Starting phenix.real_space_refine on Sun Sep 13 01:49:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4f_22667/09_2026/7k4f_22667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4f_22667/09_2026/7k4f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4f_22667/09_2026/7k4f_22667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4f_22667/09_2026/7k4f_22667.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4f_22667/09_2026/7k4f_22667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4f_22667/09_2026/7k4f_22667_neut.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.58, per 1000 atoms: 0.23 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: 1.79 Conformation dependent library (CDL) restraints added in 942.0 milliseconds 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: 0.54 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: 3.06 Time building geometry restraints manager: 2.28 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: 1.380 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.200 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 are 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/Z covalent geometry : bond 0.01166 / 0.54 (20341) covalent geometry : angle 1.38150 / 0.68 (27607) hydrogen bonds : bond 0.31640 / 20.63 ( 772) hydrogen bonds : angle 10.28336 / 7.23 ( 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 : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.9014 (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: 0.7761 (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: 0.1423 time to fit residues: 175.6831 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 : 0.748 ------------------------------------------------------------------------------- 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... ** 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: 0.8555 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 are 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/Z covalent geometry : bond 0.00401 / 0.18 (20341) covalent geometry : angle 0.84877 / 0.41 (27607) hydrogen bonds : bond 0.04900 / 3.19 ( 772) hydrogen bonds : angle 5.29895 / 3.71 ( 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 : 0.591 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: 0.8965 (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: 0.8550 (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: 0.1314 time to fit residues: 127.9602 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 : 0.759 ------------------------------------------------------------------------------- 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... ** 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: 0.8640 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 are 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/Z covalent geometry : bond 0.00484 / 0.21 (20341) covalent geometry : angle 0.86032 / 0.41 (27607) hydrogen bonds : bond 0.04396 / 2.86 ( 772) hydrogen bonds : angle 4.92495 / 3.44 ( 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 : 0.752 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: 0.8038 (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: 0.8888 (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: 0.8865 (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: 0.1237 time to fit residues: 111.0823 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 : 0.601 ------------------------------------------------------------------------------- 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... ** 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: 0.8567 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 are 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/Z covalent geometry : bond 0.00287 / 0.13 (20341) covalent geometry : angle 0.79022 / 0.37 (27607) hydrogen bonds : bond 0.03549 / 2.31 ( 772) hydrogen bonds : angle 4.52989 / 3.14 ( 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 : 0.814 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: 0.5907 (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: 0.8975 (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: 0.1368 time to fit residues: 119.4035 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 : 0.923 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 244 random chunks: chunk 78 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.0918 > 50:) chunk 137 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 127 optimal weight: 0.0980 chunk 205 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 261 GLN D 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102291 restraints weight = 37008.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105556 restraints weight = 18295.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107759 restraints weight = 11361.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109263 restraints weight = 8179.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110176 restraints weight = 6536.261| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20341 Z= 0.141 Angle : 0.787 14.495 27607 Z= 0.367 Chirality : 0.043 0.214 3118 Planarity : 0.004 0.050 3474 Dihedral : 5.913 46.088 2875 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.95 % Favored : 90.81 % Rotamer: Outliers : 6.14 % Allowed : 22.05 % Favored : 71.81 % 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 are not related in a simple way. whole: -1.93 (0.17), residues: 2448 helix: -0.05 (0.14), residues: 1368 sheet: -2.24 (0.52), residues: 76 loop : -3.01 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 355 TYR 0.018 0.001 TYR A 216 PHE 0.024 0.001 PHE D 553 TRP 0.014 0.001 TRP A 583 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (20341) covalent geometry : angle 0.78689 / 0.37 (27607) hydrogen bonds : bond 0.03532 / 2.30 ( 772) hydrogen bonds : angle 4.43002 / 3.06 ( 2220) *********************** REFINEMENT MACRO_CYCLE 5 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 585 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 454 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.9676 (mt) cc_final: 0.9393 (tt) REVERT: A 227 ASP cc_start: 0.6177 (m-30) cc_final: 0.5919 (t70) REVERT: A 239 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9112 (tm-30) REVERT: A 302 ARG cc_start: 0.7463 (tpm170) cc_final: 0.7262 (tpm170) REVERT: A 306 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 322 LYS cc_start: 0.9315 (tttt) cc_final: 0.8984 (ttmm) REVERT: A 357 ASN cc_start: 0.8240 (p0) cc_final: 0.7885 (p0) REVERT: A 440 MET cc_start: 0.8793 (ptm) cc_final: 0.8573 (tmm) REVERT: A 442 MET cc_start: 0.8857 (ttm) cc_final: 0.8618 (ttm) REVERT: A 536 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9065 (tt) REVERT: A 547 TYR cc_start: 0.8842 (m-10) cc_final: 0.8541 (m-10) REVERT: A 605 GLU cc_start: 0.8463 (tt0) cc_final: 0.7952 (tt0) REVERT: A 622 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7925 (tp30) REVERT: B 113 GLU cc_start: 0.8828 (tp30) cc_final: 0.8543 (tp30) REVERT: B 176 GLU cc_start: 0.8480 (pm20) cc_final: 0.8076 (pm20) REVERT: B 177 GLU cc_start: 0.8647 (mp0) cc_final: 0.8395 (mp0) REVERT: B 195 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9211 (tm) REVERT: B 202 ILE cc_start: 0.9612 (mt) cc_final: 0.9403 (tt) REVERT: B 239 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.9113 (tm-30) REVERT: B 279 ASP cc_start: 0.8083 (t70) cc_final: 0.7574 (t0) REVERT: B 306 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8865 (tm-30) REVERT: B 322 LYS cc_start: 0.9326 (tttt) cc_final: 0.8977 (ttmm) REVERT: B 357 ASN cc_start: 0.8307 (p0) cc_final: 0.7977 (p0) REVERT: B 363 ARG cc_start: 0.7949 (mmt180) cc_final: 0.7442 (mmp80) REVERT: B 440 MET cc_start: 0.8806 (ptm) cc_final: 0.8555 (tmm) REVERT: B 442 MET cc_start: 0.8830 (ttm) cc_final: 0.8591 (ttm) REVERT: B 536 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9076 (tt) REVERT: B 622 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7963 (tp30) REVERT: C 193 ASP cc_start: 0.7816 (m-30) cc_final: 0.7059 (t0) REVERT: C 195 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9209 (tm) REVERT: C 239 GLN cc_start: 0.9422 (OUTLIER) cc_final: 0.9075 (tm-30) REVERT: C 279 ASP cc_start: 0.8220 (t70) cc_final: 0.7727 (t0) REVERT: C 302 ARG cc_start: 0.7408 (tpm170) cc_final: 0.6683 (tpm170) REVERT: C 305 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8469 (ttp80) REVERT: C 306 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 321 TRP cc_start: 0.8888 (t60) cc_final: 0.8641 (t-100) REVERT: C 322 LYS cc_start: 0.9255 (tttt) cc_final: 0.8962 (ttmm) REVERT: C 326 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7588 (mtm-85) REVERT: C 367 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8353 (tt) REVERT: C 434 PHE cc_start: 0.8162 (t80) cc_final: 0.7869 (m-80) REVERT: C 442 MET cc_start: 0.8858 (ttm) cc_final: 0.8632 (ttm) REVERT: C 518 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: C 536 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9074 (tt) REVERT: C 577 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8893 (ttm) REVERT: C 622 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8001 (tp30) REVERT: D 54 LYS cc_start: 0.8587 (tptp) cc_final: 0.8213 (tptp) REVERT: D 71 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7321 (pmmt) REVERT: D 215 MET cc_start: 0.8738 (ttp) cc_final: 0.8412 (tmm) REVERT: D 239 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: D 279 ASP cc_start: 0.8450 (t0) cc_final: 0.7970 (t0) REVERT: D 302 ARG cc_start: 0.7789 (tpm170) cc_final: 0.7460 (tpp-160) REVERT: D 306 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8506 (tm-30) REVERT: D 322 LYS cc_start: 0.9277 (tttt) cc_final: 0.8950 (ttmm) REVERT: D 474 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7630 (ttp) REVERT: D 522 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.7804 (t-90) REVERT: D 523 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8202 (p90) REVERT: D 536 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9073 (tt) REVERT: D 605 GLU cc_start: 0.8157 (tt0) cc_final: 0.7697 (tt0) REVERT: D 622 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7698 (tp30) outliers start: 131 outliers final: 83 residues processed: 539 average time/residue: 0.1317 time to fit residues: 111.7277 Evaluate side-chains 523 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 423 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU 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 203 LEU Chi-restraints excluded: chain B residue 204 ILE 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 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 438 VAL 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 B residue 542 ASP Chi-restraints excluded: chain B residue 551 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 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 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 377 TYR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 465 VAL 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 557 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 601 THR 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 239 GLN 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 368 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 VAL 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 474 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 575 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 203 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 0.3980 chunk 198 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 370 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102961 restraints weight = 36849.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106234 restraints weight = 18263.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108432 restraints weight = 11340.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109913 restraints weight = 8189.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110819 restraints weight = 6565.338| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20341 Z= 0.142 Angle : 0.793 15.158 27607 Z= 0.368 Chirality : 0.043 0.239 3118 Planarity : 0.004 0.047 3474 Dihedral : 5.769 45.844 2875 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.62 % Favored : 91.18 % Rotamer: Outliers : 6.33 % Allowed : 23.17 % Favored : 70.50 % 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 are not related in a simple way. whole: -1.66 (0.17), residues: 2448 helix: 0.21 (0.14), residues: 1372 sheet: -2.20 (0.52), residues: 76 loop : -2.96 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 355 TYR 0.017 0.001 TYR A 216 PHE 0.027 0.001 PHE C 553 TRP 0.012 0.001 TRP A 583 HIS 0.007 0.001 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (20341) covalent geometry : angle 0.79277 / 0.37 (27607) hydrogen bonds : bond 0.03464 / 2.26 ( 772) hydrogen bonds : angle 4.38111 / 3.03 ( 2220) *********************** REFINEMENT MACRO_CYCLE 6 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 590 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 455 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7643 (mt) cc_final: 0.7422 (mt) REVERT: A 202 ILE cc_start: 0.9701 (mt) cc_final: 0.9366 (tt) REVERT: A 239 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.9090 (tm-30) REVERT: A 302 ARG cc_start: 0.7565 (tpm170) cc_final: 0.7267 (tpp-160) REVERT: A 305 ARG cc_start: 0.9008 (ttm110) cc_final: 0.8784 (ttm-80) REVERT: A 306 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 322 LYS cc_start: 0.9309 (tttt) cc_final: 0.8985 (ttmm) REVERT: A 357 ASN cc_start: 0.8327 (p0) cc_final: 0.8120 (p0) REVERT: A 440 MET cc_start: 0.8835 (ptm) cc_final: 0.8614 (tmm) REVERT: A 442 MET cc_start: 0.8855 (ttm) cc_final: 0.8613 (ttm) REVERT: A 536 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9026 (tt) REVERT: A 547 TYR cc_start: 0.8858 (m-10) cc_final: 0.8547 (m-10) REVERT: A 605 GLU cc_start: 0.8507 (tt0) cc_final: 0.8031 (tt0) REVERT: A 622 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7931 (tp30) REVERT: B 113 GLU cc_start: 0.8849 (tp30) cc_final: 0.8523 (tp30) REVERT: B 177 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8349 (tm-30) REVERT: B 195 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9208 (tm) REVERT: B 239 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9111 (tm-30) REVERT: B 279 ASP cc_start: 0.8093 (t70) cc_final: 0.7570 (t0) REVERT: B 305 ARG cc_start: 0.8968 (ttm110) cc_final: 0.8765 (ttp80) REVERT: B 306 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8860 (tm-30) REVERT: B 322 LYS cc_start: 0.9326 (tttt) cc_final: 0.8978 (ttmm) REVERT: B 363 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7468 (mmp80) REVERT: B 440 MET cc_start: 0.8825 (ptm) cc_final: 0.8602 (tmm) REVERT: B 442 MET cc_start: 0.8821 (ttm) cc_final: 0.8581 (ttm) REVERT: B 536 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9060 (tt) REVERT: B 622 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7948 (tp30) REVERT: C 195 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9228 (tm) REVERT: C 239 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9061 (tm-30) REVERT: C 279 ASP cc_start: 0.8277 (t70) cc_final: 0.7755 (t0) REVERT: C 302 ARG cc_start: 0.7446 (tpm170) cc_final: 0.6690 (tpm170) REVERT: C 305 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8455 (ttp80) REVERT: C 306 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 321 TRP cc_start: 0.8877 (t60) cc_final: 0.8608 (t-100) REVERT: C 322 LYS cc_start: 0.9230 (tttt) cc_final: 0.8935 (ttmm) REVERT: C 326 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7560 (mtm-85) REVERT: C 367 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8293 (tt) REVERT: C 442 MET cc_start: 0.8848 (ttm) cc_final: 0.8601 (ttm) REVERT: C 518 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8740 (tp30) REVERT: C 522 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.7831 (t-90) REVERT: C 523 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8555 (p90) REVERT: C 536 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9073 (tt) REVERT: C 578 MET cc_start: 0.9045 (ttm) cc_final: 0.8630 (mtm) REVERT: C 622 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7996 (tp30) REVERT: D 54 LYS cc_start: 0.8657 (tptp) cc_final: 0.8090 (tptp) REVERT: D 71 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7261 (pmmt) REVERT: D 78 MET cc_start: 0.8226 (ptp) cc_final: 0.7619 (pmm) REVERT: D 80 GLU cc_start: 0.8278 (pm20) cc_final: 0.7937 (pm20) REVERT: D 215 MET cc_start: 0.8738 (ttp) cc_final: 0.8404 (tmm) REVERT: D 239 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: D 279 ASP cc_start: 0.8440 (t0) cc_final: 0.7956 (t0) REVERT: D 302 ARG cc_start: 0.7767 (tpt170) cc_final: 0.7345 (tpp-160) REVERT: D 306 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 322 LYS cc_start: 0.9274 (tttt) cc_final: 0.8955 (ttmm) REVERT: D 349 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: D 474 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7677 (ttp) REVERT: D 522 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.7853 (t-90) REVERT: D 523 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8183 (p90) REVERT: D 536 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9086 (tt) REVERT: D 622 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7735 (tp30) outliers start: 135 outliers final: 86 residues processed: 548 average time/residue: 0.1284 time to fit residues: 111.7170 Evaluate side-chains 543 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 438 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 128 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU 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 203 LEU Chi-restraints excluded: chain B residue 204 ILE 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 340 ILE Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL 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 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 B residue 542 ASP 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 204 ILE Chi-restraints excluded: chain C residue 220 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 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 368 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 444 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 522 HIS Chi-restraints excluded: chain C residue 523 PHE 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 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL 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 349 TYR Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 VAL 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 474 MET Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 601 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 76 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100532 restraints weight = 37405.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103759 restraints weight = 18549.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105936 restraints weight = 11562.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107397 restraints weight = 8351.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108375 restraints weight = 6715.662| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20341 Z= 0.177 Angle : 0.811 15.275 27607 Z= 0.379 Chirality : 0.044 0.231 3118 Planarity : 0.004 0.044 3474 Dihedral : 5.683 45.470 2873 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.76 % Favored : 89.95 % Rotamer: Outliers : 6.66 % Allowed : 23.41 % Favored : 69.93 % 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 are not related in a simple way. whole: -1.50 (0.17), residues: 2448 helix: 0.32 (0.14), residues: 1376 sheet: -2.19 (0.52), residues: 76 loop : -2.88 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 355 TYR 0.019 0.001 TYR A 216 PHE 0.025 0.002 PHE C 553 TRP 0.027 0.001 TRP A 613 HIS 0.008 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (20341) covalent geometry : angle 0.81135 / 0.38 (27607) hydrogen bonds : bond 0.03705 / 2.42 ( 772) hydrogen bonds : angle 4.49924 / 3.11 ( 2220) *********************** REFINEMENT MACRO_CYCLE 7 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 590 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 448 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7685 (mt) cc_final: 0.7459 (mt) REVERT: A 227 ASP cc_start: 0.6265 (m-30) cc_final: 0.5934 (t70) REVERT: A 239 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.9011 (tm-30) REVERT: A 302 ARG cc_start: 0.7611 (tpm170) cc_final: 0.7131 (tpm170) REVERT: A 305 ARG cc_start: 0.9018 (ttm110) cc_final: 0.8348 (ttp80) REVERT: A 306 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 322 LYS cc_start: 0.9314 (tttt) cc_final: 0.8987 (ttmm) REVERT: A 440 MET cc_start: 0.8858 (ptm) cc_final: 0.8633 (tmm) REVERT: A 442 MET cc_start: 0.8879 (ttm) cc_final: 0.8633 (ttm) REVERT: A 536 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 547 TYR cc_start: 0.8889 (m-10) cc_final: 0.8558 (m-10) REVERT: A 605 GLU cc_start: 0.8487 (tt0) cc_final: 0.8077 (tt0) REVERT: A 622 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7923 (tp30) REVERT: B 113 GLU cc_start: 0.8880 (tp30) cc_final: 0.8568 (tp30) REVERT: B 195 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9172 (tm) REVERT: B 202 ILE cc_start: 0.9641 (mt) cc_final: 0.9362 (tt) REVERT: B 239 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: B 279 ASP cc_start: 0.8244 (t70) cc_final: 0.7726 (t0) REVERT: B 305 ARG cc_start: 0.9017 (ttm110) cc_final: 0.8268 (ttp80) REVERT: B 306 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8605 (tm-30) REVERT: B 322 LYS cc_start: 0.9291 (tttt) cc_final: 0.8967 (ttmm) REVERT: B 363 ARG cc_start: 0.7884 (mmt180) cc_final: 0.7418 (mmp80) REVERT: B 440 MET cc_start: 0.8865 (ptm) cc_final: 0.8621 (tmm) REVERT: B 442 MET cc_start: 0.8883 (ttm) cc_final: 0.8635 (ttm) REVERT: B 536 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9065 (tt) REVERT: B 622 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7977 (tp30) REVERT: C 239 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 279 ASP cc_start: 0.8286 (t70) cc_final: 0.7755 (t0) REVERT: C 302 ARG cc_start: 0.7489 (tpm170) cc_final: 0.6921 (tpm170) REVERT: C 303 GLU cc_start: 0.8565 (mp0) cc_final: 0.8286 (pm20) REVERT: C 305 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8461 (ttp80) REVERT: C 306 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8552 (tm-30) REVERT: C 321 TRP cc_start: 0.8927 (t60) cc_final: 0.8533 (t-100) REVERT: C 322 LYS cc_start: 0.9225 (tttt) cc_final: 0.8943 (ttmm) REVERT: C 326 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7585 (mtm-85) REVERT: C 367 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8315 (tt) REVERT: C 442 MET cc_start: 0.8892 (ttm) cc_final: 0.8654 (ttm) REVERT: C 518 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: C 520 LEU cc_start: 0.8928 (tt) cc_final: 0.8651 (tp) REVERT: C 522 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: C 523 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8575 (p90) REVERT: C 536 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9082 (tt) REVERT: C 578 MET cc_start: 0.9075 (ttm) cc_final: 0.8596 (mtm) REVERT: C 605 GLU cc_start: 0.8454 (tp30) cc_final: 0.8206 (tp30) REVERT: C 622 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8012 (tp30) REVERT: D 71 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7373 (pmmt) REVERT: D 215 MET cc_start: 0.8752 (ttp) cc_final: 0.8369 (tmm) REVERT: D 239 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: D 279 ASP cc_start: 0.8412 (t0) cc_final: 0.7952 (t0) REVERT: D 302 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7343 (tpp-160) REVERT: D 306 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 322 LYS cc_start: 0.9263 (tttt) cc_final: 0.8959 (ttmm) REVERT: D 326 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7628 (mtm-85) REVERT: D 349 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: D 454 MET cc_start: 0.9065 (tpt) cc_final: 0.8773 (tpt) REVERT: D 474 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7800 (ttp) REVERT: D 522 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: D 523 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8367 (p90) REVERT: D 536 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9102 (tt) REVERT: D 622 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7818 (tp30) outliers start: 142 outliers final: 101 residues processed: 545 average time/residue: 0.1399 time to fit residues: 120.7073 Evaluate side-chains 551 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 432 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 128 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 387 VAL 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 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE 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 194 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 220 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 286 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 387 VAL 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 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 220 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 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 368 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 465 VAL 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 522 HIS Chi-restraints excluded: chain C residue 523 PHE 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 557 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR 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 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 391 VAL 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 474 MET Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 240 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104756 restraints weight = 36877.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108098 restraints weight = 18170.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110354 restraints weight = 11245.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111876 restraints weight = 8069.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112910 restraints weight = 6448.172| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20341 Z= 0.123 Angle : 0.806 16.268 27607 Z= 0.370 Chirality : 0.043 0.274 3118 Planarity : 0.004 0.049 3474 Dihedral : 5.566 45.242 2873 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.62 % Favored : 91.18 % Rotamer: Outliers : 4.83 % Allowed : 25.61 % Favored : 69.56 % 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 are not related in a simple way. whole: -1.35 (0.17), residues: 2448 helix: 0.39 (0.14), residues: 1396 sheet: -1.33 (0.63), residues: 56 loop : -2.84 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 414 TYR 0.020 0.001 TYR A 216 PHE 0.026 0.001 PHE C 553 TRP 0.018 0.001 TRP A 583 HIS 0.008 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (20341) covalent geometry : angle 0.80581 / 0.37 (27607) hydrogen bonds : bond 0.03300 / 2.15 ( 772) hydrogen bonds : angle 4.24340 / 2.91 ( 2220) *********************** REFINEMENT MACRO_CYCLE 8 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 584 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 481 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8766 (pm20) cc_final: 0.8530 (pt0) REVERT: A 239 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.8967 (tm-30) REVERT: A 302 ARG cc_start: 0.7541 (tpm170) cc_final: 0.7062 (tpm170) REVERT: A 305 ARG cc_start: 0.8996 (ttm110) cc_final: 0.8387 (ttp80) REVERT: A 306 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8468 (tm-30) REVERT: A 322 LYS cc_start: 0.9316 (tttt) cc_final: 0.8974 (ttmm) REVERT: A 347 CYS cc_start: 0.8952 (t) cc_final: 0.8733 (t) REVERT: A 442 MET cc_start: 0.8851 (ttm) cc_final: 0.8603 (ttm) REVERT: A 536 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8825 (tt) REVERT: A 605 GLU cc_start: 0.8467 (tt0) cc_final: 0.8065 (tt0) REVERT: A 622 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7941 (tp30) REVERT: B 78 MET cc_start: 0.7847 (mtm) cc_final: 0.7463 (ptt) REVERT: B 113 GLU cc_start: 0.8851 (tp30) cc_final: 0.8504 (tp30) REVERT: B 195 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9011 (tm) REVERT: B 202 ILE cc_start: 0.9546 (mt) cc_final: 0.9295 (tt) REVERT: B 239 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8998 (tm-30) REVERT: B 279 ASP cc_start: 0.8210 (t70) cc_final: 0.7668 (t0) REVERT: B 306 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8592 (tm-30) REVERT: B 322 LYS cc_start: 0.9286 (tttt) cc_final: 0.8956 (ttmm) REVERT: B 442 MET cc_start: 0.8807 (ttm) cc_final: 0.8558 (ttm) REVERT: B 536 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8987 (tt) REVERT: B 622 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8009 (tp30) REVERT: C 176 GLU cc_start: 0.8803 (pt0) cc_final: 0.8366 (pm20) REVERT: C 239 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8977 (tm-30) REVERT: C 279 ASP cc_start: 0.8219 (t70) cc_final: 0.7692 (t0) REVERT: C 302 ARG cc_start: 0.7469 (tpm170) cc_final: 0.6659 (tpm170) REVERT: C 305 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8466 (ttp80) REVERT: C 306 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 322 LYS cc_start: 0.9217 (tttt) cc_final: 0.8954 (ttmm) REVERT: C 326 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7525 (mtm-85) REVERT: C 367 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8259 (tt) REVERT: C 442 MET cc_start: 0.8855 (ttm) cc_final: 0.8576 (ttm) REVERT: C 474 MET cc_start: 0.8311 (ttp) cc_final: 0.8090 (ttp) REVERT: C 522 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.7767 (t-90) REVERT: C 523 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8448 (p90) REVERT: C 622 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8013 (tp30) REVERT: D 71 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7268 (pmmt) REVERT: D 78 MET cc_start: 0.8360 (ptp) cc_final: 0.7741 (ptp) REVERT: D 239 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8556 (tm-30) REVERT: D 279 ASP cc_start: 0.8413 (t0) cc_final: 0.7930 (t0) REVERT: D 302 ARG cc_start: 0.7792 (tpt170) cc_final: 0.7360 (tpp-160) REVERT: D 306 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 322 LYS cc_start: 0.9262 (tttt) cc_final: 0.8955 (ttmm) REVERT: D 349 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7704 (m-10) REVERT: D 474 MET cc_start: 0.8061 (ttm) cc_final: 0.7774 (ttp) REVERT: D 522 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.7871 (t-90) REVERT: D 523 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8226 (p90) REVERT: D 536 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9071 (tt) REVERT: D 622 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7775 (tp30) outliers start: 103 outliers final: 61 residues processed: 556 average time/residue: 0.1342 time to fit residues: 119.0663 Evaluate side-chains 530 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 453 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN 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 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 ILE 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 204 ILE 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 444 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 465 VAL 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 B residue 551 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ILE 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 286 SER Chi-restraints excluded: chain C residue 305 ARG 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 368 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 465 VAL 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 604 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 235 VAL 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 377 TYR 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 465 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 69 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 63.3906 > 50:) chunk 103 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101517 restraints weight = 36812.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104762 restraints weight = 18451.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106959 restraints weight = 11523.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108355 restraints weight = 8315.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109409 restraints weight = 6716.348| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20341 Z= 0.161 Angle : 0.834 16.081 27607 Z= 0.385 Chirality : 0.045 0.324 3118 Planarity : 0.004 0.048 3474 Dihedral : 5.581 44.221 2873 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.84 % Favored : 89.99 % Rotamer: Outliers : 4.60 % Allowed : 26.92 % Favored : 68.48 % 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 are not related in a simple way. whole: -1.32 (0.17), residues: 2448 helix: 0.37 (0.14), residues: 1408 sheet: -1.33 (0.62), residues: 56 loop : -2.79 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 305 TYR 0.022 0.001 TYR A 216 PHE 0.026 0.002 PHE B 553 TRP 0.029 0.001 TRP A 613 HIS 0.008 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (20341) covalent geometry : angle 0.83394 / 0.39 (27607) hydrogen bonds : bond 0.03550 / 2.33 ( 772) hydrogen bonds : angle 4.37691 / 3.02 ( 2220) *********************** REFINEMENT MACRO_CYCLE 9 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 553 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 455 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7775 (mt) cc_final: 0.7547 (mt) REVERT: A 239 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8959 (tm-30) REVERT: A 302 ARG cc_start: 0.7567 (tpm170) cc_final: 0.7069 (tpm170) REVERT: A 305 ARG cc_start: 0.9018 (ttm110) cc_final: 0.8378 (ttp80) REVERT: A 306 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 322 LYS cc_start: 0.9304 (tttt) cc_final: 0.8975 (ttmm) REVERT: A 442 MET cc_start: 0.8863 (ttm) cc_final: 0.8633 (ttm) REVERT: A 481 MET cc_start: 0.9088 (mtp) cc_final: 0.8812 (ttm) REVERT: A 536 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8879 (tt) REVERT: A 578 MET cc_start: 0.8711 (ttm) cc_final: 0.8348 (mtm) REVERT: A 605 GLU cc_start: 0.8457 (tt0) cc_final: 0.8114 (tt0) REVERT: A 622 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7945 (tp30) REVERT: B 78 MET cc_start: 0.7811 (mtm) cc_final: 0.7471 (ptt) REVERT: B 113 GLU cc_start: 0.8856 (tp30) cc_final: 0.8515 (tp30) REVERT: B 195 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8975 (tm) REVERT: B 239 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8989 (tm-30) REVERT: B 279 ASP cc_start: 0.8272 (t70) cc_final: 0.7755 (t0) REVERT: B 306 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8634 (tm-30) REVERT: B 322 LYS cc_start: 0.9290 (tttt) cc_final: 0.8969 (ttmm) REVERT: B 442 MET cc_start: 0.8825 (ttm) cc_final: 0.8601 (ttm) REVERT: B 481 MET cc_start: 0.9132 (ttm) cc_final: 0.8784 (ttm) REVERT: B 485 MET cc_start: 0.9014 (tpp) cc_final: 0.8787 (ttm) REVERT: B 536 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 622 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8056 (tp30) REVERT: C 176 GLU cc_start: 0.8803 (pt0) cc_final: 0.8372 (pm20) REVERT: C 239 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8955 (tm-30) REVERT: C 279 ASP cc_start: 0.8259 (t70) cc_final: 0.7752 (t0) REVERT: C 302 ARG cc_start: 0.7508 (tpm170) cc_final: 0.6703 (tpm170) REVERT: C 305 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8481 (ttp80) REVERT: C 306 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 321 TRP cc_start: 0.9114 (t-100) cc_final: 0.8800 (t-100) REVERT: C 322 LYS cc_start: 0.9246 (tttt) cc_final: 0.8988 (ttmm) REVERT: C 326 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7693 (mtm-85) REVERT: C 367 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8226 (tt) REVERT: C 442 MET cc_start: 0.8863 (ttm) cc_final: 0.8632 (ttm) REVERT: C 522 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.7846 (t-90) REVERT: C 523 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8460 (p90) REVERT: C 622 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8022 (tp30) REVERT: D 54 LYS cc_start: 0.8544 (tptp) cc_final: 0.7983 (tptp) REVERT: D 71 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7299 (pmmt) REVERT: D 208 ASN cc_start: 0.7975 (t0) cc_final: 0.7716 (t0) REVERT: D 239 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8583 (tm-30) REVERT: D 279 ASP cc_start: 0.8387 (t0) cc_final: 0.7921 (t0) REVERT: D 302 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7367 (tpp-160) REVERT: D 306 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 322 LYS cc_start: 0.9287 (tttt) cc_final: 0.8999 (ttmm) REVERT: D 349 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: D 474 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7824 (ttp) REVERT: D 522 HIS cc_start: 0.9172 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: D 523 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8260 (p90) REVERT: D 536 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9099 (tt) REVERT: D 622 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7814 (tp30) outliers start: 98 outliers final: 66 residues processed: 523 average time/residue: 0.1315 time to fit residues: 109.9750 Evaluate side-chains 524 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 441 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 ILE 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 204 ILE 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 372 LEU Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 444 LEU 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 B residue 551 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ILE 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 286 SER Chi-restraints excluded: chain C residue 305 ARG 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 368 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 465 VAL 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 604 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 235 VAL 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 332 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 377 TYR 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 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 601 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 24 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103271 restraints weight = 36900.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106591 restraints weight = 18302.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108820 restraints weight = 11332.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110330 restraints weight = 8147.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111276 restraints weight = 6493.195| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20341 Z= 0.139 Angle : 0.836 16.844 27607 Z= 0.383 Chirality : 0.044 0.276 3118 Planarity : 0.004 0.048 3474 Dihedral : 5.537 43.866 2873 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 4.08 % Allowed : 27.72 % Favored : 68.20 % 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 are not related in a simple way. whole: -1.27 (0.17), residues: 2448 helix: 0.44 (0.14), residues: 1396 sheet: -1.32 (0.62), residues: 56 loop : -2.78 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 414 TYR 0.023 0.001 TYR A 216 PHE 0.027 0.001 PHE A 523 TRP 0.037 0.001 TRP A 583 HIS 0.007 0.001 HIS D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (20341) covalent geometry : angle 0.83615 / 0.38 (27607) hydrogen bonds : bond 0.03461 / 2.26 ( 772) hydrogen bonds : angle 4.30307 / 2.97 ( 2220) ********************** REFINEMENT MACRO_CYCLE 10 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 555 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 468 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8932 (tm-30) REVERT: A 302 ARG cc_start: 0.7572 (tpm170) cc_final: 0.7071 (tpm170) REVERT: A 305 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8373 (ttp80) REVERT: A 306 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 322 LYS cc_start: 0.9292 (tttt) cc_final: 0.8941 (ttmm) REVERT: A 536 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8851 (tt) REVERT: A 575 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8287 (pt) REVERT: A 605 GLU cc_start: 0.8389 (tt0) cc_final: 0.8077 (tt0) REVERT: A 622 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7932 (tp30) REVERT: B 91 ASN cc_start: 0.7911 (m-40) cc_final: 0.7421 (m-40) REVERT: B 113 GLU cc_start: 0.8850 (tp30) cc_final: 0.8504 (tp30) REVERT: B 195 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8878 (tm) REVERT: B 202 ILE cc_start: 0.9567 (mt) cc_final: 0.9297 (tt) REVERT: B 214 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8901 (tm-30) REVERT: B 239 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8966 (tm-30) REVERT: B 279 ASP cc_start: 0.8249 (t70) cc_final: 0.7731 (t0) REVERT: B 306 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8618 (tm-30) REVERT: B 322 LYS cc_start: 0.9284 (tttt) cc_final: 0.8986 (ttmm) REVERT: B 578 MET cc_start: 0.9081 (ttm) cc_final: 0.8764 (mtp) REVERT: B 622 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7992 (tp30) REVERT: C 67 TYR cc_start: 0.6571 (m-80) cc_final: 0.6245 (m-80) REVERT: C 177 GLU cc_start: 0.8987 (mp0) cc_final: 0.8764 (mp0) REVERT: C 239 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8948 (tm-30) REVERT: C 279 ASP cc_start: 0.8216 (t70) cc_final: 0.7698 (t0) REVERT: C 302 ARG cc_start: 0.7507 (tpm170) cc_final: 0.6737 (tpm170) REVERT: C 305 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: C 306 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 322 LYS cc_start: 0.9221 (tttt) cc_final: 0.8958 (ttmm) REVERT: C 326 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7766 (mtm-85) REVERT: C 367 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 434 PHE cc_start: 0.8194 (t80) cc_final: 0.7926 (m-80) REVERT: C 481 MET cc_start: 0.9175 (ttm) cc_final: 0.8958 (ttt) REVERT: C 522 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.7759 (t-90) REVERT: C 523 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8521 (p90) REVERT: C 622 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8018 (tp30) REVERT: D 54 LYS cc_start: 0.8531 (tptp) cc_final: 0.7993 (tptp) REVERT: D 71 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7276 (pmmt) REVERT: D 239 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8688 (tm-30) REVERT: D 279 ASP cc_start: 0.8419 (t0) cc_final: 0.7940 (t0) REVERT: D 302 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7510 (tpp-160) REVERT: D 306 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8447 (tm-30) REVERT: D 322 LYS cc_start: 0.9284 (tttt) cc_final: 0.8992 (ttmm) REVERT: D 349 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7712 (m-10) REVERT: D 474 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7817 (ttp) REVERT: D 522 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.7943 (t-90) REVERT: D 523 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8205 (p90) REVERT: D 536 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9019 (tt) REVERT: D 622 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7798 (tp30) outliers start: 87 outliers final: 61 residues processed: 529 average time/residue: 0.1332 time to fit residues: 112.8359 Evaluate side-chains 536 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 458 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 ILE 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 204 ILE 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 260 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 444 LEU 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 C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 ILE 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 260 MET Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 305 ARG 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 368 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 465 VAL 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 604 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 235 VAL 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 377 TYR 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 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 66 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 218 optimal weight: 0.0970 chunk 192 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102446 restraints weight = 37243.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105720 restraints weight = 18524.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107937 restraints weight = 11493.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109432 restraints weight = 8247.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110358 restraints weight = 6582.187| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20341 Z= 0.153 Angle : 0.847 16.906 27607 Z= 0.388 Chirality : 0.045 0.257 3118 Planarity : 0.004 0.049 3474 Dihedral : 5.532 43.595 2873 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.97 % Favored : 89.91 % Rotamer: Outliers : 4.22 % Allowed : 27.49 % Favored : 68.29 % 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 are not related in a simple way. whole: -1.26 (0.17), residues: 2448 helix: 0.43 (0.14), residues: 1384 sheet: -0.97 (0.56), residues: 64 loop : -2.74 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 305 TYR 0.036 0.001 TYR A 216 PHE 0.028 0.002 PHE B 553 TRP 0.039 0.001 TRP A 613 HIS 0.008 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (20341) covalent geometry : angle 0.84713 / 0.39 (27607) hydrogen bonds : bond 0.03580 / 2.37 ( 772) hydrogen bonds : angle 4.37528 / 3.02 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.15 seconds wall clock time: 64 minutes 12.21 seconds (3852.21 seconds total)