Starting phenix.real_space_refine on Sat Jul 4 09:42:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4d_22665/07_2026/7k4d_22665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4d_22665/07_2026/7k4d_22665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4d_22665/07_2026/7k4d_22665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4d_22665/07_2026/7k4d_22665.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4d_22665/07_2026/7k4d_22665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4d_22665/07_2026/7k4d_22665_neut.cif" } resolution = 3.66 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= 0.003 sd= 0.037 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 2 9.91 5 S 160 5.16 5 C 12811 2.51 5 N 3339 2.21 5 O 3474 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 68 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: 19801 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'VUM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'VUM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'VUM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'VUM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.17, per 1000 atoms: 0.21 Number of scatterers: 19801 At special positions: 0 Unit cell: (143.45, 143.45, 127.3, 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 2 19.99 S 160 16.00 F 15 9.00 O 3474 8.00 N 3339 7.00 C 12811 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: 1.74 Conformation dependent library (CDL) restraints added in 804.8 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 58.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.043A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.663A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.729A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.576A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.761A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.593A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.726A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.650A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.748A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.765A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.608A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.700A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.642A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.676A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.895A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.754A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.655A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.549A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.915A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.566A pdb=" N TYR A 467 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.600A pdb=" N LYS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.724A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.989A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.958A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 4.175A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.504A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.043A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.663A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.730A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.576A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.761A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.593A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.726A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.650A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.748A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.765A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.607A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.700A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.642A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.677A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.896A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.754A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 404 removed outlier: 3.654A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.549A pdb=" N VAL B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.916A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.566A pdb=" N TYR B 467 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.600A pdb=" N LYS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.725A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.989A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.958A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 585 removed outlier: 4.175A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.505A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.043A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.664A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.729A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.575A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.761A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.593A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.726A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.650A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.747A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.765A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.608A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.699A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.641A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.676A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.895A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 348 removed outlier: 3.754A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 404 removed outlier: 3.654A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.549A pdb=" N VAL C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.916A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.566A pdb=" N TYR C 467 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 removed outlier: 3.600A pdb=" N LYS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.725A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.990A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.958A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 585 removed outlier: 4.176A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.504A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.042A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.663A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.729A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.577A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.761A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 removed outlier: 3.593A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.726A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.650A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.747A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.765A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.608A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.700A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.643A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.676A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.895A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.754A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 404 removed outlier: 3.654A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.549A pdb=" N VAL D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.915A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.566A pdb=" N TYR D 467 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 removed outlier: 3.599A pdb=" N LYS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.724A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.989A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.959A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 585 removed outlier: 4.175A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.504A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.698A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 275 " --> pdb=" O TRP A 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 274 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 633 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 removed outlier: 3.698A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 275 " --> pdb=" O TRP B 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 274 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 633 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 268 through 270 removed outlier: 3.698A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 275 " --> pdb=" O TRP C 268 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 274 " --> pdb=" O ASP C 635 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 633 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 268 through 270 removed outlier: 3.698A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 275 " --> pdb=" O TRP D 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 274 " --> pdb=" O ASP D 635 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 633 " --> pdb=" O THR D 276 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 2.24 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: 6275 1.34 - 1.46: 4339 1.46 - 1.58: 9380 1.58 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 20266 Sorted by residual: bond pdb=" C01 VUM D 702 " pdb=" O01 VUM D 702 " ideal model delta sigma weight residual 1.230 1.400 -0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" C01 VUM C 701 " pdb=" O01 VUM C 701 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C01 VUM B 701 " pdb=" O01 VUM B 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C01 VUM A 701 " pdb=" O01 VUM A 701 " ideal model delta sigma weight residual 1.230 1.391 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C01 VUM D 701 " pdb=" O01 VUM D 701 " ideal model delta sigma weight residual 1.230 1.391 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 20261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 25724 2.23 - 4.46: 1482 4.46 - 6.69: 233 6.69 - 8.93: 57 8.93 - 11.16: 22 Bond angle restraints: 27518 Sorted by residual: angle pdb=" N VAL A 465 " pdb=" CA VAL A 465 " pdb=" C VAL A 465 " ideal model delta sigma weight residual 112.80 105.68 7.12 1.15e+00 7.56e-01 3.83e+01 angle pdb=" N VAL D 465 " pdb=" CA VAL D 465 " pdb=" C VAL D 465 " ideal model delta sigma weight residual 112.80 105.70 7.10 1.15e+00 7.56e-01 3.81e+01 angle pdb=" N VAL B 465 " pdb=" CA VAL B 465 " pdb=" C VAL B 465 " ideal model delta sigma weight residual 112.80 105.71 7.09 1.15e+00 7.56e-01 3.80e+01 angle pdb=" N VAL C 465 " pdb=" CA VAL C 465 " pdb=" C VAL C 465 " ideal model delta sigma weight residual 112.80 105.73 7.07 1.15e+00 7.56e-01 3.78e+01 angle pdb=" N LEU C 372 " pdb=" CA LEU C 372 " pdb=" C LEU C 372 " ideal model delta sigma weight residual 110.24 117.43 -7.19 1.30e+00 5.92e-01 3.06e+01 ... (remaining 27513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.26: 11652 23.26 - 46.52: 530 46.52 - 69.78: 25 69.78 - 93.03: 9 93.03 - 116.29: 7 Dihedral angle restraints: 12223 sinusoidal: 5063 harmonic: 7160 Sorted by residual: dihedral pdb=" CA ILE D 540 " pdb=" C ILE D 540 " pdb=" N ILE D 541 " pdb=" CA ILE D 541 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE A 540 " pdb=" C ILE A 540 " pdb=" N ILE A 541 " pdb=" CA ILE A 541 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE C 540 " pdb=" C ILE C 540 " pdb=" N ILE C 541 " pdb=" CA ILE C 541 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 12220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1962 0.048 - 0.097: 898 0.097 - 0.145: 195 0.145 - 0.193: 27 0.193 - 0.241: 28 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CB ILE B 540 " pdb=" CA ILE B 540 " pdb=" CG1 ILE B 540 " pdb=" CG2 ILE B 540 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE D 540 " pdb=" CA ILE D 540 " pdb=" CG1 ILE D 540 " pdb=" CG2 ILE D 540 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 3107 not shown) Planarity restraints: 3458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 476 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO D 477 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 477 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 477 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO C 477 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 477 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " 0.048 5.00e-02 4.00e+02 ... (remaining 3455 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2567 2.74 - 3.28: 18385 3.28 - 3.82: 29914 3.82 - 4.36: 34717 4.36 - 4.90: 57926 Nonbonded interactions: 143509 Sorted by model distance: nonbonded pdb=" OH TYR C 623 " pdb=" OE2 GLU D 35 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN A 118 " pdb=" OH TYR D 270 " model vdw 2.337 3.120 nonbonded pdb=" OH TYR A 623 " pdb=" OE2 GLU B 35 " model vdw 2.357 3.040 nonbonded pdb=" OH TYR B 623 " pdb=" OE2 GLU C 35 " model vdw 2.379 3.040 nonbonded pdb=" O TYR A 349 " pdb=" NH1 ARG A 385 " model vdw 2.400 3.120 ... (remaining 143504 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 28 through 701) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 28 through 701) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.850 Find NCS groups from input model: 0.460 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 : 0.010 0.170 20266 Z= 0.446 Angle : 1.216 11.157 27518 Z= 0.661 Chirality : 0.058 0.241 3110 Planarity : 0.008 0.087 3458 Dihedral : 12.492 116.292 7599 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.38 % Allowed : 6.59 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.15 (0.11), residues: 2440 helix: -4.58 (0.06), residues: 1224 sheet: -2.92 (0.59), residues: 56 loop : -3.52 (0.15), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 305 TYR 0.021 0.002 TYR A 547 PHE 0.028 0.003 PHE A 162 TRP 0.017 0.002 TRP C 321 HIS 0.020 0.002 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.45 (20266) covalent geometry : angle 1.21568 / 0.66 (27518) hydrogen bonds : bond 0.34136 / 22.50 ( 696) hydrogen bonds : angle 9.89534 / 6.99 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 636 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7848 (m110) cc_final: 0.6837 (t0) REVERT: A 84 HIS cc_start: 0.7950 (m90) cc_final: 0.7552 (m90) REVERT: A 91 ASN cc_start: 0.8037 (m110) cc_final: 0.7689 (m-40) REVERT: A 96 MET cc_start: 0.7937 (tmm) cc_final: 0.7315 (tmm) REVERT: A 100 GLU cc_start: 0.8419 (tp30) cc_final: 0.8153 (mt-10) REVERT: A 128 GLN cc_start: 0.7106 (pt0) cc_final: 0.6403 (tm-30) REVERT: A 146 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7542 (tpp-160) REVERT: A 214 GLN cc_start: 0.8188 (mt0) cc_final: 0.7297 (tm-30) REVERT: A 250 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8138 (tp30) REVERT: A 262 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8519 (tptt) REVERT: A 284 ASP cc_start: 0.8915 (t70) cc_final: 0.8654 (t0) REVERT: A 300 LYS cc_start: 0.8437 (pmtt) cc_final: 0.7896 (ttmt) REVERT: A 303 GLU cc_start: 0.8368 (tt0) cc_final: 0.8094 (tt0) REVERT: A 440 MET cc_start: 0.8906 (ttp) cc_final: 0.7912 (mmp) REVERT: A 470 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.8259 (ptp90) REVERT: A 502 LEU cc_start: 0.8291 (tp) cc_final: 0.7922 (tt) REVERT: A 547 TYR cc_start: 0.8068 (m-10) cc_final: 0.7755 (m-10) REVERT: A 577 MET cc_start: 0.7297 (mtp) cc_final: 0.6963 (mtp) REVERT: A 619 CYS cc_start: 0.7776 (p) cc_final: 0.7395 (p) REVERT: A 637 GLN cc_start: 0.8547 (tp40) cc_final: 0.8277 (tt0) REVERT: B 34 ASP cc_start: 0.8167 (m-30) cc_final: 0.7942 (m-30) REVERT: B 62 ASN cc_start: 0.7843 (m110) cc_final: 0.6698 (t0) REVERT: B 84 HIS cc_start: 0.8017 (m90) cc_final: 0.7569 (m90) REVERT: B 91 ASN cc_start: 0.8064 (m110) cc_final: 0.7650 (m-40) REVERT: B 96 MET cc_start: 0.8004 (tmm) cc_final: 0.7290 (tmm) REVERT: B 100 GLU cc_start: 0.8426 (tp30) cc_final: 0.8175 (mt-10) REVERT: B 128 GLN cc_start: 0.7067 (pt0) cc_final: 0.6181 (pp30) REVERT: B 144 SER cc_start: 0.8115 (m) cc_final: 0.7599 (p) REVERT: B 146 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7546 (tpp-160) REVERT: B 214 GLN cc_start: 0.8289 (mt0) cc_final: 0.7448 (tm-30) REVERT: B 250 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8123 (tp30) REVERT: B 270 TYR cc_start: 0.7923 (t80) cc_final: 0.7485 (t80) REVERT: B 300 LYS cc_start: 0.8308 (pmtt) cc_final: 0.7808 (ttmt) REVERT: B 303 GLU cc_start: 0.8391 (tt0) cc_final: 0.8154 (tt0) REVERT: B 368 LEU cc_start: 0.6348 (mp) cc_final: 0.6058 (mp) REVERT: B 440 MET cc_start: 0.8910 (ttp) cc_final: 0.8028 (mmp) REVERT: B 464 ASN cc_start: 0.7377 (t0) cc_final: 0.6795 (t0) REVERT: B 470 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.8237 (ptp90) REVERT: B 502 LEU cc_start: 0.8329 (tp) cc_final: 0.7961 (tt) REVERT: B 577 MET cc_start: 0.7317 (mtp) cc_final: 0.7045 (ttm) REVERT: B 637 GLN cc_start: 0.8559 (tp40) cc_final: 0.8337 (tt0) REVERT: C 59 GLN cc_start: 0.8358 (tp-100) cc_final: 0.8031 (tp-100) REVERT: C 62 ASN cc_start: 0.7929 (m110) cc_final: 0.6898 (t0) REVERT: C 71 LYS cc_start: 0.7226 (mttt) cc_final: 0.6437 (mmpt) REVERT: C 84 HIS cc_start: 0.8216 (m90) cc_final: 0.7648 (m90) REVERT: C 91 ASN cc_start: 0.7859 (m110) cc_final: 0.7453 (m-40) REVERT: C 144 SER cc_start: 0.8287 (m) cc_final: 0.7772 (p) REVERT: C 146 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7347 (tpp-160) REVERT: C 193 ASP cc_start: 0.7305 (p0) cc_final: 0.6625 (p0) REVERT: C 214 GLN cc_start: 0.8237 (mt0) cc_final: 0.7683 (tm-30) REVERT: C 250 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7684 (tp30) REVERT: C 262 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8571 (tptt) REVERT: C 294 GLU cc_start: 0.8018 (tp30) cc_final: 0.7582 (tt0) REVERT: C 315 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7944 (tp30) REVERT: C 355 ARG cc_start: 0.7754 (ttt-90) cc_final: 0.7239 (ttt-90) REVERT: C 440 MET cc_start: 0.8875 (ttp) cc_final: 0.7738 (tpt) REVERT: C 481 MET cc_start: 0.7802 (tpp) cc_final: 0.7426 (tpp) REVERT: C 546 ASN cc_start: 0.8596 (t0) cc_final: 0.8161 (t0) REVERT: C 578 MET cc_start: 0.8271 (mmt) cc_final: 0.7528 (mmt) REVERT: C 637 GLN cc_start: 0.8596 (tp40) cc_final: 0.8340 (tt0) REVERT: D 34 ASP cc_start: 0.8173 (m-30) cc_final: 0.7960 (m-30) REVERT: D 62 ASN cc_start: 0.7767 (m110) cc_final: 0.6733 (t0) REVERT: D 84 HIS cc_start: 0.8247 (m90) cc_final: 0.7825 (m90) REVERT: D 91 ASN cc_start: 0.8242 (m110) cc_final: 0.7839 (m-40) REVERT: D 96 MET cc_start: 0.8098 (tmm) cc_final: 0.7825 (tmm) REVERT: D 100 GLU cc_start: 0.8381 (tp30) cc_final: 0.8070 (mt-10) REVERT: D 128 GLN cc_start: 0.7006 (pt0) cc_final: 0.6606 (pp30) REVERT: D 137 LEU cc_start: 0.9244 (mt) cc_final: 0.8919 (tt) REVERT: D 144 SER cc_start: 0.8173 (m) cc_final: 0.7669 (p) REVERT: D 146 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7623 (tpp-160) REVERT: D 193 ASP cc_start: 0.7610 (p0) cc_final: 0.7198 (p0) REVERT: D 214 GLN cc_start: 0.8318 (mt0) cc_final: 0.7368 (tm-30) REVERT: D 250 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8161 (tp30) REVERT: D 262 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8593 (mmtt) REVERT: D 268 TRP cc_start: 0.8182 (p-90) cc_final: 0.7803 (p-90) REVERT: D 282 GLU cc_start: 0.7408 (tt0) cc_final: 0.6921 (tt0) REVERT: D 303 GLU cc_start: 0.8370 (tt0) cc_final: 0.8099 (tt0) REVERT: D 323 ARG cc_start: 0.8279 (ptt180) cc_final: 0.7818 (ptt90) REVERT: D 440 MET cc_start: 0.8890 (ttp) cc_final: 0.7824 (mmp) REVERT: D 502 LEU cc_start: 0.8499 (tp) cc_final: 0.8216 (tt) REVERT: D 637 GLN cc_start: 0.8442 (tp40) cc_final: 0.8242 (tt0) outliers start: 8 outliers final: 0 residues processed: 636 average time/residue: 0.1359 time to fit residues: 130.2379 Evaluate side-chains 445 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 HIS A 206 GLN A 239 GLN A 267 GLN A 357 ASN A 358 ASN A 464 ASN A 548 ASN A 572 ASN A 596 GLN B 59 GLN B 165 HIS B 206 GLN B 239 GLN B 267 GLN B 357 ASN B 358 ASN B 464 ASN B 548 ASN B 572 ASN B 596 GLN C 165 HIS C 206 GLN C 239 GLN C 267 GLN C 357 ASN C 358 ASN C 464 ASN C 473 GLN C 548 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN D 165 HIS D 206 GLN D 239 GLN D 267 GLN D 357 ASN D 358 ASN D 464 ASN D 473 GLN D 548 ASN D 572 ASN D 596 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143965 restraints weight = 27394.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148183 restraints weight = 14421.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150978 restraints weight = 9426.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152797 restraints weight = 7163.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153924 restraints weight = 6000.521| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20266 Z= 0.166 Angle : 0.711 8.621 27518 Z= 0.367 Chirality : 0.042 0.174 3110 Planarity : 0.006 0.066 3458 Dihedral : 7.914 83.378 2879 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.06 % Allowed : 12.76 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.13), residues: 2440 helix: -2.79 (0.11), residues: 1340 sheet: -2.55 (0.63), residues: 56 loop : -3.57 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.019 0.002 TYR B 324 PHE 0.016 0.002 PHE B 211 TRP 0.012 0.001 TRP C 321 HIS 0.007 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (20266) covalent geometry : angle 0.71061 / 0.37 (27518) hydrogen bonds : bond 0.04833 / 3.14 ( 696) hydrogen bonds : angle 5.29909 / 3.67 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 502 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7704 (m110) cc_final: 0.6721 (t0) REVERT: A 71 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7072 (mmpt) REVERT: A 128 GLN cc_start: 0.7112 (pt0) cc_final: 0.6337 (tm-30) REVERT: A 153 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7707 (mtt90) REVERT: A 201 HIS cc_start: 0.8550 (m170) cc_final: 0.8332 (m90) REVERT: A 211 PHE cc_start: 0.7700 (p90) cc_final: 0.7342 (p90) REVERT: A 262 LYS cc_start: 0.8821 (tmtt) cc_final: 0.8556 (tptt) REVERT: A 268 TRP cc_start: 0.7791 (p-90) cc_final: 0.7553 (p-90) REVERT: A 282 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 284 ASP cc_start: 0.8760 (t70) cc_final: 0.8544 (t0) REVERT: A 300 LYS cc_start: 0.8344 (pmtt) cc_final: 0.8008 (ttmt) REVERT: A 303 GLU cc_start: 0.8438 (tt0) cc_final: 0.8194 (tt0) REVERT: A 315 GLU cc_start: 0.8058 (tp30) cc_final: 0.7639 (mm-30) REVERT: A 378 MET cc_start: 0.7596 (ttm) cc_final: 0.7100 (ttt) REVERT: A 440 MET cc_start: 0.8469 (ttp) cc_final: 0.7757 (tpt) REVERT: A 540 ILE cc_start: 0.8143 (mt) cc_final: 0.7862 (mt) REVERT: A 542 ASP cc_start: 0.7454 (m-30) cc_final: 0.7198 (m-30) REVERT: A 629 TRP cc_start: 0.5923 (m-10) cc_final: 0.5259 (m-10) REVERT: A 637 GLN cc_start: 0.8412 (tp40) cc_final: 0.8139 (tt0) REVERT: B 62 ASN cc_start: 0.7730 (m110) cc_final: 0.6841 (t0) REVERT: B 71 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7122 (mmpt) REVERT: B 91 ASN cc_start: 0.7508 (m110) cc_final: 0.7270 (m-40) REVERT: B 128 GLN cc_start: 0.7014 (pt0) cc_final: 0.6239 (tm-30) REVERT: B 153 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7829 (mtt90) REVERT: B 193 ASP cc_start: 0.8080 (p0) cc_final: 0.7381 (p0) REVERT: B 211 PHE cc_start: 0.7700 (p90) cc_final: 0.7252 (p90) REVERT: B 300 LYS cc_start: 0.8328 (pmtt) cc_final: 0.7940 (ttmt) REVERT: B 303 GLU cc_start: 0.8382 (tt0) cc_final: 0.8160 (tt0) REVERT: B 315 GLU cc_start: 0.8016 (tp30) cc_final: 0.7570 (mm-30) REVERT: B 440 MET cc_start: 0.8572 (ttp) cc_final: 0.7816 (tpt) REVERT: B 464 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.6950 (t0) REVERT: B 470 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.8353 (ptp-170) REVERT: B 481 MET cc_start: 0.7709 (tpp) cc_final: 0.7260 (tpp) REVERT: B 540 ILE cc_start: 0.8116 (mt) cc_final: 0.7847 (mt) REVERT: B 621 ARG cc_start: 0.6575 (ptt-90) cc_final: 0.6364 (ttp80) REVERT: B 637 GLN cc_start: 0.8335 (tp40) cc_final: 0.8055 (tt0) REVERT: C 59 GLN cc_start: 0.8276 (tp-100) cc_final: 0.8070 (tp-100) REVERT: C 62 ASN cc_start: 0.7827 (m110) cc_final: 0.6922 (t0) REVERT: C 146 ARG cc_start: 0.7692 (mmm160) cc_final: 0.7488 (tpp-160) REVERT: C 164 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: C 180 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8313 (ttm170) REVERT: C 193 ASP cc_start: 0.7953 (p0) cc_final: 0.7340 (p0) REVERT: C 195 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7873 (tm) REVERT: C 214 GLN cc_start: 0.8291 (mt0) cc_final: 0.7402 (tm-30) REVERT: C 215 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8781 (ttt) REVERT: C 216 TYR cc_start: 0.9221 (t80) cc_final: 0.8922 (t80) REVERT: C 262 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8470 (tptt) REVERT: C 268 TRP cc_start: 0.8286 (p-90) cc_final: 0.7953 (p-90) REVERT: C 294 GLU cc_start: 0.7743 (tp30) cc_final: 0.7356 (tt0) REVERT: C 315 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7559 (tp30) REVERT: C 440 MET cc_start: 0.8589 (ttp) cc_final: 0.7556 (tpt) REVERT: C 464 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7655 (t0) REVERT: C 536 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7914 (tt) REVERT: C 574 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.3853 (tt) REVERT: D 38 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (tt) REVERT: D 62 ASN cc_start: 0.7830 (m110) cc_final: 0.6875 (t0) REVERT: D 71 LYS cc_start: 0.7337 (mtpt) cc_final: 0.7036 (mtpt) REVERT: D 91 ASN cc_start: 0.7625 (m110) cc_final: 0.7135 (m-40) REVERT: D 99 MET cc_start: 0.8005 (mmm) cc_final: 0.7627 (mmm) REVERT: D 144 SER cc_start: 0.8294 (m) cc_final: 0.7721 (p) REVERT: D 146 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7154 (tpp-160) REVERT: D 153 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7773 (mtt90) REVERT: D 193 ASP cc_start: 0.8140 (p0) cc_final: 0.7404 (p0) REVERT: D 211 PHE cc_start: 0.7615 (p90) cc_final: 0.7260 (p90) REVERT: D 214 GLN cc_start: 0.8216 (mt0) cc_final: 0.7202 (tm-30) REVERT: D 215 MET cc_start: 0.8743 (ttt) cc_final: 0.8536 (ttt) REVERT: D 250 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8091 (tp30) REVERT: D 262 LYS cc_start: 0.8792 (tmtt) cc_final: 0.8547 (tptt) REVERT: D 300 LYS cc_start: 0.8356 (pmtt) cc_final: 0.7926 (ttmt) REVERT: D 303 GLU cc_start: 0.8350 (tt0) cc_final: 0.8020 (tt0) REVERT: D 315 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7638 (mm-30) REVERT: D 331 MET cc_start: 0.5025 (ttp) cc_final: 0.4378 (tmm) REVERT: D 440 MET cc_start: 0.8457 (ttp) cc_final: 0.7589 (tpt) REVERT: D 454 MET cc_start: 0.8466 (tpp) cc_final: 0.7689 (tpt) REVERT: D 464 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7066 (t0) REVERT: D 637 GLN cc_start: 0.8357 (tp40) cc_final: 0.8118 (tt0) outliers start: 65 outliers final: 20 residues processed: 547 average time/residue: 0.1298 time to fit residues: 109.6027 Evaluate side-chains 458 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 429 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 464 ASN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 224 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN B 59 GLN C 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN D 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139674 restraints weight = 27516.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143719 restraints weight = 14861.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146401 restraints weight = 9883.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148145 restraints weight = 7586.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149161 restraints weight = 6412.946| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20266 Z= 0.134 Angle : 0.662 8.483 27518 Z= 0.334 Chirality : 0.041 0.173 3110 Planarity : 0.005 0.057 3458 Dihedral : 7.079 59.213 2879 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.11 % Allowed : 17.18 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.15), residues: 2440 helix: -1.70 (0.13), residues: 1312 sheet: -2.47 (0.61), residues: 56 loop : -3.22 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 443 TYR 0.023 0.002 TYR D 324 PHE 0.041 0.001 PHE C 211 TRP 0.010 0.001 TRP C 321 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (20266) covalent geometry : angle 0.66184 / 0.33 (27518) hydrogen bonds : bond 0.03984 / 2.58 ( 696) hydrogen bonds : angle 4.67740 / 3.23 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 459 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7789 (m110) cc_final: 0.6847 (t0) REVERT: A 71 LYS cc_start: 0.7591 (mtpt) cc_final: 0.6974 (mmpt) REVERT: A 99 MET cc_start: 0.7840 (mmm) cc_final: 0.7442 (mmm) REVERT: A 153 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7696 (mtt90) REVERT: A 180 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8047 (ttm-80) REVERT: A 211 PHE cc_start: 0.7657 (p90) cc_final: 0.7390 (p90) REVERT: A 239 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: A 262 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8555 (tptt) REVERT: A 268 TRP cc_start: 0.7856 (p-90) cc_final: 0.7566 (p-90) REVERT: A 282 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 300 LYS cc_start: 0.8360 (pmtt) cc_final: 0.8015 (ttmt) REVERT: A 303 GLU cc_start: 0.8412 (tt0) cc_final: 0.8166 (tt0) REVERT: A 378 MET cc_start: 0.7731 (ttm) cc_final: 0.7188 (ttt) REVERT: A 390 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7388 (tt) REVERT: A 440 MET cc_start: 0.8604 (ttp) cc_final: 0.7874 (tpp) REVERT: A 445 ILE cc_start: 0.8491 (tt) cc_final: 0.8290 (tp) REVERT: A 577 MET cc_start: 0.7340 (mtp) cc_final: 0.7093 (mtp) REVERT: A 637 GLN cc_start: 0.8314 (tp40) cc_final: 0.8069 (tt0) REVERT: B 62 ASN cc_start: 0.7788 (m110) cc_final: 0.6918 (t0) REVERT: B 71 LYS cc_start: 0.7435 (mtpt) cc_final: 0.6892 (mmpt) REVERT: B 99 MET cc_start: 0.7857 (mmm) cc_final: 0.7573 (mmm) REVERT: B 153 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7842 (mtt90) REVERT: B 180 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8137 (ttm-80) REVERT: B 211 PHE cc_start: 0.7637 (p90) cc_final: 0.7313 (p90) REVERT: B 239 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: B 294 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7248 (tt0) REVERT: B 300 LYS cc_start: 0.8333 (pmtt) cc_final: 0.7962 (ttmt) REVERT: B 303 GLU cc_start: 0.8414 (tt0) cc_final: 0.8168 (tt0) REVERT: B 315 GLU cc_start: 0.8057 (tp30) cc_final: 0.7622 (mm-30) REVERT: B 440 MET cc_start: 0.8631 (ttp) cc_final: 0.7920 (tpp) REVERT: B 464 ASN cc_start: 0.7532 (t0) cc_final: 0.6833 (t0) REVERT: B 481 MET cc_start: 0.7828 (tpp) cc_final: 0.7337 (tpp) REVERT: B 540 ILE cc_start: 0.8259 (mt) cc_final: 0.7936 (mt) REVERT: B 574 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.3818 (mt) REVERT: B 637 GLN cc_start: 0.8276 (tp40) cc_final: 0.8061 (tt0) REVERT: C 62 ASN cc_start: 0.7882 (m110) cc_final: 0.6931 (t0) REVERT: C 153 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7894 (mtt90) REVERT: C 180 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8331 (ttm170) REVERT: C 193 ASP cc_start: 0.8045 (p0) cc_final: 0.7578 (p0) REVERT: C 214 GLN cc_start: 0.8258 (mt0) cc_final: 0.7552 (tm-30) REVERT: C 239 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: C 250 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8149 (tp30) REVERT: C 262 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8503 (tptt) REVERT: C 268 TRP cc_start: 0.8351 (p-90) cc_final: 0.8051 (p-90) REVERT: C 294 GLU cc_start: 0.7702 (tp30) cc_final: 0.7404 (tt0) REVERT: C 390 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8040 (tm) REVERT: C 401 LEU cc_start: 0.8335 (mt) cc_final: 0.8103 (tt) REVERT: C 440 MET cc_start: 0.8690 (ttp) cc_final: 0.7670 (tpt) REVERT: C 464 ASN cc_start: 0.7802 (t0) cc_final: 0.7271 (t0) REVERT: C 536 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7999 (tt) REVERT: D 38 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8183 (tt) REVERT: D 62 ASN cc_start: 0.7825 (m110) cc_final: 0.6866 (t0) REVERT: D 71 LYS cc_start: 0.7325 (mtpt) cc_final: 0.7040 (mtpt) REVERT: D 91 ASN cc_start: 0.7558 (m110) cc_final: 0.7213 (m-40) REVERT: D 99 MET cc_start: 0.7908 (mmm) cc_final: 0.7573 (mmm) REVERT: D 146 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7484 (tpp-160) REVERT: D 180 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8103 (ttm-80) REVERT: D 193 ASP cc_start: 0.8047 (p0) cc_final: 0.7802 (p0) REVERT: D 211 PHE cc_start: 0.7505 (p90) cc_final: 0.7156 (p90) REVERT: D 214 GLN cc_start: 0.8215 (mt0) cc_final: 0.7266 (tm-30) REVERT: D 239 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: D 250 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8177 (tp30) REVERT: D 282 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7906 (mt-10) REVERT: D 300 LYS cc_start: 0.8357 (pmtt) cc_final: 0.7933 (ttmt) REVERT: D 303 GLU cc_start: 0.8270 (tt0) cc_final: 0.7982 (tt0) REVERT: D 390 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7466 (tt) REVERT: D 401 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8564 (mt) REVERT: D 440 MET cc_start: 0.8654 (ttp) cc_final: 0.7711 (tpp) REVERT: D 464 ASN cc_start: 0.7461 (t0) cc_final: 0.6563 (t0) REVERT: D 470 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.8368 (ptp-170) REVERT: D 574 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.3940 (mt) REVERT: D 637 GLN cc_start: 0.8354 (tp40) cc_final: 0.8137 (tt0) outliers start: 66 outliers final: 21 residues processed: 495 average time/residue: 0.1266 time to fit residues: 97.5739 Evaluate side-chains 460 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 427 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 150 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 149 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 234 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 HIS B 59 GLN B 258 HIS C 59 GLN C 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149017 restraints weight = 27354.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153428 restraints weight = 14231.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156356 restraints weight = 9199.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158243 restraints weight = 6916.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159539 restraints weight = 5755.704| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20266 Z= 0.105 Angle : 0.609 7.298 27518 Z= 0.305 Chirality : 0.039 0.167 3110 Planarity : 0.004 0.058 3458 Dihedral : 6.339 42.736 2879 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.39 % Allowed : 18.08 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.16), residues: 2440 helix: -1.01 (0.14), residues: 1304 sheet: -2.13 (0.65), residues: 56 loop : -3.01 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 443 TYR 0.024 0.001 TYR A 324 PHE 0.023 0.001 PHE C 211 TRP 0.009 0.001 TRP B 613 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (20266) covalent geometry : angle 0.60905 / 0.30 (27518) hydrogen bonds : bond 0.03017 / 1.95 ( 696) hydrogen bonds : angle 4.14919 / 2.87 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 469 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7788 (m110) cc_final: 0.6866 (t0) REVERT: A 71 LYS cc_start: 0.7471 (mtpt) cc_final: 0.6914 (mmpt) REVERT: A 99 MET cc_start: 0.7806 (mmm) cc_final: 0.7342 (mmm) REVERT: A 153 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7667 (mtt90) REVERT: A 180 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8135 (ttm-80) REVERT: A 211 PHE cc_start: 0.7453 (p90) cc_final: 0.7215 (p90) REVERT: A 239 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: A 262 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8467 (tptt) REVERT: A 268 TRP cc_start: 0.7987 (p-90) cc_final: 0.7631 (p-90) REVERT: A 282 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7886 (mt-10) REVERT: A 300 LYS cc_start: 0.8324 (pmtt) cc_final: 0.7980 (ttmt) REVERT: A 303 GLU cc_start: 0.8400 (tt0) cc_final: 0.8106 (tt0) REVERT: A 315 GLU cc_start: 0.7976 (tp30) cc_final: 0.7520 (mm-30) REVERT: A 440 MET cc_start: 0.8545 (ttp) cc_final: 0.7845 (tpp) REVERT: A 464 ASN cc_start: 0.7795 (t0) cc_final: 0.7071 (t0) REVERT: A 540 ILE cc_start: 0.8169 (mt) cc_final: 0.7700 (tt) REVERT: B 62 ASN cc_start: 0.7838 (m110) cc_final: 0.7001 (t0) REVERT: B 71 LYS cc_start: 0.7288 (mtpt) cc_final: 0.6808 (mmpt) REVERT: B 99 MET cc_start: 0.7847 (mmm) cc_final: 0.7534 (mmm) REVERT: B 153 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7688 (mtt90) REVERT: B 180 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8110 (ttm110) REVERT: B 211 PHE cc_start: 0.7454 (p90) cc_final: 0.7130 (p90) REVERT: B 239 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: B 250 GLU cc_start: 0.8038 (tp30) cc_final: 0.7824 (mm-30) REVERT: B 282 GLU cc_start: 0.8055 (tp30) cc_final: 0.7840 (tp30) REVERT: B 294 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7264 (tt0) REVERT: B 300 LYS cc_start: 0.8267 (pmtt) cc_final: 0.7862 (ttmt) REVERT: B 303 GLU cc_start: 0.8413 (tt0) cc_final: 0.8140 (tt0) REVERT: B 315 GLU cc_start: 0.7978 (tp30) cc_final: 0.7495 (mm-30) REVERT: B 440 MET cc_start: 0.8607 (ttp) cc_final: 0.7618 (tpp) REVERT: B 464 ASN cc_start: 0.7373 (t0) cc_final: 0.6938 (t0) REVERT: B 481 MET cc_start: 0.7809 (tpp) cc_final: 0.7309 (tpp) REVERT: B 540 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7751 (tt) REVERT: B 574 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.3458 (mt) REVERT: C 99 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6938 (tmm) REVERT: C 153 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7853 (mtt90) REVERT: C 180 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8086 (ttm-80) REVERT: C 215 MET cc_start: 0.8711 (ttt) cc_final: 0.8389 (ttp) REVERT: C 239 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: C 252 ASN cc_start: 0.8371 (t0) cc_final: 0.8067 (t0) REVERT: C 262 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8278 (tptt) REVERT: C 268 TRP cc_start: 0.8256 (p-90) cc_final: 0.7923 (p-90) REVERT: C 440 MET cc_start: 0.8582 (ttp) cc_final: 0.7604 (tpt) REVERT: C 464 ASN cc_start: 0.7675 (t0) cc_final: 0.7403 (t0) REVERT: C 536 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7787 (tt) REVERT: C 574 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.4378 (mp) REVERT: C 634 GLU cc_start: 0.8371 (pm20) cc_final: 0.7626 (mp0) REVERT: D 62 ASN cc_start: 0.7889 (m110) cc_final: 0.6953 (t0) REVERT: D 91 ASN cc_start: 0.7309 (m110) cc_final: 0.7075 (m-40) REVERT: D 99 MET cc_start: 0.7863 (mmm) cc_final: 0.7491 (mmm) REVERT: D 180 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8088 (ttm110) REVERT: D 211 PHE cc_start: 0.7358 (p90) cc_final: 0.7034 (p90) REVERT: D 239 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: D 250 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8152 (tp30) REVERT: D 282 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7953 (mt-10) REVERT: D 294 GLU cc_start: 0.7307 (tt0) cc_final: 0.6981 (tt0) REVERT: D 300 LYS cc_start: 0.8361 (pmtt) cc_final: 0.7932 (ttmt) REVERT: D 303 GLU cc_start: 0.8311 (tt0) cc_final: 0.7967 (tt0) REVERT: D 401 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (mt) REVERT: D 440 MET cc_start: 0.8452 (ttp) cc_final: 0.7518 (tpp) REVERT: D 464 ASN cc_start: 0.7428 (t0) cc_final: 0.6752 (t0) REVERT: D 629 TRP cc_start: 0.5383 (m-10) cc_final: 0.4911 (m-10) REVERT: D 637 GLN cc_start: 0.8284 (tp40) cc_final: 0.8059 (tt0) outliers start: 72 outliers final: 24 residues processed: 511 average time/residue: 0.1210 time to fit residues: 96.4604 Evaluate side-chains 453 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 419 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 103 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 135 optimal weight: 0.0070 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN B 91 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 128 GLN C 370 GLN C 426 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135542 restraints weight = 27553.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139460 restraints weight = 14937.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142076 restraints weight = 10026.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143751 restraints weight = 7766.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144737 restraints weight = 6591.163| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20266 Z= 0.237 Angle : 0.767 10.660 27518 Z= 0.376 Chirality : 0.046 0.165 3110 Planarity : 0.005 0.052 3458 Dihedral : 6.840 52.373 2879 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.99 % Allowed : 19.35 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.16), residues: 2440 helix: -0.88 (0.14), residues: 1312 sheet: -2.40 (0.61), residues: 56 loop : -2.96 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 470 TYR 0.027 0.002 TYR C 623 PHE 0.023 0.002 PHE C 211 TRP 0.019 0.002 TRP D 629 HIS 0.007 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (20266) covalent geometry : angle 0.76665 / 0.38 (27518) hydrogen bonds : bond 0.04372 / 2.82 ( 696) hydrogen bonds : angle 4.81206 / 3.30 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 444 time to evaluate : 0.614 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 62 ASN cc_start: 0.7904 (m110) cc_final: 0.7035 (t0) REVERT: A 71 LYS cc_start: 0.7444 (mtpt) cc_final: 0.6956 (mmpt) REVERT: A 99 MET cc_start: 0.7860 (mmm) cc_final: 0.7533 (mmm) REVERT: A 144 SER cc_start: 0.8438 (m) cc_final: 0.7812 (p) REVERT: A 180 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8232 (ttm-80) REVERT: A 214 GLN cc_start: 0.7993 (mt0) cc_final: 0.7314 (tm-30) REVERT: A 239 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: A 250 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8044 (tp30) REVERT: A 262 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8614 (tptt) REVERT: A 268 TRP cc_start: 0.7745 (p-90) cc_final: 0.7524 (p-90) REVERT: A 282 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7946 (mt-10) REVERT: A 303 GLU cc_start: 0.8408 (tt0) cc_final: 0.8084 (tt0) REVERT: A 378 MET cc_start: 0.7932 (ttm) cc_final: 0.7496 (ttt) REVERT: A 401 LEU cc_start: 0.8471 (mt) cc_final: 0.8067 (tt) REVERT: A 440 MET cc_start: 0.8552 (ttp) cc_final: 0.7500 (tpp) REVERT: A 454 MET cc_start: 0.8374 (tpp) cc_final: 0.7982 (tpt) REVERT: A 490 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6839 (tt) REVERT: A 540 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 62 ASN cc_start: 0.7816 (m110) cc_final: 0.7006 (t0) REVERT: B 71 LYS cc_start: 0.7207 (mtpt) cc_final: 0.6827 (mmpt) REVERT: B 99 MET cc_start: 0.7829 (mmm) cc_final: 0.7550 (mmm) REVERT: B 144 SER cc_start: 0.8504 (m) cc_final: 0.7820 (p) REVERT: B 153 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7721 (mtt90) REVERT: B 180 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.7838 (mtp85) REVERT: B 214 GLN cc_start: 0.8103 (mt0) cc_final: 0.7492 (tm-30) REVERT: B 239 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: B 282 GLU cc_start: 0.8142 (tp30) cc_final: 0.7882 (tp30) REVERT: B 303 GLU cc_start: 0.8416 (tt0) cc_final: 0.8107 (tt0) REVERT: B 315 GLU cc_start: 0.8033 (tp30) cc_final: 0.7596 (tp30) REVERT: B 401 LEU cc_start: 0.8501 (mt) cc_final: 0.8100 (tt) REVERT: B 440 MET cc_start: 0.8579 (ttp) cc_final: 0.7663 (tpt) REVERT: B 454 MET cc_start: 0.8423 (tpp) cc_final: 0.7904 (tpt) REVERT: B 464 ASN cc_start: 0.7862 (t0) cc_final: 0.7262 (t0) REVERT: B 490 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6788 (tt) REVERT: B 574 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4694 (mp) REVERT: B 577 MET cc_start: 0.7594 (ttm) cc_final: 0.7156 (ttm) REVERT: B 615 ARG cc_start: 0.7576 (ttm170) cc_final: 0.6985 (ttm170) REVERT: B 629 TRP cc_start: 0.6555 (m-10) cc_final: 0.5706 (m-10) REVERT: C 99 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6871 (tmm) REVERT: C 180 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8134 (ttm-80) REVERT: C 211 PHE cc_start: 0.7734 (p90) cc_final: 0.7300 (p90) REVERT: C 214 GLN cc_start: 0.8460 (mt0) cc_final: 0.7754 (tm-30) REVERT: C 239 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: C 250 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8201 (tp30) REVERT: C 262 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8327 (tptt) REVERT: C 268 TRP cc_start: 0.8312 (p-90) cc_final: 0.7975 (p-90) REVERT: C 300 LYS cc_start: 0.8393 (pmtt) cc_final: 0.7620 (tmtt) REVERT: C 440 MET cc_start: 0.8628 (ttp) cc_final: 0.7481 (tpt) REVERT: C 524 TYR cc_start: 0.8079 (p90) cc_final: 0.7851 (p90) REVERT: C 542 ASP cc_start: 0.7832 (m-30) cc_final: 0.7618 (m-30) REVERT: C 574 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5066 (mp) REVERT: D 62 ASN cc_start: 0.7932 (m110) cc_final: 0.7007 (t0) REVERT: D 99 MET cc_start: 0.7867 (mmm) cc_final: 0.7504 (mmm) REVERT: D 144 SER cc_start: 0.8567 (m) cc_final: 0.7937 (p) REVERT: D 146 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6915 (tpt170) REVERT: D 180 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.7819 (mtp85) REVERT: D 214 GLN cc_start: 0.8178 (mt0) cc_final: 0.7400 (tm-30) REVERT: D 239 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: D 250 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8113 (tp30) REVERT: D 282 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8109 (mt-10) REVERT: D 303 GLU cc_start: 0.8373 (tt0) cc_final: 0.8035 (tt0) REVERT: D 378 MET cc_start: 0.8015 (ttm) cc_final: 0.7490 (ttt) REVERT: D 401 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8247 (tt) REVERT: D 440 MET cc_start: 0.8721 (ttp) cc_final: 0.7589 (tpt) REVERT: D 470 ARG cc_start: 0.8735 (ptp-170) cc_final: 0.8256 (ptp-170) REVERT: D 540 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8154 (mt) REVERT: D 577 MET cc_start: 0.7716 (ttm) cc_final: 0.7434 (ttm) outliers start: 106 outliers final: 54 residues processed: 511 average time/residue: 0.1205 time to fit residues: 97.0856 Evaluate side-chains 477 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 410 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 209 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 226 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 128 GLN C 370 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138950 restraints weight = 27233.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143002 restraints weight = 14685.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145673 restraints weight = 9823.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147396 restraints weight = 7585.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148404 restraints weight = 6440.657| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20266 Z= 0.152 Angle : 0.657 7.799 27518 Z= 0.324 Chirality : 0.042 0.163 3110 Planarity : 0.004 0.053 3458 Dihedral : 6.345 51.956 2879 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.95 % Allowed : 21.14 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.16), residues: 2440 helix: -0.48 (0.14), residues: 1312 sheet: -2.27 (0.63), residues: 56 loop : -2.90 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 414 TYR 0.026 0.002 TYR C 623 PHE 0.014 0.001 PHE C 211 TRP 0.014 0.001 TRP D 629 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (20266) covalent geometry : angle 0.65698 / 0.32 (27518) hydrogen bonds : bond 0.03303 / 2.13 ( 696) hydrogen bonds : angle 4.35962 / 3.00 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 436 time to evaluate : 0.647 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 62 ASN cc_start: 0.7843 (m110) cc_final: 0.6979 (t0) REVERT: A 71 LYS cc_start: 0.7509 (mtpt) cc_final: 0.7031 (mmpt) REVERT: A 99 MET cc_start: 0.7855 (mmm) cc_final: 0.7563 (mmm) REVERT: A 144 SER cc_start: 0.8442 (m) cc_final: 0.7811 (p) REVERT: A 180 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8140 (ttm-80) REVERT: A 214 GLN cc_start: 0.7868 (mt0) cc_final: 0.7273 (tm-30) REVERT: A 239 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: A 250 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7996 (tp30) REVERT: A 262 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8400 (tptt) REVERT: A 282 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7955 (mt-10) REVERT: A 294 GLU cc_start: 0.7267 (tt0) cc_final: 0.7060 (tt0) REVERT: A 303 GLU cc_start: 0.8420 (tt0) cc_final: 0.8094 (tt0) REVERT: A 378 MET cc_start: 0.7934 (ttm) cc_final: 0.7482 (ttt) REVERT: A 401 LEU cc_start: 0.8375 (mt) cc_final: 0.8070 (tt) REVERT: A 440 MET cc_start: 0.8477 (ttp) cc_final: 0.7403 (tpt) REVERT: A 454 MET cc_start: 0.8427 (tpp) cc_final: 0.8054 (tpt) REVERT: A 540 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8129 (mt) REVERT: A 574 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.4476 (mp) REVERT: B 62 ASN cc_start: 0.7857 (m110) cc_final: 0.7078 (t0) REVERT: B 71 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6822 (mmpt) REVERT: B 99 MET cc_start: 0.7843 (mmm) cc_final: 0.7597 (mmm) REVERT: B 144 SER cc_start: 0.8498 (m) cc_final: 0.7809 (p) REVERT: B 180 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8054 (ttm-80) REVERT: B 214 GLN cc_start: 0.7813 (mt0) cc_final: 0.7205 (tm-30) REVERT: B 239 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: B 282 GLU cc_start: 0.8104 (tp30) cc_final: 0.7825 (tp30) REVERT: B 294 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7364 (tt0) REVERT: B 303 GLU cc_start: 0.8422 (tt0) cc_final: 0.8118 (tt0) REVERT: B 315 GLU cc_start: 0.8019 (tp30) cc_final: 0.7573 (tp30) REVERT: B 401 LEU cc_start: 0.8463 (mt) cc_final: 0.8217 (tt) REVERT: B 440 MET cc_start: 0.8563 (ttp) cc_final: 0.7611 (tpt) REVERT: B 454 MET cc_start: 0.8464 (tpp) cc_final: 0.7901 (tpt) REVERT: B 464 ASN cc_start: 0.7799 (t0) cc_final: 0.7364 (t0) REVERT: B 541 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8311 (mt) REVERT: B 577 MET cc_start: 0.7588 (ttm) cc_final: 0.6882 (ttm) REVERT: B 615 ARG cc_start: 0.7508 (ttm170) cc_final: 0.6924 (ttm170) REVERT: B 629 TRP cc_start: 0.6727 (m-10) cc_final: 0.5856 (m-10) REVERT: C 99 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6871 (tmm) REVERT: C 128 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6549 (tm130) REVERT: C 180 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8157 (ttm-80) REVERT: C 214 GLN cc_start: 0.8387 (mt0) cc_final: 0.7671 (tm-30) REVERT: C 215 MET cc_start: 0.8945 (ttt) cc_final: 0.8705 (ttt) REVERT: C 239 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: C 250 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8198 (tp30) REVERT: C 262 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8306 (tptt) REVERT: C 268 TRP cc_start: 0.8248 (p-90) cc_final: 0.7929 (p-90) REVERT: C 300 LYS cc_start: 0.8392 (pmtt) cc_final: 0.7504 (tmtt) REVERT: C 440 MET cc_start: 0.8576 (ttp) cc_final: 0.7286 (tpt) REVERT: C 454 MET cc_start: 0.8366 (tpp) cc_final: 0.8124 (tpt) REVERT: C 464 ASN cc_start: 0.7907 (t0) cc_final: 0.7570 (t0) REVERT: C 524 TYR cc_start: 0.8020 (p90) cc_final: 0.7805 (p90) REVERT: C 542 ASP cc_start: 0.7714 (m-30) cc_final: 0.7439 (m-30) REVERT: C 574 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5296 (mt) REVERT: C 629 TRP cc_start: 0.7118 (m-10) cc_final: 0.6764 (m-10) REVERT: C 634 GLU cc_start: 0.8536 (pm20) cc_final: 0.8213 (pm20) REVERT: D 62 ASN cc_start: 0.7901 (m110) cc_final: 0.7027 (t0) REVERT: D 71 LYS cc_start: 0.7325 (mtpt) cc_final: 0.6820 (mmpt) REVERT: D 99 MET cc_start: 0.7902 (mmm) cc_final: 0.7580 (mmm) REVERT: D 144 SER cc_start: 0.8514 (m) cc_final: 0.7826 (p) REVERT: D 180 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8059 (ttm-80) REVERT: D 214 GLN cc_start: 0.8062 (mt0) cc_final: 0.7410 (tm-30) REVERT: D 239 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: D 250 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8261 (tp30) REVERT: D 282 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8099 (mt-10) REVERT: D 294 GLU cc_start: 0.7543 (tt0) cc_final: 0.7260 (tt0) REVERT: D 303 GLU cc_start: 0.8368 (tt0) cc_final: 0.8024 (tt0) REVERT: D 378 MET cc_start: 0.7968 (ttm) cc_final: 0.7429 (ttt) REVERT: D 401 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8344 (tt) REVERT: D 414 ARG cc_start: 0.7555 (mmt-90) cc_final: 0.7238 (tpp80) REVERT: D 440 MET cc_start: 0.8582 (ttp) cc_final: 0.7385 (tpt) REVERT: D 464 ASN cc_start: 0.7785 (t0) cc_final: 0.7244 (t0) REVERT: D 574 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.4716 (mp) REVERT: D 577 MET cc_start: 0.7507 (ttm) cc_final: 0.7119 (ttm) outliers start: 84 outliers final: 48 residues processed: 486 average time/residue: 0.1204 time to fit residues: 92.4585 Evaluate side-chains 469 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 409 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.0010 chunk 179 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 chunk 198 optimal weight: 0.0050 chunk 142 optimal weight: 0.0270 chunk 113 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.2458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144500 restraints weight = 27458.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148671 restraints weight = 14924.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151465 restraints weight = 9933.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153329 restraints weight = 7612.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154523 restraints weight = 6389.795| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20266 Z= 0.103 Angle : 0.615 7.634 27518 Z= 0.302 Chirality : 0.040 0.208 3110 Planarity : 0.004 0.051 3458 Dihedral : 5.774 45.437 2879 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.97 % Allowed : 22.32 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.85 (0.17), residues: 2440 helix: 0.02 (0.15), residues: 1300 sheet: -2.12 (0.65), residues: 56 loop : -2.83 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 470 TYR 0.024 0.001 TYR C 623 PHE 0.015 0.001 PHE B 415 TRP 0.010 0.001 TRP C 613 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (20266) covalent geometry : angle 0.61537 / 0.30 (27518) hydrogen bonds : bond 0.02565 / 1.65 ( 696) hydrogen bonds : angle 3.88621 / 2.68 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 442 time to evaluate : 0.607 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 62 ASN cc_start: 0.7817 (m110) cc_final: 0.6978 (t0) REVERT: A 71 LYS cc_start: 0.7409 (mtpt) cc_final: 0.6974 (mmpt) REVERT: A 99 MET cc_start: 0.7804 (mmm) cc_final: 0.7514 (mmm) REVERT: A 130 MET cc_start: 0.7812 (mmm) cc_final: 0.7528 (mpp) REVERT: A 167 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 180 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8184 (ttm-80) REVERT: A 239 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: A 250 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7911 (tp30) REVERT: A 255 MET cc_start: 0.8744 (tpp) cc_final: 0.8272 (tpp) REVERT: A 262 LYS cc_start: 0.8626 (tmtt) cc_final: 0.8277 (tptt) REVERT: A 268 TRP cc_start: 0.7803 (p-90) cc_final: 0.7296 (p-90) REVERT: A 282 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 290 GLN cc_start: 0.6660 (mm110) cc_final: 0.6407 (mm110) REVERT: A 294 GLU cc_start: 0.7237 (tt0) cc_final: 0.6928 (tt0) REVERT: A 303 GLU cc_start: 0.8376 (tt0) cc_final: 0.8051 (tt0) REVERT: A 315 GLU cc_start: 0.7944 (tp30) cc_final: 0.7537 (mm-30) REVERT: A 378 MET cc_start: 0.8051 (ttm) cc_final: 0.7515 (ttt) REVERT: A 401 LEU cc_start: 0.8472 (mt) cc_final: 0.8164 (tt) REVERT: A 440 MET cc_start: 0.8270 (ttp) cc_final: 0.7475 (tpp) REVERT: A 454 MET cc_start: 0.8462 (tpp) cc_final: 0.8078 (tpt) REVERT: A 574 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4638 (mp) REVERT: A 577 MET cc_start: 0.7313 (ttm) cc_final: 0.6574 (ttm) REVERT: A 578 MET cc_start: 0.8303 (mmt) cc_final: 0.7618 (mmt) REVERT: B 62 ASN cc_start: 0.7797 (m110) cc_final: 0.7019 (t0) REVERT: B 71 LYS cc_start: 0.7237 (mtpt) cc_final: 0.6867 (mmpt) REVERT: B 99 MET cc_start: 0.7811 (mmm) cc_final: 0.7593 (mmm) REVERT: B 180 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8196 (ttm-80) REVERT: B 239 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 282 GLU cc_start: 0.7957 (tp30) cc_final: 0.7718 (tp30) REVERT: B 294 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7317 (tt0) REVERT: B 303 GLU cc_start: 0.8380 (tt0) cc_final: 0.8020 (tt0) REVERT: B 315 GLU cc_start: 0.7965 (tp30) cc_final: 0.7507 (mm-30) REVERT: B 373 LEU cc_start: 0.7661 (mp) cc_final: 0.7224 (tp) REVERT: B 401 LEU cc_start: 0.8536 (mt) cc_final: 0.8315 (tt) REVERT: B 440 MET cc_start: 0.8352 (ttp) cc_final: 0.7424 (tpt) REVERT: B 464 ASN cc_start: 0.7597 (t0) cc_final: 0.7318 (t0) REVERT: B 577 MET cc_start: 0.7507 (ttm) cc_final: 0.6665 (ttm) REVERT: B 629 TRP cc_start: 0.6590 (m-10) cc_final: 0.6012 (m-10) REVERT: C 99 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6896 (tmm) REVERT: C 100 GLU cc_start: 0.8476 (tp30) cc_final: 0.8090 (mt-10) REVERT: C 214 GLN cc_start: 0.8192 (mt0) cc_final: 0.7535 (tm-30) REVERT: C 239 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: C 250 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8186 (tp30) REVERT: C 262 LYS cc_start: 0.8553 (tmtt) cc_final: 0.8226 (tptt) REVERT: C 268 TRP cc_start: 0.8215 (p-90) cc_final: 0.7909 (p-90) REVERT: C 440 MET cc_start: 0.8405 (ttp) cc_final: 0.7115 (tpt) REVERT: C 524 TYR cc_start: 0.7840 (p90) cc_final: 0.7597 (p90) REVERT: C 542 ASP cc_start: 0.7441 (m-30) cc_final: 0.7218 (m-30) REVERT: C 574 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.4999 (tp) REVERT: D 62 ASN cc_start: 0.7984 (m110) cc_final: 0.7066 (t0) REVERT: D 71 LYS cc_start: 0.7139 (mtpt) cc_final: 0.6283 (mmpt) REVERT: D 99 MET cc_start: 0.7847 (mmm) cc_final: 0.7450 (mmm) REVERT: D 100 GLU cc_start: 0.8328 (tp30) cc_final: 0.7773 (mt-10) REVERT: D 180 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8210 (ttm-80) REVERT: D 211 PHE cc_start: 0.7226 (p90) cc_final: 0.6966 (p90) REVERT: D 239 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: D 250 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8189 (tp30) REVERT: D 282 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 294 GLU cc_start: 0.7513 (tt0) cc_final: 0.7212 (tt0) REVERT: D 303 GLU cc_start: 0.8338 (tt0) cc_final: 0.7992 (tt0) REVERT: D 378 MET cc_start: 0.7998 (ttm) cc_final: 0.7540 (ttt) REVERT: D 401 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8323 (tp) REVERT: D 440 MET cc_start: 0.8319 (ttp) cc_final: 0.7370 (tpp) REVERT: D 464 ASN cc_start: 0.7549 (t0) cc_final: 0.7183 (t0) REVERT: D 574 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.4704 (mp) outliers start: 63 outliers final: 34 residues processed: 476 average time/residue: 0.1151 time to fit residues: 86.9660 Evaluate side-chains 445 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 401 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 464 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 128 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142783 restraints weight = 27461.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146817 restraints weight = 14959.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149522 restraints weight = 9967.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151166 restraints weight = 7636.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152408 restraints weight = 6478.759| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20266 Z= 0.118 Angle : 0.641 9.165 27518 Z= 0.311 Chirality : 0.041 0.326 3110 Planarity : 0.004 0.048 3458 Dihedral : 5.769 47.345 2879 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.20 % Allowed : 22.93 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.17), residues: 2440 helix: 0.18 (0.15), residues: 1300 sheet: -2.11 (0.65), residues: 56 loop : -2.87 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 153 TYR 0.026 0.001 TYR C 623 PHE 0.021 0.001 PHE B 415 TRP 0.027 0.001 TRP C 629 HIS 0.004 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (20266) covalent geometry : angle 0.64091 / 0.31 (27518) hydrogen bonds : bond 0.02855 / 1.85 ( 696) hydrogen bonds : angle 3.92971 / 2.70 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 412 time to evaluate : 0.790 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: A 62 ASN cc_start: 0.7856 (m110) cc_final: 0.7008 (t0) REVERT: A 71 LYS cc_start: 0.7417 (mtpt) cc_final: 0.6987 (mmpt) REVERT: A 99 MET cc_start: 0.7838 (mmm) cc_final: 0.7522 (mmm) REVERT: A 130 MET cc_start: 0.7863 (mmm) cc_final: 0.7567 (mpp) REVERT: A 167 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 180 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8192 (ttm-80) REVERT: A 214 GLN cc_start: 0.7772 (mt0) cc_final: 0.7238 (tm-30) REVERT: A 239 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: A 262 LYS cc_start: 0.8633 (tmtt) cc_final: 0.8310 (tptt) REVERT: A 282 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 294 GLU cc_start: 0.7250 (tt0) cc_final: 0.7029 (tt0) REVERT: A 303 GLU cc_start: 0.8378 (tt0) cc_final: 0.8059 (tt0) REVERT: A 315 GLU cc_start: 0.7882 (tp30) cc_final: 0.7480 (mm-30) REVERT: A 378 MET cc_start: 0.8055 (ttm) cc_final: 0.7557 (ttt) REVERT: A 401 LEU cc_start: 0.8492 (mt) cc_final: 0.8172 (tt) REVERT: A 414 ARG cc_start: 0.7359 (mmt-90) cc_final: 0.7023 (tpp80) REVERT: A 440 MET cc_start: 0.8337 (ttp) cc_final: 0.7454 (tpp) REVERT: A 454 MET cc_start: 0.8460 (tpp) cc_final: 0.8139 (tpt) REVERT: A 574 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4154 (mt) REVERT: A 578 MET cc_start: 0.8279 (mmt) cc_final: 0.7554 (mmt) REVERT: B 62 ASN cc_start: 0.7818 (m110) cc_final: 0.7027 (t0) REVERT: B 71 LYS cc_start: 0.7209 (mtpt) cc_final: 0.6855 (mmpt) REVERT: B 99 MET cc_start: 0.7800 (mmm) cc_final: 0.7575 (mmm) REVERT: B 180 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7881 (ttm-80) REVERT: B 211 PHE cc_start: 0.7354 (p90) cc_final: 0.7080 (p90) REVERT: B 214 GLN cc_start: 0.7664 (mt0) cc_final: 0.7137 (tm-30) REVERT: B 239 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: B 282 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: B 294 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7200 (tt0) REVERT: B 303 GLU cc_start: 0.8366 (tt0) cc_final: 0.8013 (tt0) REVERT: B 315 GLU cc_start: 0.7983 (tp30) cc_final: 0.7604 (tp30) REVERT: B 401 LEU cc_start: 0.8512 (mt) cc_final: 0.8224 (tt) REVERT: B 414 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7247 (mmm160) REVERT: B 440 MET cc_start: 0.8429 (ttp) cc_final: 0.7429 (tpt) REVERT: B 464 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7414 (t0) REVERT: B 485 MET cc_start: 0.8570 (tpp) cc_final: 0.8139 (ttm) REVERT: B 577 MET cc_start: 0.7735 (ttm) cc_final: 0.7051 (ttm) REVERT: C 55 ASP cc_start: 0.8734 (t0) cc_final: 0.8223 (t70) REVERT: C 99 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6888 (tmm) REVERT: C 217 ASN cc_start: 0.8694 (t0) cc_final: 0.8316 (m-40) REVERT: C 239 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: C 262 LYS cc_start: 0.8569 (tmtt) cc_final: 0.8205 (tptt) REVERT: C 268 TRP cc_start: 0.8236 (p-90) cc_final: 0.7919 (p-90) REVERT: C 300 LYS cc_start: 0.8374 (pmtt) cc_final: 0.7503 (tmtt) REVERT: C 414 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7630 (tpp-160) REVERT: C 440 MET cc_start: 0.8410 (ttp) cc_final: 0.7080 (tpt) REVERT: C 524 TYR cc_start: 0.7818 (p90) cc_final: 0.7617 (p90) REVERT: C 574 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.4997 (mp) REVERT: C 578 MET cc_start: 0.8326 (tpp) cc_final: 0.8112 (tpp) REVERT: C 625 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8041 (mp) REVERT: D 62 ASN cc_start: 0.7994 (m110) cc_final: 0.7079 (t0) REVERT: D 71 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6373 (mmtt) REVERT: D 78 MET cc_start: 0.7158 (mtm) cc_final: 0.6953 (mtm) REVERT: D 99 MET cc_start: 0.7864 (mmm) cc_final: 0.7451 (mmm) REVERT: D 180 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8158 (ttm-80) REVERT: D 211 PHE cc_start: 0.7216 (p90) cc_final: 0.6967 (p90) REVERT: D 214 GLN cc_start: 0.7758 (mt0) cc_final: 0.7287 (tm-30) REVERT: D 239 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: D 250 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8135 (tp30) REVERT: D 282 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8092 (mt-10) REVERT: D 294 GLU cc_start: 0.7546 (tt0) cc_final: 0.7215 (tt0) REVERT: D 303 GLU cc_start: 0.8341 (tt0) cc_final: 0.7995 (tt0) REVERT: D 378 MET cc_start: 0.8019 (ttm) cc_final: 0.7567 (ttt) REVERT: D 401 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8464 (mt) REVERT: D 440 MET cc_start: 0.8318 (ttp) cc_final: 0.7404 (tpp) REVERT: D 464 ASN cc_start: 0.7745 (t0) cc_final: 0.7337 (t0) outliers start: 68 outliers final: 39 residues processed: 451 average time/residue: 0.1266 time to fit residues: 91.4107 Evaluate side-chains 445 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 394 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 233 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 137 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4046 r_free = 0.4046 target = 0.181431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144870 restraints weight = 26919.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149092 restraints weight = 14411.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151900 restraints weight = 9465.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153762 restraints weight = 7175.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154947 restraints weight = 5991.172| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20266 Z= 0.123 Angle : 0.645 7.285 27518 Z= 0.315 Chirality : 0.041 0.264 3110 Planarity : 0.004 0.044 3458 Dihedral : 5.778 51.358 2879 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.35 % Allowed : 23.59 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2440 helix: 0.29 (0.15), residues: 1292 sheet: -2.01 (0.67), residues: 56 loop : -2.74 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.026 0.001 TYR C 623 PHE 0.017 0.001 PHE D 415 TRP 0.061 0.001 TRP C 629 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (20266) covalent geometry : angle 0.64451 / 0.32 (27518) hydrogen bonds : bond 0.02932 / 1.90 ( 696) hydrogen bonds : angle 3.94630 / 2.71 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 413 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7880 (m110) cc_final: 0.7056 (t0) REVERT: A 71 LYS cc_start: 0.7383 (mtpt) cc_final: 0.6597 (mmpt) REVERT: A 99 MET cc_start: 0.7846 (mmm) cc_final: 0.7546 (mmm) REVERT: A 167 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 180 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8149 (ttm-80) REVERT: A 214 GLN cc_start: 0.7709 (mt0) cc_final: 0.7216 (tm-30) REVERT: A 239 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: A 262 LYS cc_start: 0.8672 (tmtt) cc_final: 0.8322 (tptt) REVERT: A 282 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 303 GLU cc_start: 0.8364 (tt0) cc_final: 0.8036 (tt0) REVERT: A 315 GLU cc_start: 0.7885 (tp30) cc_final: 0.7496 (mm-30) REVERT: A 378 MET cc_start: 0.8070 (ttm) cc_final: 0.7585 (ttt) REVERT: A 401 LEU cc_start: 0.8449 (mt) cc_final: 0.8162 (tt) REVERT: A 414 ARG cc_start: 0.7269 (mmt-90) cc_final: 0.6945 (tpp80) REVERT: A 440 MET cc_start: 0.8360 (ttp) cc_final: 0.7151 (tpt) REVERT: A 454 MET cc_start: 0.8446 (tpp) cc_final: 0.8110 (tpt) REVERT: A 574 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.4283 (mt) REVERT: A 577 MET cc_start: 0.7385 (ttm) cc_final: 0.7012 (ttm) REVERT: A 578 MET cc_start: 0.8310 (mmt) cc_final: 0.7444 (mmt) REVERT: B 62 ASN cc_start: 0.7846 (m110) cc_final: 0.7086 (t0) REVERT: B 71 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6323 (mmpt) REVERT: B 99 MET cc_start: 0.7782 (mmm) cc_final: 0.7571 (mmm) REVERT: B 180 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.7887 (ttm-80) REVERT: B 211 PHE cc_start: 0.7328 (p90) cc_final: 0.7056 (p90) REVERT: B 214 GLN cc_start: 0.7629 (mt0) cc_final: 0.7145 (tm-30) REVERT: B 239 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: B 282 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: B 294 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7204 (tt0) REVERT: B 303 GLU cc_start: 0.8362 (tt0) cc_final: 0.8005 (tt0) REVERT: B 315 GLU cc_start: 0.7960 (tp30) cc_final: 0.7598 (tp30) REVERT: B 401 LEU cc_start: 0.8493 (mt) cc_final: 0.8231 (tt) REVERT: B 414 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7261 (mmm160) REVERT: B 440 MET cc_start: 0.8464 (ttp) cc_final: 0.7442 (tpt) REVERT: B 577 MET cc_start: 0.7761 (ttm) cc_final: 0.7080 (ttm) REVERT: C 55 ASP cc_start: 0.8684 (t0) cc_final: 0.8114 (t70) REVERT: C 75 ARG cc_start: 0.7770 (mmt90) cc_final: 0.7552 (mmt90) REVERT: C 99 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6913 (tmm) REVERT: C 180 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.7834 (mtp85) REVERT: C 214 GLN cc_start: 0.7981 (mt0) cc_final: 0.7411 (tm-30) REVERT: C 217 ASN cc_start: 0.8620 (t0) cc_final: 0.8218 (m-40) REVERT: C 239 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: C 262 LYS cc_start: 0.8593 (tmtt) cc_final: 0.8187 (tptt) REVERT: C 268 TRP cc_start: 0.8232 (p-90) cc_final: 0.7934 (p-90) REVERT: C 414 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7868 (mmm160) REVERT: C 440 MET cc_start: 0.8361 (ttp) cc_final: 0.7115 (tpt) REVERT: C 574 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.4990 (tp) REVERT: C 625 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8094 (mp) REVERT: D 62 ASN cc_start: 0.7990 (m110) cc_final: 0.7046 (t0) REVERT: D 71 LYS cc_start: 0.7035 (mtpt) cc_final: 0.6777 (mmtm) REVERT: D 78 MET cc_start: 0.7177 (mtm) cc_final: 0.6957 (mtm) REVERT: D 99 MET cc_start: 0.7852 (mmm) cc_final: 0.7448 (mmm) REVERT: D 100 GLU cc_start: 0.8363 (tp30) cc_final: 0.7775 (mt-10) REVERT: D 180 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8108 (ttm-80) REVERT: D 211 PHE cc_start: 0.7268 (p90) cc_final: 0.6955 (p90) REVERT: D 214 GLN cc_start: 0.7802 (mt0) cc_final: 0.7353 (tm-30) REVERT: D 239 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: D 250 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8186 (tp30) REVERT: D 282 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 294 GLU cc_start: 0.7536 (tt0) cc_final: 0.7285 (tt0) REVERT: D 303 GLU cc_start: 0.8337 (tt0) cc_final: 0.7977 (tt0) REVERT: D 378 MET cc_start: 0.8049 (ttm) cc_final: 0.7649 (ttt) REVERT: D 401 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8253 (tp) REVERT: D 414 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7142 (mmm160) REVERT: D 440 MET cc_start: 0.8345 (ttp) cc_final: 0.7113 (tpt) REVERT: D 464 ASN cc_start: 0.7754 (t0) cc_final: 0.7334 (t0) REVERT: D 485 MET cc_start: 0.8680 (tpp) cc_final: 0.8171 (ttm) REVERT: D 574 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.4803 (mp) REVERT: D 577 MET cc_start: 0.7381 (ttm) cc_final: 0.6937 (ttm) outliers start: 50 outliers final: 34 residues processed: 440 average time/residue: 0.1269 time to fit residues: 89.0283 Evaluate side-chains 440 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 394 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 0.8980 chunk 188 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 207 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145911 restraints weight = 27433.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150039 restraints weight = 14871.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152770 restraints weight = 9856.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154540 restraints weight = 7531.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155765 restraints weight = 6319.718| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20266 Z= 0.107 Angle : 0.633 11.004 27518 Z= 0.309 Chirality : 0.040 0.198 3110 Planarity : 0.004 0.046 3458 Dihedral : 5.552 48.793 2879 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.35 % Allowed : 23.96 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2440 helix: 0.34 (0.15), residues: 1328 sheet: -2.07 (0.65), residues: 56 loop : -2.90 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 153 TYR 0.021 0.001 TYR C 623 PHE 0.017 0.001 PHE B 415 TRP 0.059 0.001 TRP C 629 HIS 0.004 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (20266) covalent geometry : angle 0.63322 / 0.31 (27518) hydrogen bonds : bond 0.02663 / 1.72 ( 696) hydrogen bonds : angle 3.75346 / 2.58 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 419 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7867 (m110) cc_final: 0.7021 (t0) REVERT: A 71 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6541 (mmtt) REVERT: A 99 MET cc_start: 0.7802 (mmm) cc_final: 0.7547 (mmm) REVERT: A 100 GLU cc_start: 0.8430 (tp30) cc_final: 0.8029 (mt-10) REVERT: A 167 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8413 (mt) REVERT: A 180 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8110 (ttm-80) REVERT: A 239 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 262 LYS cc_start: 0.8582 (tmtt) cc_final: 0.8191 (tptt) REVERT: A 282 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7918 (mt-10) REVERT: A 294 GLU cc_start: 0.7021 (tt0) cc_final: 0.6744 (tt0) REVERT: A 303 GLU cc_start: 0.8331 (tt0) cc_final: 0.7970 (tt0) REVERT: A 315 GLU cc_start: 0.7860 (tp30) cc_final: 0.7481 (mm-30) REVERT: A 378 MET cc_start: 0.8038 (ttm) cc_final: 0.7627 (ttt) REVERT: A 401 LEU cc_start: 0.8514 (mt) cc_final: 0.8204 (tt) REVERT: A 440 MET cc_start: 0.8365 (ttp) cc_final: 0.7150 (tpt) REVERT: A 454 MET cc_start: 0.8494 (tpp) cc_final: 0.8097 (tpt) REVERT: A 485 MET cc_start: 0.8428 (tpp) cc_final: 0.7553 (ttm) REVERT: A 574 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.4026 (mt) REVERT: A 577 MET cc_start: 0.7401 (ttm) cc_final: 0.7037 (ttm) REVERT: A 578 MET cc_start: 0.8316 (mmt) cc_final: 0.7766 (mmt) REVERT: B 62 ASN cc_start: 0.7844 (m110) cc_final: 0.7061 (t0) REVERT: B 71 LYS cc_start: 0.6933 (mtpt) cc_final: 0.6346 (mmpt) REVERT: B 180 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8005 (ttm-80) REVERT: B 211 PHE cc_start: 0.7196 (p90) cc_final: 0.6976 (p90) REVERT: B 239 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: B 294 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7128 (tt0) REVERT: B 303 GLU cc_start: 0.8337 (tt0) cc_final: 0.7992 (tt0) REVERT: B 315 GLU cc_start: 0.7923 (tp30) cc_final: 0.7474 (tp30) REVERT: B 373 LEU cc_start: 0.7698 (mp) cc_final: 0.7205 (tp) REVERT: B 414 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7358 (mmm160) REVERT: B 440 MET cc_start: 0.8410 (ttp) cc_final: 0.7258 (tpt) REVERT: B 485 MET cc_start: 0.8473 (tpp) cc_final: 0.7818 (ttm) REVERT: B 577 MET cc_start: 0.7756 (ttm) cc_final: 0.6796 (ttm) REVERT: C 55 ASP cc_start: 0.8628 (t0) cc_final: 0.8031 (t70) REVERT: C 99 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: C 180 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.7941 (ttm-80) REVERT: C 217 ASN cc_start: 0.8554 (t0) cc_final: 0.8171 (m-40) REVERT: C 239 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: C 262 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8163 (tptt) REVERT: C 268 TRP cc_start: 0.8228 (p-90) cc_final: 0.7956 (p-90) REVERT: C 410 MET cc_start: 0.7119 (tmm) cc_final: 0.6911 (tmm) REVERT: C 440 MET cc_start: 0.8256 (ttp) cc_final: 0.6992 (tpt) REVERT: D 62 ASN cc_start: 0.8020 (m110) cc_final: 0.7066 (t0) REVERT: D 99 MET cc_start: 0.7897 (mmm) cc_final: 0.7474 (mmm) REVERT: D 100 GLU cc_start: 0.8393 (tp30) cc_final: 0.7846 (mt-10) REVERT: D 180 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8148 (ttm-80) REVERT: D 211 PHE cc_start: 0.7153 (p90) cc_final: 0.6887 (p90) REVERT: D 214 GLN cc_start: 0.7768 (mt0) cc_final: 0.7310 (tm-30) REVERT: D 239 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: D 250 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8100 (tp30) REVERT: D 282 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8057 (mt-10) REVERT: D 294 GLU cc_start: 0.7464 (tt0) cc_final: 0.7128 (tt0) REVERT: D 303 GLU cc_start: 0.8290 (tt0) cc_final: 0.7950 (tt0) REVERT: D 378 MET cc_start: 0.7967 (ttm) cc_final: 0.7603 (ttt) REVERT: D 414 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7322 (mmm160) REVERT: D 440 MET cc_start: 0.8339 (ttp) cc_final: 0.7061 (tpt) REVERT: D 464 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7415 (t0) REVERT: D 485 MET cc_start: 0.8575 (tpp) cc_final: 0.8088 (ttm) REVERT: D 574 LEU cc_start: 0.5331 (OUTLIER) cc_final: 0.4715 (mp) REVERT: D 577 MET cc_start: 0.7274 (ttm) cc_final: 0.6978 (ttm) outliers start: 50 outliers final: 30 residues processed: 442 average time/residue: 0.1237 time to fit residues: 87.2850 Evaluate side-chains 424 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 385 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 119 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 143 optimal weight: 0.0040 chunk 29 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN B 91 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 91 ASN D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.183895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147708 restraints weight = 26975.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151859 restraints weight = 14624.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154626 restraints weight = 9717.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156430 restraints weight = 7429.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157468 restraints weight = 6252.409| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.370 20266 Z= 0.261 Angle : 0.814 59.132 27518 Z= 0.440 Chirality : 0.048 1.393 3110 Planarity : 0.006 0.158 3458 Dihedral : 5.553 48.807 2879 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.98 % Allowed : 24.81 % Favored : 73.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.17), residues: 2440 helix: 0.36 (0.15), residues: 1328 sheet: -2.10 (0.64), residues: 56 loop : -2.90 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.001 ARG C 414 TYR 0.041 0.001 TYR C 216 PHE 0.031 0.001 PHE A 630 TRP 0.107 0.002 TRP B 629 HIS 0.015 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (20266) covalent geometry : angle 0.81428 / 0.44 (27518) hydrogen bonds : bond 0.02662 / 1.72 ( 696) hydrogen bonds : angle 3.74890 / 2.58 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.83 seconds wall clock time: 62 minutes 29.20 seconds (3749.20 seconds total)