Starting phenix.real_space_refine on Sat Jul 4 09:44:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4f_22667/07_2026/7k4f_22667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4f_22667/07_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_22667/07_2026/7k4f_22667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4f_22667/07_2026/7k4f_22667.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4f_22667/07_2026/7k4f_22667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4f_22667/07_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-dev-6108/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, 60 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'5GK': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 4.79, per 1000 atoms: 0.24 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: 1.77 Conformation dependent library (CDL) restraints added in 955.1 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: 3.23 Time building geometry restraints manager: 2.32 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.880 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- 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 : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.8701 (p) REVERT: A 167 LEU cc_start: 0.8857 (pt) cc_final: 0.8583 (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: 0.7871 (t0) REVERT: A 255 MET cc_start: 0.9371 (mmm) cc_final: 0.9146 (mmt) 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: 0.7344 (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: 0.8540 (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: 0.8937 (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: 0.8051 (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: 0.7783 (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: 0.8543 (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: 0.8606 (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: 0.8098 (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: 0.8531 (tm-30) REVERT: D 322 LYS cc_start: 0.9190 (tttt) cc_final: 0.8789 (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: 0.6817 (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: 0.8774 (tpp) REVERT: D 622 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 627 ASP cc_start: 0.8915 (m-30) cc_final: 0.8675 (m-30) outliers start: 32 outliers final: 6 residues processed: 805 average time/residue: 0.1489 time to fit residues: 182.8518 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 : 0.807 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.129848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105027 restraints weight = 37004.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108291 restraints weight = 17928.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110484 restraints weight = 11048.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111927 restraints weight = 7937.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112886 restraints weight = 6373.511| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20341 Z= 0.178 Angle : 0.852 10.511 27607 Z= 0.417 Chirality : 0.045 0.202 3118 Planarity : 0.006 0.066 3474 Dihedral : 7.498 49.280 2887 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.25 % Favored : 91.38 % Rotamer: Outliers : 5.16 % Allowed : 15.15 % Favored : 79.69 % 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: -4.05 (0.14), residues: 2448 helix: -2.18 (0.11), residues: 1356 sheet: -1.50 (0.59), residues: 56 loop : -3.42 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 363 TYR 0.013 0.002 TYR D 67 PHE 0.014 0.002 PHE B 553 TRP 0.023 0.002 TRP C 613 HIS 0.006 0.001 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (20341) covalent geometry : angle 0.85245 / 0.42 (27607) hydrogen bonds : bond 0.05128 / 3.34 ( 772) hydrogen bonds : angle 5.36090 / 3.75 ( 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 655 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 545 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7520 (pmmt) REVERT: A 150 THR cc_start: 0.9292 (p) cc_final: 0.8629 (p) REVERT: A 167 LEU cc_start: 0.8817 (pt) cc_final: 0.8600 (tp) REVERT: A 177 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8464 (tm-30) REVERT: A 195 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8977 (tm) REVERT: A 302 ARG cc_start: 0.7588 (tpm170) cc_final: 0.6619 (tpm170) REVERT: A 305 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8212 (ttp80) REVERT: A 306 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 322 LYS cc_start: 0.9270 (tttt) cc_final: 0.8993 (ttmm) REVERT: A 347 CYS cc_start: 0.8888 (t) cc_final: 0.8601 (t) REVERT: A 442 MET cc_start: 0.8914 (ttm) cc_final: 0.8622 (ttm) REVERT: A 536 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 547 TYR cc_start: 0.8954 (m-10) cc_final: 0.8658 (m-10) REVERT: A 577 MET cc_start: 0.8632 (ptm) cc_final: 0.8142 (ptm) REVERT: A 622 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7995 (tp30) REVERT: B 150 THR cc_start: 0.9259 (p) cc_final: 0.8696 (p) REVERT: B 176 GLU cc_start: 0.8627 (pm20) cc_final: 0.7771 (pm20) REVERT: B 195 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9103 (tm) REVERT: B 270 TYR cc_start: 0.9017 (t80) cc_final: 0.8810 (t80) REVERT: B 279 ASP cc_start: 0.8061 (t70) cc_final: 0.7612 (t70) REVERT: B 300 LYS cc_start: 0.8302 (mttt) cc_final: 0.8086 (mttt) REVERT: B 302 ARG cc_start: 0.7646 (tpm170) cc_final: 0.6812 (tpm170) REVERT: B 305 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8196 (ttp80) REVERT: B 306 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8863 (tm-30) REVERT: B 322 LYS cc_start: 0.9285 (tttt) cc_final: 0.8946 (ttmm) REVERT: B 345 MET cc_start: 0.8567 (tpp) cc_final: 0.8352 (mmt) REVERT: B 347 CYS cc_start: 0.8940 (t) cc_final: 0.8548 (t) REVERT: B 363 ARG cc_start: 0.7995 (mmt180) cc_final: 0.7523 (mmp80) REVERT: B 442 MET cc_start: 0.8859 (ttm) cc_final: 0.8601 (ttm) REVERT: B 536 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8967 (tt) REVERT: C 150 THR cc_start: 0.9259 (p) cc_final: 0.8702 (p) REVERT: C 176 GLU cc_start: 0.8581 (pm20) cc_final: 0.7915 (pm20) REVERT: C 195 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9161 (tm) REVERT: C 270 TYR cc_start: 0.8928 (t80) cc_final: 0.8560 (t80) REVERT: C 279 ASP cc_start: 0.8087 (t70) cc_final: 0.7668 (t70) REVERT: C 302 ARG cc_start: 0.7567 (tpm170) cc_final: 0.6875 (tpm170) REVERT: C 305 ARG cc_start: 0.8882 (ttp80) cc_final: 0.8342 (ttp80) REVERT: C 306 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8932 (tm-30) REVERT: C 321 TRP cc_start: 0.8888 (t60) cc_final: 0.8496 (t-100) REVERT: C 322 LYS cc_start: 0.9282 (tttt) cc_final: 0.8980 (ttmm) REVERT: C 347 CYS cc_start: 0.8959 (t) cc_final: 0.8669 (t) REVERT: C 442 MET cc_start: 0.8817 (ttm) cc_final: 0.8560 (ttm) REVERT: C 536 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9010 (tt) REVERT: C 622 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7934 (tp30) REVERT: D 208 ASN cc_start: 0.8272 (t0) cc_final: 0.7920 (t0) REVERT: D 306 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8535 (tm-30) REVERT: D 322 LYS cc_start: 0.9182 (tttt) cc_final: 0.8846 (ttmm) REVERT: D 367 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8127 (tt) REVERT: D 434 PHE cc_start: 0.8545 (t80) cc_final: 0.7986 (t80) REVERT: D 473 GLN cc_start: 0.8594 (tp40) cc_final: 0.7905 (pm20) REVERT: D 495 TRP cc_start: 0.8834 (m100) cc_final: 0.8528 (m100) REVERT: D 522 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.7840 (t-90) REVERT: D 536 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8874 (tt) REVERT: D 578 MET cc_start: 0.8942 (ttm) cc_final: 0.8672 (mtm) REVERT: D 622 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7670 (tp30) outliers start: 110 outliers final: 47 residues processed: 619 average time/residue: 0.1378 time to fit residues: 134.3730 Evaluate side-chains 496 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 439 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 71 LYS 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 167 LEU Chi-restraints excluded: chain D residue 220 LEU 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 399 ILE Chi-restraints excluded: chain D residue 404 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: 6.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100609 restraints weight = 37383.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103855 restraints weight = 18468.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106002 restraints weight = 11493.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107411 restraints weight = 8329.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108403 restraints weight = 6763.321| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20341 Z= 0.189 Angle : 0.846 12.238 27607 Z= 0.403 Chirality : 0.045 0.198 3118 Planarity : 0.005 0.050 3474 Dihedral : 6.735 47.263 2879 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.56 % Favored : 90.20 % Rotamer: Outliers : 6.71 % Allowed : 18.06 % Favored : 75.23 % 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: -2.99 (0.16), residues: 2448 helix: -1.07 (0.13), residues: 1360 sheet: -2.25 (0.51), residues: 76 loop : -3.26 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 305 TYR 0.014 0.002 TYR D 89 PHE 0.014 0.002 PHE B 425 TRP 0.018 0.002 TRP A 613 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (20341) covalent geometry : angle 0.84556 / 0.40 (27607) hydrogen bonds : bond 0.04267 / 2.78 ( 772) hydrogen bonds : angle 4.90186 / 3.42 ( 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: 143 poor density : 472 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8666 (pm20) cc_final: 0.7930 (pm20) REVERT: A 178 ILE cc_start: 0.9417 (mm) cc_final: 0.9205 (tt) REVERT: A 195 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9138 (tm) REVERT: A 279 ASP cc_start: 0.8199 (t0) cc_final: 0.7997 (t0) REVERT: A 302 ARG cc_start: 0.7470 (tpm170) cc_final: 0.6534 (tpm170) REVERT: A 305 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8260 (ttp80) REVERT: A 306 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8796 (tm-30) REVERT: A 321 TRP cc_start: 0.9090 (t-100) cc_final: 0.8742 (t-100) REVERT: A 322 LYS cc_start: 0.9315 (tttt) cc_final: 0.9063 (ttmm) REVERT: A 442 MET cc_start: 0.8827 (ttm) cc_final: 0.8560 (ttm) REVERT: A 464 ASN cc_start: 0.8677 (t0) cc_final: 0.8416 (t0) REVERT: A 523 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8468 (p90) REVERT: A 536 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 622 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7966 (tp30) REVERT: B 71 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7690 (pmmt) REVERT: B 195 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9152 (tm) REVERT: B 279 ASP cc_start: 0.8105 (t70) cc_final: 0.7624 (t0) REVERT: B 302 ARG cc_start: 0.7556 (tpm170) cc_final: 0.6569 (tpm170) REVERT: B 305 ARG cc_start: 0.8896 (ttm110) cc_final: 0.8217 (ttp80) REVERT: B 306 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8924 (tm-30) REVERT: B 322 LYS cc_start: 0.9310 (tttt) cc_final: 0.9006 (ttmm) REVERT: B 363 ARG cc_start: 0.7950 (mmt180) cc_final: 0.7448 (mmp80) REVERT: B 442 MET cc_start: 0.8875 (ttm) cc_final: 0.8619 (ttm) REVERT: C 195 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9198 (tm) REVERT: C 279 ASP cc_start: 0.8185 (t70) cc_final: 0.7737 (t0) REVERT: C 305 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8549 (ttp80) REVERT: C 321 TRP cc_start: 0.8918 (t60) cc_final: 0.8621 (t-100) REVERT: C 322 LYS cc_start: 0.9284 (tttt) cc_final: 0.8947 (ttmm) REVERT: C 326 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7582 (ttm110) REVERT: C 347 CYS cc_start: 0.8828 (t) cc_final: 0.8574 (t) REVERT: C 367 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8407 (tt) REVERT: C 442 MET cc_start: 0.8863 (ttm) cc_final: 0.8613 (ttm) REVERT: C 621 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8207 (ttm170) REVERT: C 622 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7990 (tp30) REVERT: D 164 GLU cc_start: 0.7921 (mp0) cc_final: 0.7598 (mp0) REVERT: D 167 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8594 (tp) REVERT: D 208 ASN cc_start: 0.8136 (t0) cc_final: 0.7809 (t0) REVERT: D 279 ASP cc_start: 0.8457 (t70) cc_final: 0.8097 (t0) REVERT: D 303 GLU cc_start: 0.8469 (mp0) cc_final: 0.8048 (pm20) REVERT: D 306 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8533 (tm-30) REVERT: D 322 LYS cc_start: 0.9288 (tttt) cc_final: 0.8949 (ttmm) REVERT: D 363 ARG cc_start: 0.7822 (mmp80) cc_final: 0.7535 (mmp80) REVERT: D 442 MET cc_start: 0.8808 (ttm) cc_final: 0.8341 (ttm) REVERT: D 495 TRP cc_start: 0.8837 (m100) cc_final: 0.8448 (m100) REVERT: D 522 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.8169 (t-90) REVERT: D 536 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9086 (tt) REVERT: D 542 ASP cc_start: 0.7163 (t70) cc_final: 0.6837 (p0) REVERT: D 577 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8919 (ttm) outliers start: 143 outliers final: 74 residues processed: 562 average time/residue: 0.1389 time to fit residues: 123.7176 Evaluate side-chains 508 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 422 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 157 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 232 LEU 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 523 PHE 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 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 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 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 391 VAL Chi-restraints excluded: chain C residue 398 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 486 ILE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 195 LEU 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 402 VAL Chi-restraints excluded: chain D residue 404 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 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 577 MET 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: 9.9990 chunk 231 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** 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 41 GLN D 426 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100235 restraints weight = 37447.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103476 restraints weight = 18542.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105658 restraints weight = 11544.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107126 restraints weight = 8342.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107957 restraints weight = 6702.021| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20341 Z= 0.174 Angle : 0.810 13.300 27607 Z= 0.385 Chirality : 0.044 0.209 3118 Planarity : 0.005 0.044 3474 Dihedral : 6.381 46.819 2877 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.91 % Favored : 90.73 % Rotamer: Outliers : 6.85 % Allowed : 20.36 % Favored : 72.80 % 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: -2.42 (0.16), residues: 2448 helix: -0.51 (0.14), residues: 1356 sheet: -2.19 (0.51), residues: 76 loop : -3.14 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 355 TYR 0.017 0.001 TYR A 216 PHE 0.025 0.002 PHE D 553 TRP 0.025 0.001 TRP A 613 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (20341) covalent geometry : angle 0.81042 / 0.38 (27607) hydrogen bonds : bond 0.03859 / 2.52 ( 772) hydrogen bonds : angle 4.73132 / 3.28 ( 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 606 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 460 time to evaluate : 0.635 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 195 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9098 (tm) REVERT: A 239 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.9074 (tm-30) REVERT: A 279 ASP cc_start: 0.8295 (t0) cc_final: 0.8080 (t0) REVERT: A 302 ARG cc_start: 0.7509 (tpm170) cc_final: 0.6534 (tpm170) REVERT: A 305 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8266 (ttp80) REVERT: A 306 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8785 (tm-30) REVERT: A 322 LYS cc_start: 0.9328 (tttt) cc_final: 0.9001 (ttmm) REVERT: A 440 MET cc_start: 0.8693 (ptm) cc_final: 0.8423 (tmm) REVERT: A 442 MET cc_start: 0.8828 (ttm) cc_final: 0.8574 (ttm) REVERT: A 464 ASN cc_start: 0.8723 (t0) cc_final: 0.8187 (t0) REVERT: A 523 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8568 (p90) REVERT: A 547 TYR cc_start: 0.8873 (m-10) cc_final: 0.8513 (m-10) REVERT: A 622 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7941 (tp30) REVERT: B 176 GLU cc_start: 0.8372 (pm20) cc_final: 0.8145 (pm20) REVERT: B 195 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9164 (tm) REVERT: B 239 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: B 279 ASP cc_start: 0.8127 (t70) cc_final: 0.7630 (t0) REVERT: B 306 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8887 (tm-30) REVERT: B 322 LYS cc_start: 0.9334 (tttt) cc_final: 0.8984 (ttmm) REVERT: B 363 ARG cc_start: 0.7967 (mmt180) cc_final: 0.7345 (mmp80) REVERT: B 440 MET cc_start: 0.8755 (ptm) cc_final: 0.8429 (tmm) REVERT: B 442 MET cc_start: 0.8864 (ttm) cc_final: 0.8595 (ttm) REVERT: B 536 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8965 (tt) REVERT: B 622 GLU cc_start: 0.7721 (tp30) cc_final: 0.7448 (tp30) REVERT: C 176 GLU cc_start: 0.8391 (pm20) cc_final: 0.8037 (pm20) REVERT: C 177 GLU cc_start: 0.8678 (mp0) cc_final: 0.8435 (mp0) REVERT: C 195 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9249 (tm) REVERT: C 239 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: C 279 ASP cc_start: 0.8207 (t70) cc_final: 0.7733 (t0) REVERT: C 302 ARG cc_start: 0.7539 (tpm170) cc_final: 0.7304 (tpm170) REVERT: C 306 GLN cc_start: 0.9307 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 321 TRP cc_start: 0.8938 (t60) cc_final: 0.8626 (t-100) REVERT: C 322 LYS cc_start: 0.9262 (tttt) cc_final: 0.8938 (ttmm) REVERT: C 326 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7560 (mtm110) REVERT: C 367 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8375 (tt) REVERT: C 442 MET cc_start: 0.8820 (ttm) cc_final: 0.8566 (ttm) REVERT: C 518 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: C 522 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.7804 (t-90) REVERT: C 523 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8511 (p90) REVERT: C 536 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9011 (tt) REVERT: C 621 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8155 (ttm170) REVERT: C 622 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8003 (tp30) REVERT: D 54 LYS cc_start: 0.8598 (tptp) cc_final: 0.8206 (tptp) REVERT: D 71 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7310 (pmmt) REVERT: D 164 GLU cc_start: 0.7972 (mp0) cc_final: 0.7701 (mp0) REVERT: D 167 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8623 (tp) REVERT: D 208 ASN cc_start: 0.8098 (t0) cc_final: 0.7789 (t0) REVERT: D 239 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: D 279 ASP cc_start: 0.8437 (t0) cc_final: 0.8088 (t0) REVERT: D 303 GLU cc_start: 0.8447 (mp0) cc_final: 0.8050 (pm20) REVERT: D 305 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8689 (ttm-80) REVERT: D 306 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8533 (tm-30) REVERT: D 322 LYS cc_start: 0.9296 (tttt) cc_final: 0.8968 (ttmm) REVERT: D 367 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8400 (tt) REVERT: D 403 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: D 522 HIS cc_start: 0.9099 (OUTLIER) cc_final: 0.7864 (t-90) REVERT: D 523 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8224 (p90) REVERT: D 536 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9086 (tt) REVERT: D 542 ASP cc_start: 0.7192 (t70) cc_final: 0.6858 (p0) REVERT: D 547 TYR cc_start: 0.9087 (m-10) cc_final: 0.8874 (m-10) outliers start: 146 outliers final: 89 residues processed: 558 average time/residue: 0.1320 time to fit residues: 115.0977 Evaluate side-chains 531 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 420 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 195 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 338 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 391 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 459 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 568 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 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 295 LEU 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 355 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 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 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 B residue 604 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 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR 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 387 VAL Chi-restraints excluded: chain C residue 391 VAL 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 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 601 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 LEU 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 367 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 404 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 551 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 78 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 95 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** ** B 357 ASN ** 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 = 0.3530 r_free = 0.3530 target = 0.126338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100955 restraints weight = 37290.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104208 restraints weight = 18458.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106386 restraints weight = 11510.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107816 restraints weight = 8340.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108825 restraints weight = 6730.326| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20341 Z= 0.142 Angle : 0.788 14.712 27607 Z= 0.370 Chirality : 0.043 0.226 3118 Planarity : 0.004 0.046 3474 Dihedral : 6.113 46.263 2877 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.99 % Favored : 90.69 % Rotamer: Outliers : 6.33 % Allowed : 21.81 % Favored : 71.86 % 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: -2.01 (0.17), residues: 2448 helix: -0.11 (0.14), residues: 1360 sheet: -2.29 (0.51), residues: 76 loop : -3.03 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 414 TYR 0.018 0.001 TYR A 216 PHE 0.022 0.001 PHE D 553 TRP 0.014 0.001 TRP A 583 HIS 0.005 0.001 HIS D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (20341) covalent geometry : angle 0.78778 / 0.37 (27607) hydrogen bonds : bond 0.03597 / 2.35 ( 772) hydrogen bonds : angle 4.49138 / 3.11 ( 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 603 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 468 time to evaluate : 0.789 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 132 LEU cc_start: 0.9142 (mp) cc_final: 0.8892 (tp) REVERT: A 195 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9090 (tm) REVERT: A 227 ASP cc_start: 0.6220 (m-30) cc_final: 0.5926 (t70) REVERT: A 239 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.9109 (tm-30) REVERT: A 279 ASP cc_start: 0.8323 (t0) cc_final: 0.8102 (t0) REVERT: A 306 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 322 LYS cc_start: 0.9316 (tttt) cc_final: 0.8986 (ttmm) REVERT: A 440 MET cc_start: 0.8784 (ptm) cc_final: 0.8548 (tmm) REVERT: A 442 MET cc_start: 0.8807 (ttm) cc_final: 0.8555 (ttm) REVERT: A 464 ASN cc_start: 0.8693 (t0) cc_final: 0.8260 (t0) REVERT: A 523 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8508 (p90) REVERT: A 536 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9093 (tt) REVERT: A 622 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7939 (tp30) REVERT: B 195 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9171 (tm) REVERT: B 202 ILE cc_start: 0.9653 (mt) cc_final: 0.9435 (tt) REVERT: B 239 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9072 (tm-30) REVERT: B 279 ASP cc_start: 0.8100 (t70) cc_final: 0.7597 (t0) REVERT: B 305 ARG cc_start: 0.8919 (ttm110) cc_final: 0.8688 (ttm-80) REVERT: B 306 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8878 (tm-30) REVERT: B 322 LYS cc_start: 0.9317 (tttt) cc_final: 0.8981 (ttmm) REVERT: B 363 ARG cc_start: 0.7930 (mmt180) cc_final: 0.7423 (mmp80) REVERT: B 440 MET cc_start: 0.8776 (ptm) cc_final: 0.8521 (tmm) REVERT: B 442 MET cc_start: 0.8848 (ttm) cc_final: 0.8605 (ttm) REVERT: B 533 THR cc_start: 0.9662 (m) cc_final: 0.9462 (t) REVERT: B 536 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 622 GLU cc_start: 0.7766 (tp30) cc_final: 0.7481 (tp30) REVERT: C 177 GLU cc_start: 0.8634 (mp0) cc_final: 0.8404 (tm-30) REVERT: C 195 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9243 (tm) REVERT: C 239 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9067 (tm-30) REVERT: C 279 ASP cc_start: 0.8228 (t70) cc_final: 0.7735 (t0) REVERT: C 302 ARG cc_start: 0.7537 (tpm170) cc_final: 0.7293 (tpm170) REVERT: C 306 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 321 TRP cc_start: 0.8910 (t60) cc_final: 0.8634 (t-100) REVERT: C 322 LYS cc_start: 0.9256 (tttt) cc_final: 0.8958 (ttmm) REVERT: C 326 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7587 (mtm-85) REVERT: C 357 ASN cc_start: 0.8063 (p0) cc_final: 0.7821 (p0) REVERT: C 367 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8351 (tt) REVERT: C 442 MET cc_start: 0.8838 (ttm) cc_final: 0.8572 (ttm) REVERT: C 518 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: C 523 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8478 (p90) REVERT: C 536 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8944 (tt) REVERT: C 605 GLU cc_start: 0.8285 (tt0) cc_final: 0.7891 (tt0) REVERT: C 621 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8107 (ttm170) REVERT: C 622 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8005 (tp30) REVERT: D 54 LYS cc_start: 0.8680 (tptp) cc_final: 0.8175 (tptp) REVERT: D 71 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7289 (pmmt) REVERT: D 215 MET cc_start: 0.8775 (ttp) cc_final: 0.8439 (tmm) REVERT: D 239 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8592 (tm-30) REVERT: D 279 ASP cc_start: 0.8420 (t0) cc_final: 0.8064 (t0) REVERT: D 303 GLU cc_start: 0.8427 (mp0) cc_final: 0.8219 (pm20) REVERT: D 306 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 322 LYS cc_start: 0.9297 (tttt) cc_final: 0.8973 (ttmm) REVERT: D 403 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: D 522 HIS cc_start: 0.9099 (OUTLIER) cc_final: 0.7867 (t-90) REVERT: D 523 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8098 (p90) REVERT: D 536 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9076 (tt) REVERT: D 542 ASP cc_start: 0.7100 (t70) cc_final: 0.6192 (p0) REVERT: D 574 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8644 (tt) REVERT: D 578 MET cc_start: 0.9020 (ttm) cc_final: 0.8492 (mtm) outliers start: 135 outliers final: 83 residues processed: 555 average time/residue: 0.1242 time to fit residues: 108.0603 Evaluate side-chains 538 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 434 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 195 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 355 ARG 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 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 ILE 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 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 355 ARG 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 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 542 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 195 LEU 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 377 TYR 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 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 523 PHE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 LEU 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 GLU 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 574 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 203 optimal weight: 0.0980 chunk 145 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099011 restraints weight = 37152.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102203 restraints weight = 18585.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104354 restraints weight = 11641.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105803 restraints weight = 8458.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106722 restraints weight = 6821.218| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20341 Z= 0.184 Angle : 0.812 14.767 27607 Z= 0.383 Chirality : 0.044 0.216 3118 Planarity : 0.004 0.046 3474 Dihedral : 5.964 47.610 2875 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.21 % Favored : 89.54 % Rotamer: Outliers : 7.88 % Allowed : 21.25 % Favored : 70.87 % 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: -1.77 (0.17), residues: 2448 helix: 0.08 (0.14), residues: 1376 sheet: -2.36 (0.51), residues: 76 loop : -2.95 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.018 0.001 TYR A 216 PHE 0.020 0.002 PHE D 553 TRP 0.012 0.001 TRP A 583 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (20341) covalent geometry : angle 0.81166 / 0.38 (27607) hydrogen bonds : bond 0.03786 / 2.47 ( 772) hydrogen bonds : angle 4.56084 / 3.17 ( 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 615 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 447 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7687 (mt) cc_final: 0.7465 (mt) REVERT: A 132 LEU cc_start: 0.9122 (mp) cc_final: 0.8914 (tp) REVERT: A 239 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: A 279 ASP cc_start: 0.8427 (t0) cc_final: 0.8211 (t0) REVERT: A 305 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8625 (ttp80) REVERT: A 306 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 322 LYS cc_start: 0.9301 (tttt) cc_final: 0.8980 (ttmm) REVERT: A 440 MET cc_start: 0.8839 (ptm) cc_final: 0.8609 (tmm) REVERT: A 442 MET cc_start: 0.8829 (ttm) cc_final: 0.8586 (ttm) REVERT: A 464 ASN cc_start: 0.8771 (t0) cc_final: 0.8408 (t0) REVERT: A 536 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9105 (tt) REVERT: A 547 TYR cc_start: 0.8847 (m-10) cc_final: 0.8513 (m-10) REVERT: A 622 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7907 (tp30) REVERT: B 176 GLU cc_start: 0.8438 (pm20) cc_final: 0.7806 (pm20) REVERT: B 177 GLU cc_start: 0.8386 (mp0) cc_final: 0.7647 (mp0) REVERT: B 195 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9239 (tm) REVERT: B 239 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9092 (tm-30) REVERT: B 279 ASP cc_start: 0.8166 (t70) cc_final: 0.7645 (t0) REVERT: B 305 ARG cc_start: 0.9064 (ttm110) cc_final: 0.8757 (ttm-80) REVERT: B 306 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8871 (tm-30) REVERT: B 322 LYS cc_start: 0.9298 (tttt) cc_final: 0.8977 (ttmm) REVERT: B 363 ARG cc_start: 0.7907 (mmt180) cc_final: 0.7430 (mmp80) REVERT: B 440 MET cc_start: 0.8827 (ptm) cc_final: 0.8571 (tmm) REVERT: B 442 MET cc_start: 0.8851 (ttm) cc_final: 0.8599 (ttm) REVERT: B 489 ASP cc_start: 0.8340 (m-30) cc_final: 0.8126 (t0) REVERT: B 536 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9082 (tt) REVERT: B 622 GLU cc_start: 0.7782 (tp30) cc_final: 0.7500 (tp30) REVERT: C 195 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9264 (tm) REVERT: C 239 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.9051 (tm-30) REVERT: C 279 ASP cc_start: 0.8333 (t70) cc_final: 0.7839 (t0) REVERT: C 302 ARG cc_start: 0.7524 (tpm170) cc_final: 0.6817 (tpm170) REVERT: C 303 GLU cc_start: 0.8519 (mp0) cc_final: 0.8274 (pm20) REVERT: C 305 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8355 (ttp80) REVERT: C 306 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 322 LYS cc_start: 0.9247 (tttt) cc_final: 0.8958 (ttmm) REVERT: C 326 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7685 (mtm-85) REVERT: C 357 ASN cc_start: 0.7931 (p0) cc_final: 0.7724 (p0) REVERT: C 367 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8324 (tt) REVERT: C 442 MET cc_start: 0.8866 (ttm) cc_final: 0.8614 (ttm) REVERT: C 518 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: C 522 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.7756 (t-90) REVERT: C 523 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8494 (p90) REVERT: C 536 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9050 (tt) REVERT: C 621 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7969 (ttm170) REVERT: C 622 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7959 (tp30) REVERT: D 71 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7318 (pmmt) REVERT: D 208 ASN cc_start: 0.8016 (t0) cc_final: 0.7733 (t0) REVERT: D 215 MET cc_start: 0.8747 (ttp) cc_final: 0.8406 (tmm) REVERT: D 239 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: D 279 ASP cc_start: 0.8427 (t0) cc_final: 0.8062 (t0) REVERT: D 302 ARG cc_start: 0.7857 (tpt170) cc_final: 0.7466 (tpp-160) REVERT: D 306 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 322 LYS cc_start: 0.9278 (tttt) cc_final: 0.8976 (ttmm) REVERT: D 326 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7613 (mtm-85) REVERT: D 349 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: D 367 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8313 (tt) REVERT: D 403 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: D 522 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.7904 (t-90) REVERT: D 523 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8323 (p90) REVERT: D 536 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9114 (tt) REVERT: D 622 GLU cc_start: 0.8227 (mp0) cc_final: 0.7858 (tp30) outliers start: 168 outliers final: 112 residues processed: 561 average time/residue: 0.1302 time to fit residues: 114.8600 Evaluate side-chains 561 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 428 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 81 THR 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 355 ARG 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 391 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 549 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR 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 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 332 LEU 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 352 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 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 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 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 81 THR 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 340 ILE 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 391 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 438 VAL 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 557 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 195 LEU 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 355 ARG Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 367 LEU 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 403 GLU 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 523 PHE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 76 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 204 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** 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 = 0.3511 r_free = 0.3511 target = 0.124993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099602 restraints weight = 37459.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102815 restraints weight = 18667.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104959 restraints weight = 11665.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106430 restraints weight = 8488.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107203 restraints weight = 6819.815| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20341 Z= 0.176 Angle : 0.825 15.445 27607 Z= 0.386 Chirality : 0.044 0.239 3118 Planarity : 0.005 0.048 3474 Dihedral : 5.848 45.685 2873 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.89 % Favored : 89.87 % Rotamer: Outliers : 7.04 % Allowed : 22.61 % Favored : 70.36 % 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: -1.55 (0.17), residues: 2448 helix: 0.25 (0.14), residues: 1360 sheet: -1.68 (0.60), residues: 56 loop : -2.83 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 414 TYR 0.021 0.001 TYR A 216 PHE 0.021 0.002 PHE A 523 TRP 0.017 0.001 TRP B 583 HIS 0.007 0.001 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20341) covalent geometry : angle 0.82488 / 0.39 (27607) hydrogen bonds : bond 0.03689 / 2.41 ( 772) hydrogen bonds : angle 4.50782 / 3.13 ( 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 592 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 442 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7706 (mt) cc_final: 0.7505 (mt) REVERT: A 239 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.8990 (tm-30) REVERT: A 279 ASP cc_start: 0.8441 (t0) cc_final: 0.8216 (t0) REVERT: A 306 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8545 (tm-30) REVERT: A 322 LYS cc_start: 0.9302 (tttt) cc_final: 0.8980 (ttmm) REVERT: A 440 MET cc_start: 0.8850 (ptm) cc_final: 0.8611 (tmm) REVERT: A 442 MET cc_start: 0.8810 (ttm) cc_final: 0.8560 (ttm) REVERT: A 454 MET cc_start: 0.8935 (tpp) cc_final: 0.8724 (tpp) REVERT: A 464 ASN cc_start: 0.8851 (t0) cc_final: 0.8472 (t0) REVERT: A 536 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9091 (tt) REVERT: A 547 TYR cc_start: 0.8849 (m-10) cc_final: 0.8524 (m-10) REVERT: A 622 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7935 (tp30) REVERT: B 195 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9179 (tm) REVERT: B 239 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: B 279 ASP cc_start: 0.8248 (t70) cc_final: 0.7728 (t0) REVERT: B 302 ARG cc_start: 0.7737 (tpm170) cc_final: 0.7277 (tpp-160) REVERT: B 305 ARG cc_start: 0.9042 (ttm110) cc_final: 0.8801 (ttm-80) REVERT: B 306 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 322 LYS cc_start: 0.9282 (tttt) cc_final: 0.8957 (ttmm) REVERT: B 363 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7435 (mmp80) REVERT: B 440 MET cc_start: 0.8844 (ptm) cc_final: 0.8597 (tmm) REVERT: B 442 MET cc_start: 0.8844 (ttm) cc_final: 0.8587 (ttm) REVERT: B 489 ASP cc_start: 0.8388 (m-30) cc_final: 0.8148 (t0) REVERT: B 536 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9040 (tt) REVERT: B 622 GLU cc_start: 0.7785 (tp30) cc_final: 0.7487 (tp30) REVERT: C 195 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9288 (tm) REVERT: C 202 ILE cc_start: 0.9668 (mt) cc_final: 0.9418 (tt) REVERT: C 239 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: C 279 ASP cc_start: 0.8349 (t70) cc_final: 0.7813 (t0) REVERT: C 302 ARG cc_start: 0.7497 (tpm170) cc_final: 0.6590 (tpm170) REVERT: C 305 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8416 (ttp80) REVERT: C 306 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8575 (tm-30) REVERT: C 322 LYS cc_start: 0.9244 (tttt) cc_final: 0.8957 (ttmm) REVERT: C 326 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7656 (mtm-85) REVERT: C 367 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8320 (tt) REVERT: C 442 MET cc_start: 0.8870 (ttm) cc_final: 0.8610 (ttm) REVERT: C 518 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: C 522 HIS cc_start: 0.9102 (OUTLIER) cc_final: 0.7818 (t-90) REVERT: C 523 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8567 (p90) REVERT: C 536 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9045 (tt) REVERT: C 621 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: C 622 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7954 (tp30) REVERT: D 71 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7326 (pmmt) REVERT: D 208 ASN cc_start: 0.8024 (t0) cc_final: 0.7734 (t0) REVERT: D 215 MET cc_start: 0.8746 (ttp) cc_final: 0.8366 (tmm) REVERT: D 239 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: D 279 ASP cc_start: 0.8416 (t0) cc_final: 0.8043 (t0) REVERT: D 302 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7320 (tpp-160) REVERT: D 306 GLN cc_start: 0.9283 (tm-30) cc_final: 0.8513 (tm-30) REVERT: D 322 LYS cc_start: 0.9286 (tttt) cc_final: 0.8992 (ttmm) REVERT: D 326 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7671 (mtm-85) REVERT: D 349 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7840 (m-10) REVERT: D 403 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: D 522 HIS cc_start: 0.9163 (OUTLIER) cc_final: 0.7910 (t-90) REVERT: D 523 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8310 (p90) REVERT: D 536 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9113 (tt) REVERT: D 578 MET cc_start: 0.9028 (ttm) cc_final: 0.8741 (mtp) REVERT: D 622 GLU cc_start: 0.8214 (mp0) cc_final: 0.7880 (tp30) outliers start: 150 outliers final: 108 residues processed: 546 average time/residue: 0.1252 time to fit residues: 108.2793 Evaluate side-chains 552 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 423 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 78 MET Chi-restraints excluded: chain A residue 81 THR 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 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 549 VAL 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 B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR 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 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 352 LEU Chi-restraints excluded: chain B residue 355 ARG 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 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 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 81 THR 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 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 340 ILE 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 557 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 203 LEU 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 355 ARG Chi-restraints excluded: chain D residue 368 LEU 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 403 GLU 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 523 PHE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain D residue 551 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 240 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** 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 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 = 0.3543 r_free = 0.3543 target = 0.127237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102537 restraints weight = 36922.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105757 restraints weight = 18581.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107917 restraints weight = 11626.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109306 restraints weight = 8415.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110334 restraints weight = 6811.709| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5237 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= 0.125 Angle : 0.814 16.372 27607 Z= 0.374 Chirality : 0.043 0.253 3118 Planarity : 0.004 0.056 3474 Dihedral : 5.681 45.482 2873 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 5.25 % Allowed : 24.95 % Favored : 69.79 % 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: -1.37 (0.17), residues: 2448 helix: 0.41 (0.14), residues: 1360 sheet: -1.45 (0.62), residues: 56 loop : -2.79 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 305 TYR 0.014 0.001 TYR A 216 PHE 0.018 0.001 PHE A 523 TRP 0.035 0.001 TRP A 583 HIS 0.009 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (20341) covalent geometry : angle 0.81420 / 0.37 (27607) hydrogen bonds : bond 0.03372 / 2.20 ( 772) hydrogen bonds : angle 4.23374 / 2.92 ( 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 590 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 478 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.9339 (t80) cc_final: 0.9136 (t80) REVERT: A 227 ASP cc_start: 0.6219 (m-30) cc_final: 0.6003 (t70) REVERT: A 239 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8978 (tm-30) REVERT: A 279 ASP cc_start: 0.8370 (t0) cc_final: 0.8168 (t0) REVERT: A 306 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8499 (tm-30) REVERT: A 322 LYS cc_start: 0.9262 (tttt) cc_final: 0.8941 (ttmm) REVERT: A 440 MET cc_start: 0.8878 (ptm) cc_final: 0.8666 (tmm) REVERT: A 442 MET cc_start: 0.8846 (ttm) cc_final: 0.8565 (ttm) REVERT: A 454 MET cc_start: 0.8934 (tpp) cc_final: 0.8732 (tpp) REVERT: A 464 ASN cc_start: 0.8655 (t0) cc_final: 0.8313 (t0) REVERT: A 536 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 622 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7950 (tp30) REVERT: B 195 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8986 (tm) REVERT: B 239 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.9014 (tm-30) REVERT: B 279 ASP cc_start: 0.8207 (t70) cc_final: 0.7647 (t0) REVERT: B 302 ARG cc_start: 0.7694 (tpm170) cc_final: 0.7215 (tpp-160) REVERT: B 305 ARG cc_start: 0.8997 (ttm110) cc_final: 0.8747 (ttm-80) REVERT: B 306 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8841 (tm-30) REVERT: B 322 LYS cc_start: 0.9294 (tttt) cc_final: 0.8972 (ttmm) REVERT: B 363 ARG cc_start: 0.7836 (mmt180) cc_final: 0.7374 (mmp80) REVERT: B 440 MET cc_start: 0.8872 (ptm) cc_final: 0.8651 (tmm) REVERT: B 442 MET cc_start: 0.8839 (ttm) cc_final: 0.8556 (ttm) REVERT: B 578 MET cc_start: 0.9108 (ttm) cc_final: 0.8663 (mtp) REVERT: C 195 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9248 (tm) REVERT: C 202 ILE cc_start: 0.9643 (mt) cc_final: 0.9406 (tt) REVERT: C 239 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9007 (tm-30) REVERT: C 279 ASP cc_start: 0.8272 (t70) cc_final: 0.7730 (t0) REVERT: C 302 ARG cc_start: 0.7476 (tpm170) cc_final: 0.6582 (tpm170) REVERT: C 305 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8390 (ttp80) REVERT: C 306 GLN cc_start: 0.9301 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 321 TRP cc_start: 0.8857 (t60) cc_final: 0.8584 (t-100) REVERT: C 322 LYS cc_start: 0.9231 (tttt) cc_final: 0.8964 (ttmm) REVERT: C 326 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7327 (mtm-85) REVERT: C 367 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8273 (tt) REVERT: C 442 MET cc_start: 0.8866 (ttm) cc_final: 0.8581 (ttm) REVERT: C 518 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: C 523 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8525 (p90) REVERT: C 536 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8938 (tt) REVERT: C 578 MET cc_start: 0.9146 (ttm) cc_final: 0.8738 (mtm) REVERT: C 621 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7969 (ttm170) REVERT: C 622 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7943 (tp30) REVERT: D 44 ILE cc_start: 0.9147 (tp) cc_final: 0.8923 (tt) REVERT: D 71 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7276 (pmmt) REVERT: D 215 MET cc_start: 0.8737 (ttp) cc_final: 0.8289 (tmm) REVERT: D 239 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: D 279 ASP cc_start: 0.8379 (t0) cc_final: 0.8003 (t0) REVERT: D 302 ARG cc_start: 0.7807 (tpt170) cc_final: 0.7341 (tpp-160) REVERT: D 306 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8412 (tm-30) REVERT: D 322 LYS cc_start: 0.9267 (tttt) cc_final: 0.8964 (ttmm) REVERT: D 349 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: D 355 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6776 (ttm170) REVERT: D 403 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: D 522 HIS cc_start: 0.9103 (OUTLIER) cc_final: 0.7913 (t-90) REVERT: D 523 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8265 (p90) REVERT: D 578 MET cc_start: 0.9039 (ttm) cc_final: 0.8805 (mtp) REVERT: D 622 GLU cc_start: 0.8160 (mp0) cc_final: 0.7890 (tp30) outliers start: 112 outliers final: 65 residues processed: 565 average time/residue: 0.1276 time to fit residues: 114.5696 Evaluate side-chains 530 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 446 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 332 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 377 TYR 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 523 PHE 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 575 ILE Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 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 377 TYR 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 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 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 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 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 523 PHE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 403 GLU 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 485 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 551 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 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 = 0.3485 r_free = 0.3485 target = 0.122975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098136 restraints weight = 37265.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101183 restraints weight = 19221.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103249 restraints weight = 12209.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104554 restraints weight = 8946.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105544 restraints weight = 7307.115| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20341 Z= 0.225 Angle : 0.878 15.700 27607 Z= 0.411 Chirality : 0.046 0.238 3118 Planarity : 0.005 0.049 3474 Dihedral : 5.860 44.882 2873 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.19 % Favored : 88.64 % Rotamer: Outliers : 5.44 % Allowed : 25.14 % Favored : 69.42 % 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: -1.53 (0.17), residues: 2448 helix: 0.28 (0.14), residues: 1380 sheet: -1.98 (0.48), residues: 84 loop : -2.90 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 305 TYR 0.025 0.002 TYR B 467 PHE 0.027 0.002 PHE B 553 TRP 0.032 0.001 TRP A 613 HIS 0.008 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (20341) covalent geometry : angle 0.87827 / 0.41 (27607) hydrogen bonds : bond 0.03991 / 2.63 ( 772) hydrogen bonds : angle 4.65260 / 3.23 ( 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 545 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 429 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7796 (mt) cc_final: 0.7591 (mt) REVERT: A 239 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8963 (tm-30) REVERT: A 279 ASP cc_start: 0.8490 (t0) cc_final: 0.8266 (t0) REVERT: A 306 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 322 LYS cc_start: 0.9318 (tttt) cc_final: 0.8984 (ttmm) REVERT: A 442 MET cc_start: 0.8864 (ttm) cc_final: 0.8628 (ttm) REVERT: A 536 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9020 (tt) REVERT: A 622 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7924 (tp30) REVERT: B 195 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9037 (tm) REVERT: B 239 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: B 279 ASP cc_start: 0.8327 (t70) cc_final: 0.7815 (t0) REVERT: B 302 ARG cc_start: 0.7729 (tpm170) cc_final: 0.7262 (tpp-160) REVERT: B 305 ARG cc_start: 0.9068 (ttm110) cc_final: 0.8818 (ttm-80) REVERT: B 306 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 322 LYS cc_start: 0.9269 (tttt) cc_final: 0.8954 (ttmm) REVERT: B 357 ASN cc_start: 0.7710 (p0) cc_final: 0.6982 (p0) REVERT: B 363 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7397 (mmp80) REVERT: B 440 MET cc_start: 0.8907 (ptm) cc_final: 0.8692 (tmm) REVERT: B 442 MET cc_start: 0.8845 (ttm) cc_final: 0.8606 (ttm) REVERT: C 195 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9278 (tm) REVERT: C 202 ILE cc_start: 0.9678 (mt) cc_final: 0.9400 (tt) REVERT: C 239 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8988 (tm-30) REVERT: C 279 ASP cc_start: 0.8369 (t70) cc_final: 0.7853 (t0) REVERT: C 302 ARG cc_start: 0.7541 (tpm170) cc_final: 0.6852 (tpm170) REVERT: C 303 GLU cc_start: 0.8552 (mp0) cc_final: 0.8302 (pm20) REVERT: C 305 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: C 306 GLN cc_start: 0.9333 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 322 LYS cc_start: 0.9238 (tttt) cc_final: 0.8956 (ttmm) REVERT: C 326 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7743 (mtm-85) REVERT: C 345 MET cc_start: 0.7644 (mmt) cc_final: 0.7294 (mmt) REVERT: C 367 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 442 MET cc_start: 0.8867 (ttm) cc_final: 0.8635 (ttm) REVERT: C 522 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.7966 (t-90) REVERT: C 523 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8599 (p90) REVERT: C 536 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9049 (tt) REVERT: C 621 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7966 (ttm170) REVERT: C 622 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7915 (tp30) REVERT: D 44 ILE cc_start: 0.9235 (tp) cc_final: 0.9014 (tt) REVERT: D 71 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7381 (pmmt) REVERT: D 208 ASN cc_start: 0.8060 (t0) cc_final: 0.7758 (t0) REVERT: D 215 MET cc_start: 0.8705 (ttp) cc_final: 0.8229 (tmm) REVERT: D 239 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: D 279 ASP cc_start: 0.8460 (t0) cc_final: 0.8076 (t0) REVERT: D 302 ARG cc_start: 0.7862 (tpt170) cc_final: 0.7372 (tpp-160) REVERT: D 306 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 322 LYS cc_start: 0.9289 (tttt) cc_final: 0.8997 (ttmm) REVERT: D 326 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7752 (mtm-85) REVERT: D 355 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6977 (ttm170) REVERT: D 403 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: D 522 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8072 (t-90) REVERT: D 523 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8405 (p90) REVERT: D 536 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9133 (tt) REVERT: D 578 MET cc_start: 0.9033 (ttm) cc_final: 0.8747 (mtm) REVERT: D 622 GLU cc_start: 0.8248 (mp0) cc_final: 0.7918 (tp30) outliers start: 116 outliers final: 76 residues processed: 512 average time/residue: 0.1334 time to fit residues: 108.0085 Evaluate side-chains 520 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 425 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 150 THR 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 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 387 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 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 564 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR 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 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 372 LEU Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 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 194 SER 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 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 391 VAL 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 557 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 203 LEU 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 403 GLU 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 485 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 551 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 24 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 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** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS D 40 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099493 restraints weight = 37395.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102632 restraints weight = 19002.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104767 restraints weight = 11947.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106184 restraints weight = 8688.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107068 restraints weight = 7015.283| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5338 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= 0.181 Angle : 0.867 16.765 27607 Z= 0.400 Chirality : 0.045 0.244 3118 Planarity : 0.004 0.049 3474 Dihedral : 5.842 45.200 2873 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.33 % Favored : 89.46 % Rotamer: Outliers : 5.07 % Allowed : 25.52 % Favored : 69.42 % 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: -1.40 (0.17), residues: 2448 helix: 0.35 (0.14), residues: 1368 sheet: -1.55 (0.61), residues: 56 loop : -2.76 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 305 TYR 0.030 0.001 TYR B 467 PHE 0.031 0.002 PHE A 523 TRP 0.035 0.001 TRP A 583 HIS 0.009 0.001 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (20341) covalent geometry : angle 0.86668 / 0.40 (27607) hydrogen bonds : bond 0.03787 / 2.50 ( 772) hydrogen bonds : angle 4.52830 / 3.13 ( 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 549 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 441 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7819 (mt) cc_final: 0.7608 (mt) REVERT: A 239 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8944 (tm-30) REVERT: A 279 ASP cc_start: 0.8452 (t0) cc_final: 0.8237 (t0) REVERT: A 305 ARG cc_start: 0.8963 (ttp-110) cc_final: 0.8709 (ttm-80) REVERT: A 306 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 322 LYS cc_start: 0.9303 (tttt) cc_final: 0.8972 (ttmm) REVERT: A 442 MET cc_start: 0.8880 (ttm) cc_final: 0.8629 (ttm) REVERT: A 536 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8989 (tt) REVERT: A 622 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7936 (tp30) REVERT: B 195 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9020 (tm) REVERT: B 239 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8973 (tm-30) REVERT: B 279 ASP cc_start: 0.8304 (t70) cc_final: 0.7782 (t0) REVERT: B 302 ARG cc_start: 0.7732 (tpm170) cc_final: 0.7256 (tpp-160) REVERT: B 305 ARG cc_start: 0.9066 (ttm110) cc_final: 0.8811 (ttm-80) REVERT: B 306 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8612 (tm-30) REVERT: B 322 LYS cc_start: 0.9271 (tttt) cc_final: 0.8950 (ttmm) REVERT: B 442 MET cc_start: 0.8814 (ttm) cc_final: 0.8556 (ttm) REVERT: B 481 MET cc_start: 0.9165 (ttm) cc_final: 0.8960 (ttt) REVERT: C 195 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9265 (tm) REVERT: C 202 ILE cc_start: 0.9659 (mt) cc_final: 0.9398 (tt) REVERT: C 239 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8973 (tm-30) REVERT: C 279 ASP cc_start: 0.8329 (t70) cc_final: 0.7817 (t0) REVERT: C 302 ARG cc_start: 0.7486 (tpm170) cc_final: 0.6818 (tpm170) REVERT: C 303 GLU cc_start: 0.8584 (mp0) cc_final: 0.8325 (pm20) REVERT: C 305 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8443 (ttp80) REVERT: C 306 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 322 LYS cc_start: 0.9240 (tttt) cc_final: 0.8947 (ttmm) REVERT: C 326 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7638 (mtm-85) REVERT: C 367 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8204 (tt) REVERT: C 442 MET cc_start: 0.8843 (ttm) cc_final: 0.8596 (ttm) REVERT: C 522 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.7862 (t-90) REVERT: C 523 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8575 (p90) REVERT: C 536 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9022 (tt) REVERT: C 621 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7917 (ttm170) REVERT: C 622 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7922 (tp30) REVERT: D 44 ILE cc_start: 0.9207 (tp) cc_final: 0.8981 (tt) REVERT: D 71 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7314 (pmmt) REVERT: D 208 ASN cc_start: 0.8027 (t0) cc_final: 0.7731 (t0) REVERT: D 215 MET cc_start: 0.8670 (ttp) cc_final: 0.8260 (tmm) REVERT: D 239 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8589 (tm-30) REVERT: D 279 ASP cc_start: 0.8436 (t0) cc_final: 0.8047 (t0) REVERT: D 302 ARG cc_start: 0.7886 (tpt170) cc_final: 0.7411 (tpp-160) REVERT: D 306 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8461 (tm-30) REVERT: D 322 LYS cc_start: 0.9292 (tttt) cc_final: 0.8990 (ttmm) REVERT: D 326 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7689 (mtm-85) REVERT: D 355 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6892 (ttm170) REVERT: D 403 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: D 522 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8022 (t-90) REVERT: D 523 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8397 (p90) REVERT: D 536 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9121 (tt) REVERT: D 578 MET cc_start: 0.9045 (ttm) cc_final: 0.8761 (mtm) REVERT: D 622 GLU cc_start: 0.8212 (mp0) cc_final: 0.7855 (tp30) outliers start: 108 outliers final: 75 residues processed: 521 average time/residue: 0.1344 time to fit residues: 110.8924 Evaluate side-chains 523 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 429 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP 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 377 TYR Chi-restraints excluded: chain A residue 387 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 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 B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR 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 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 372 LEU Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 194 SER 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 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 438 VAL 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 536 LEU Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 203 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 338 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 403 GLU 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 465 VAL Chi-restraints excluded: chain D residue 485 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 532 SER Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 66 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 110 optimal weight: 0.0370 chunk 207 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- 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** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 582 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099724 restraints weight = 37367.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102984 restraints weight = 18542.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105107 restraints weight = 11506.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106623 restraints weight = 8354.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107564 restraints weight = 6665.226| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5400 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= 0.172 Angle : 0.860 16.637 27607 Z= 0.397 Chirality : 0.046 0.244 3118 Planarity : 0.004 0.049 3474 Dihedral : 5.793 45.000 2873 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.70 % Favored : 89.05 % Rotamer: Outliers : 5.16 % Allowed : 25.75 % Favored : 69.09 % 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: -1.36 (0.17), residues: 2448 helix: 0.30 (0.14), residues: 1392 sheet: -1.28 (0.55), residues: 64 loop : -2.71 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 305 TYR 0.031 0.001 TYR A 216 PHE 0.033 0.002 PHE A 523 TRP 0.042 0.002 TRP B 583 HIS 0.009 0.001 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (20341) covalent geometry : angle 0.85971 / 0.40 (27607) hydrogen bonds : bond 0.03740 / 2.46 ( 772) hydrogen bonds : angle 4.51963 / 3.12 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3693.15 seconds wall clock time: 64 minutes 26.08 seconds (3866.08 seconds total)