 124 - 125: 31.827 distance: 125 - 126: 35.679 distance: 125 - 127: 34.448 distance: 128 - 129: 6.646 distance: 129 - 130: 52.697 distance: 129 - 132: 51.784 distance: 130 - 131: 38.928 distance: 130 - 136: 34.231 distance: 132 - 133: 57.502 distance: 132 - 134: 39.581