Starting phenix.real_space_refine on Thu Mar 5 06:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4d_22665/03_2026/7k4d_22665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4d_22665/03_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_22665/03_2026/7k4d_22665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4d_22665/03_2026/7k4d_22665.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4d_22665/03_2026/7k4d_22665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4d_22665/03_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-5986/lib/python3.9/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, 33 Unusual residues: {' CA': 2, 'VUM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 4.41, per 1000 atoms: 0.22 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: 1.42 Conformation dependent library (CDL) restraints added in 673.1 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: 0.49 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: 2.66 Time building geometry restraints manager: 1.91 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.040 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 covalent geometry : bond 0.00958 (20266) covalent geometry : angle 1.21568 (27518) hydrogen bonds : bond 0.34136 ( 696) hydrogen bonds : angle 9.89534 ( 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 : 0.648 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7848 (m110) cc_final: 0.6836 (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: 0.7316 (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: 0.7543 (tpp-160) REVERT: A 214 GLN cc_start: 0.8188 (mt0) cc_final: 0.7298 (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: 0.8095 (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: 0.7752 (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: 0.7396 (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: 0.7649 (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: 0.7809 (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: 0.6793 (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: 0.7962 (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: 0.7647 (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: 0.8570 (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 440 MET cc_start: 0.8875 (ttp) cc_final: 0.7737 (tpt) REVERT: C 481 MET cc_start: 0.7802 (tpp) cc_final: 0.7427 (tpp) REVERT: C 546 ASN cc_start: 0.8596 (t0) cc_final: 0.8160 (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: 0.7959 (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: 0.6607 (pp30) REVERT: D 137 LEU cc_start: 0.9244 (mt) cc_final: 0.8920 (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: 0.7199 (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: 0.8217 (tt) REVERT: D 637 GLN cc_start: 0.8442 (tp40) cc_final: 0.8241 (tt0) outliers start: 8 outliers final: 0 residues processed: 636 average time/residue: 0.1471 time to fit residues: 140.2747 Evaluate side-chains 444 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 128 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143793 restraints weight = 27428.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147858 restraints weight = 14820.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150540 restraints weight = 9874.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152280 restraints weight = 7601.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153257 restraints weight = 6426.804| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20266 Z= 0.167 Angle : 0.711 8.716 27518 Z= 0.367 Chirality : 0.042 0.179 3110 Planarity : 0.006 0.066 3458 Dihedral : 7.954 85.787 2879 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.06 % Allowed : 12.81 % Favored : 84.13 % 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: -4.67 (0.13), residues: 2440 helix: -2.73 (0.11), residues: 1340 sheet: -2.58 (0.62), residues: 56 loop : -3.57 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 615 TYR 0.019 0.002 TYR B 324 PHE 0.016 0.002 PHE B 211 TRP 0.013 0.001 TRP C 629 HIS 0.007 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00390 (20266) covalent geometry : angle 0.71150 (27518) hydrogen bonds : bond 0.04850 ( 696) hydrogen bonds : angle 5.31462 ( 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 565 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 500 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7720 (m110) cc_final: 0.6697 (t0) REVERT: A 71 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7061 (mmpt) REVERT: A 91 ASN cc_start: 0.7639 (m110) cc_final: 0.7431 (m-40) REVERT: A 128 GLN cc_start: 0.7179 (pt0) cc_final: 0.6388 (tm-30) REVERT: A 153 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7746 (mtt90) REVERT: A 211 PHE cc_start: 0.7721 (p90) cc_final: 0.7380 (p90) REVERT: A 268 TRP cc_start: 0.7816 (p-90) cc_final: 0.7593 (p-90) REVERT: A 282 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 300 LYS cc_start: 0.8347 (pmtt) cc_final: 0.8043 (ttmt) REVERT: A 303 GLU cc_start: 0.8407 (tt0) cc_final: 0.8184 (tt0) REVERT: A 378 MET cc_start: 0.7649 (ttm) cc_final: 0.7136 (ttt) REVERT: A 440 MET cc_start: 0.8538 (ttp) cc_final: 0.7826 (tpt) REVERT: A 540 ILE cc_start: 0.8227 (mt) cc_final: 0.7923 (mt) REVERT: A 542 ASP cc_start: 0.7374 (m-30) cc_final: 0.7166 (m-30) REVERT: A 629 TRP cc_start: 0.5865 (m-10) cc_final: 0.5230 (m-10) REVERT: A 637 GLN cc_start: 0.8409 (tp40) cc_final: 0.8170 (tt0) REVERT: B 62 ASN cc_start: 0.7750 (m110) cc_final: 0.6831 (t0) REVERT: B 71 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7111 (mmpt) REVERT: B 91 ASN cc_start: 0.7589 (m110) cc_final: 0.7355 (m-40) REVERT: B 128 GLN cc_start: 0.7144 (pt0) cc_final: 0.6330 (tm-30) REVERT: B 164 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 211 PHE cc_start: 0.7743 (p90) cc_final: 0.7308 (p90) REVERT: B 300 LYS cc_start: 0.8334 (pmtt) cc_final: 0.7955 (ttmt) REVERT: B 315 GLU cc_start: 0.8018 (tp30) cc_final: 0.7562 (mm-30) REVERT: B 440 MET cc_start: 0.8627 (ttp) cc_final: 0.7909 (tpt) REVERT: B 464 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.6921 (t0) REVERT: B 470 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8353 (ptp-170) REVERT: B 481 MET cc_start: 0.7728 (tpp) cc_final: 0.7275 (tpp) REVERT: B 540 ILE cc_start: 0.8212 (mt) cc_final: 0.7927 (mt) REVERT: B 637 GLN cc_start: 0.8334 (tp40) cc_final: 0.8090 (tt0) REVERT: C 59 GLN cc_start: 0.8281 (tp-100) cc_final: 0.8080 (tp-100) REVERT: C 62 ASN cc_start: 0.7836 (m110) cc_final: 0.6899 (t0) REVERT: C 164 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: C 180 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8310 (ttm170) REVERT: C 193 ASP cc_start: 0.7972 (p0) cc_final: 0.7373 (p0) REVERT: C 195 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8006 (tm) REVERT: C 214 GLN cc_start: 0.8284 (mt0) cc_final: 0.7449 (tm-30) REVERT: C 216 TYR cc_start: 0.9288 (t80) cc_final: 0.8967 (t80) REVERT: C 262 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8522 (tptt) REVERT: C 268 TRP cc_start: 0.8375 (p-90) cc_final: 0.8050 (p-90) REVERT: C 294 GLU cc_start: 0.7664 (tp30) cc_final: 0.7352 (tt0) REVERT: C 315 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7620 (tp30) REVERT: C 440 MET cc_start: 0.8660 (ttp) cc_final: 0.7637 (tpt) REVERT: C 464 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7561 (t0) REVERT: C 536 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8079 (tt) REVERT: C 542 ASP cc_start: 0.7673 (m-30) cc_final: 0.7226 (m-30) REVERT: C 546 ASN cc_start: 0.8578 (t0) cc_final: 0.8357 (t0) REVERT: C 574 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.4072 (tt) REVERT: D 38 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8232 (tt) REVERT: D 62 ASN cc_start: 0.7854 (m110) cc_final: 0.6851 (t0) REVERT: D 71 LYS cc_start: 0.7334 (mtpt) cc_final: 0.7038 (mtpt) REVERT: D 91 ASN cc_start: 0.7702 (m110) cc_final: 0.7218 (m-40) REVERT: D 99 MET cc_start: 0.8013 (mmm) cc_final: 0.7639 (mmm) REVERT: D 144 SER cc_start: 0.8272 (m) cc_final: 0.7696 (p) REVERT: D 146 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7232 (tpp-160) REVERT: D 193 ASP cc_start: 0.8130 (p0) cc_final: 0.7378 (p0) REVERT: D 211 PHE cc_start: 0.7641 (p90) cc_final: 0.7285 (p90) REVERT: D 214 GLN cc_start: 0.8199 (mt0) cc_final: 0.7238 (tm-30) REVERT: D 300 LYS cc_start: 0.8350 (pmtt) cc_final: 0.7968 (ttmt) REVERT: D 303 GLU cc_start: 0.8320 (tt0) cc_final: 0.8029 (tt0) REVERT: D 315 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 440 MET cc_start: 0.8539 (ttp) cc_final: 0.7655 (tpt) REVERT: D 454 MET cc_start: 0.8563 (tpp) cc_final: 0.7799 (tpt) REVERT: D 464 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7045 (t0) REVERT: D 577 MET cc_start: 0.7737 (mtm) cc_final: 0.7488 (ttm) REVERT: D 637 GLN cc_start: 0.8364 (tp40) cc_final: 0.8151 (tt0) outliers start: 65 outliers final: 22 residues processed: 545 average time/residue: 0.1424 time to fit residues: 120.0245 Evaluate side-chains 455 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 424 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 GLU 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 341 ILE 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 464 ASN Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 597 ILE 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: 0.8980 chunk 86 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN B 59 GLN C 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS C 596 GLN D 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146678 restraints weight = 27492.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150980 restraints weight = 14397.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153854 restraints weight = 9340.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155703 restraints weight = 7037.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156909 restraints weight = 5872.392| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20266 Z= 0.120 Angle : 0.653 8.813 27518 Z= 0.330 Chirality : 0.040 0.187 3110 Planarity : 0.005 0.056 3458 Dihedral : 6.988 58.886 2879 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.92 % Allowed : 17.00 % Favored : 80.08 % 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: -3.53 (0.15), residues: 2440 helix: -1.68 (0.13), residues: 1312 sheet: -2.47 (0.61), residues: 56 loop : -3.19 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 443 TYR 0.021 0.001 TYR A 324 PHE 0.042 0.001 PHE C 211 TRP 0.011 0.001 TRP C 321 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00273 (20266) covalent geometry : angle 0.65332 (27518) hydrogen bonds : bond 0.03817 ( 696) hydrogen bonds : angle 4.57966 ( 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 528 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 466 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7763 (m110) cc_final: 0.6823 (t0) REVERT: A 71 LYS cc_start: 0.7633 (mtpt) cc_final: 0.6970 (mmpt) REVERT: A 91 ASN cc_start: 0.7545 (m110) cc_final: 0.7324 (m-40) REVERT: A 99 MET cc_start: 0.7796 (mmm) cc_final: 0.7404 (mmm) REVERT: A 153 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7677 (mtt90) REVERT: A 180 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8040 (ttm-80) REVERT: A 211 PHE cc_start: 0.7640 (p90) cc_final: 0.7362 (p90) REVERT: A 239 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: A 268 TRP cc_start: 0.7897 (p-90) cc_final: 0.7667 (p-90) REVERT: A 282 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 300 LYS cc_start: 0.8345 (pmtt) cc_final: 0.7992 (ttmt) REVERT: A 303 GLU cc_start: 0.8436 (tt0) cc_final: 0.8125 (tt0) REVERT: A 378 MET cc_start: 0.7667 (ttm) cc_final: 0.7142 (ttt) REVERT: A 390 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7311 (tt) REVERT: A 440 MET cc_start: 0.8630 (ttp) cc_final: 0.7865 (tpp) REVERT: A 629 TRP cc_start: 0.5962 (m-10) cc_final: 0.5172 (m-10) REVERT: A 637 GLN cc_start: 0.8351 (tp40) cc_final: 0.8078 (tt0) REVERT: B 62 ASN cc_start: 0.7783 (m110) cc_final: 0.6924 (t0) REVERT: B 71 LYS cc_start: 0.7439 (mtpt) cc_final: 0.6892 (mmpt) REVERT: B 99 MET cc_start: 0.7834 (mmm) cc_final: 0.7537 (mmm) REVERT: B 180 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8166 (ttm-80) REVERT: B 193 ASP cc_start: 0.8186 (p0) cc_final: 0.7610 (p0) REVERT: B 211 PHE cc_start: 0.7569 (p90) cc_final: 0.7206 (p90) REVERT: B 239 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: B 268 TRP cc_start: 0.7674 (p-90) cc_final: 0.7348 (p-90) REVERT: B 294 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7259 (tt0) REVERT: B 300 LYS cc_start: 0.8317 (pmtt) cc_final: 0.7938 (ttmt) REVERT: B 315 GLU cc_start: 0.8034 (tp30) cc_final: 0.7595 (mm-30) REVERT: B 440 MET cc_start: 0.8559 (ttp) cc_final: 0.7897 (tpp) REVERT: B 464 ASN cc_start: 0.7330 (t0) cc_final: 0.6679 (t0) REVERT: B 470 ARG cc_start: 0.8579 (ptp-170) cc_final: 0.8360 (ptp-170) REVERT: B 481 MET cc_start: 0.7734 (tpp) cc_final: 0.7252 (tpp) REVERT: B 574 LEU cc_start: 0.5187 (OUTLIER) cc_final: 0.3548 (mt) REVERT: B 637 GLN cc_start: 0.8268 (tp40) cc_final: 0.8023 (tt0) REVERT: C 62 ASN cc_start: 0.7876 (m110) cc_final: 0.6935 (t0) REVERT: C 153 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7846 (mtt90) REVERT: C 180 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8337 (ttm170) REVERT: C 193 ASP cc_start: 0.8005 (p0) cc_final: 0.7646 (p0) REVERT: C 214 GLN cc_start: 0.8147 (mt0) cc_final: 0.7439 (tm-30) REVERT: C 239 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: C 250 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8144 (tp30) REVERT: C 262 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8448 (tptt) REVERT: C 268 TRP cc_start: 0.8302 (p-90) cc_final: 0.7999 (p-90) REVERT: C 294 GLU cc_start: 0.7674 (tp30) cc_final: 0.7290 (tt0) REVERT: C 390 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7948 (tm) REVERT: C 401 LEU cc_start: 0.8282 (mt) cc_final: 0.8064 (tt) REVERT: C 440 MET cc_start: 0.8647 (ttp) cc_final: 0.7626 (tpt) REVERT: C 464 ASN cc_start: 0.7620 (t0) cc_final: 0.7126 (t0) REVERT: C 536 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7875 (tt) REVERT: C 542 ASP cc_start: 0.7505 (m-30) cc_final: 0.6932 (m-30) REVERT: C 564 ILE cc_start: 0.7918 (tp) cc_final: 0.7708 (tp) REVERT: D 62 ASN cc_start: 0.7816 (m110) cc_final: 0.6872 (t0) REVERT: D 71 LYS cc_start: 0.7316 (mtpt) cc_final: 0.7057 (mtpt) REVERT: D 91 ASN cc_start: 0.7480 (m110) cc_final: 0.7183 (m-40) REVERT: D 146 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7434 (tpp-160) REVERT: D 180 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8193 (ttm-80) REVERT: D 211 PHE cc_start: 0.7450 (p90) cc_final: 0.7101 (p90) REVERT: D 239 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: D 268 TRP cc_start: 0.7532 (p-90) cc_final: 0.7272 (p-90) REVERT: D 282 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7937 (mt-10) REVERT: D 300 LYS cc_start: 0.8347 (pmtt) cc_final: 0.7926 (ttmt) REVERT: D 303 GLU cc_start: 0.8289 (tt0) cc_final: 0.8048 (tt0) REVERT: D 390 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7282 (tt) REVERT: D 401 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8571 (mt) REVERT: D 440 MET cc_start: 0.8587 (ttp) cc_final: 0.7661 (tpp) REVERT: D 464 ASN cc_start: 0.7271 (t0) cc_final: 0.6389 (t0) REVERT: D 574 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.3904 (mt) REVERT: D 578 MET cc_start: 0.8381 (mmt) cc_final: 0.7848 (mmt) REVERT: D 637 GLN cc_start: 0.8356 (tp40) cc_final: 0.8107 (tt0) outliers start: 62 outliers final: 18 residues processed: 499 average time/residue: 0.1359 time to fit residues: 105.4157 Evaluate side-chains 449 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 420 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 390 LEU 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 239 GLN Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 172 CYS 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 536 LEU Chi-restraints excluded: chain C residue 590 ASP 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 390 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 480 ILE 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: 0.7980 chunk 121 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 174 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 149 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS B 59 GLN B 258 HIS C 59 GLN C 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140986 restraints weight = 27548.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145100 restraints weight = 14771.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147828 restraints weight = 9826.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149597 restraints weight = 7542.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150611 restraints weight = 6372.365| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20266 Z= 0.121 Angle : 0.625 7.374 27518 Z= 0.312 Chirality : 0.040 0.186 3110 Planarity : 0.004 0.057 3458 Dihedral : 6.428 42.605 2879 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.48 % Allowed : 18.31 % Favored : 78.20 % 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: -2.82 (0.16), residues: 2440 helix: -0.99 (0.14), residues: 1304 sheet: -2.23 (0.64), residues: 56 loop : -3.00 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 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 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00276 (20266) covalent geometry : angle 0.62496 (27518) hydrogen bonds : bond 0.03250 ( 696) hydrogen bonds : angle 4.24345 ( 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 522 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 448 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7759 (m110) cc_final: 0.6857 (t0) REVERT: A 71 LYS cc_start: 0.7416 (mtpt) cc_final: 0.6861 (mmpt) REVERT: A 99 MET cc_start: 0.7791 (mmm) cc_final: 0.7349 (mmm) REVERT: A 153 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7687 (mtt90) REVERT: A 180 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8134 (ttm-80) REVERT: A 211 PHE cc_start: 0.7506 (p90) cc_final: 0.7228 (p90) REVERT: A 239 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: A 268 TRP cc_start: 0.7946 (p-90) cc_final: 0.7707 (p-90) REVERT: A 282 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 300 LYS cc_start: 0.8346 (pmtt) cc_final: 0.7985 (ttmt) REVERT: A 303 GLU cc_start: 0.8402 (tt0) cc_final: 0.8112 (tt0) REVERT: A 315 GLU cc_start: 0.7995 (tp30) cc_final: 0.7537 (mm-30) REVERT: A 440 MET cc_start: 0.8579 (ttp) cc_final: 0.7592 (tpp) REVERT: A 464 ASN cc_start: 0.7635 (t0) cc_final: 0.6954 (t0) REVERT: A 470 ARG cc_start: 0.8671 (ptp-170) cc_final: 0.8429 (ptp-170) REVERT: A 490 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6853 (tt) REVERT: A 637 GLN cc_start: 0.8251 (tp40) cc_final: 0.8038 (tt0) REVERT: B 62 ASN cc_start: 0.7760 (m110) cc_final: 0.6935 (t0) REVERT: B 71 LYS cc_start: 0.7291 (mtpt) cc_final: 0.6809 (mmpt) REVERT: B 99 MET cc_start: 0.7858 (mmm) cc_final: 0.7549 (mmm) REVERT: B 180 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8099 (ttm-80) REVERT: B 239 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: B 250 GLU cc_start: 0.7990 (tp30) cc_final: 0.7775 (mm-30) REVERT: B 268 TRP cc_start: 0.7824 (p-90) cc_final: 0.7493 (p-90) REVERT: B 282 GLU cc_start: 0.8068 (tp30) cc_final: 0.7845 (tp30) REVERT: B 294 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7135 (tt0) REVERT: B 300 LYS cc_start: 0.8265 (pmtt) cc_final: 0.7847 (ttmt) REVERT: B 303 GLU cc_start: 0.8439 (tt0) cc_final: 0.8130 (tt0) REVERT: B 315 GLU cc_start: 0.8019 (tp30) cc_final: 0.7521 (mm-30) REVERT: B 324 TYR cc_start: 0.7385 (m-80) cc_final: 0.7068 (m-80) REVERT: B 414 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7392 (tpp80) REVERT: B 440 MET cc_start: 0.8634 (ttp) cc_final: 0.7744 (tpt) REVERT: B 454 MET cc_start: 0.8525 (tpp) cc_final: 0.8229 (tpt) REVERT: B 464 ASN cc_start: 0.7452 (t0) cc_final: 0.7014 (t0) REVERT: B 481 MET cc_start: 0.7978 (tpp) cc_final: 0.7396 (tpp) REVERT: B 540 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7762 (tt) REVERT: B 542 ASP cc_start: 0.7730 (m-30) cc_final: 0.7285 (m-30) REVERT: B 574 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.3589 (mt) REVERT: B 577 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7377 (ttm) REVERT: C 99 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6889 (tmm) REVERT: C 180 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8114 (ttm-80) REVERT: C 214 GLN cc_start: 0.8170 (mt0) cc_final: 0.7456 (tm-30) REVERT: C 215 MET cc_start: 0.8740 (ttt) cc_final: 0.8517 (ttt) REVERT: C 239 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: C 262 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8394 (tptt) REVERT: C 268 TRP cc_start: 0.8289 (p-90) cc_final: 0.7989 (p-90) REVERT: C 294 GLU cc_start: 0.7796 (tp30) cc_final: 0.7539 (tt0) REVERT: C 440 MET cc_start: 0.8616 (ttp) cc_final: 0.7631 (tpt) REVERT: C 464 ASN cc_start: 0.7705 (t0) cc_final: 0.7433 (t0) REVERT: C 536 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7907 (tt) REVERT: C 542 ASP cc_start: 0.7541 (m-30) cc_final: 0.7005 (m-30) REVERT: C 574 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.4420 (mp) REVERT: C 634 GLU cc_start: 0.8396 (pm20) cc_final: 0.7637 (mp0) REVERT: D 62 ASN cc_start: 0.7874 (m110) cc_final: 0.6949 (t0) REVERT: D 71 LYS cc_start: 0.7232 (mtpt) cc_final: 0.7017 (mtpt) REVERT: D 99 MET cc_start: 0.7678 (mmm) cc_final: 0.7251 (tmm) REVERT: D 180 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8132 (ttm-80) REVERT: D 211 PHE cc_start: 0.7450 (p90) cc_final: 0.7101 (p90) REVERT: D 239 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: D 268 TRP cc_start: 0.7805 (p-90) cc_final: 0.7348 (p-90) REVERT: D 282 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 294 GLU cc_start: 0.7312 (tt0) cc_final: 0.7008 (tt0) REVERT: D 300 LYS cc_start: 0.8340 (pmtt) cc_final: 0.7900 (ttmt) REVERT: D 303 GLU cc_start: 0.8328 (tt0) cc_final: 0.8047 (tt0) REVERT: D 401 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 440 MET cc_start: 0.8504 (ttp) cc_final: 0.7595 (tpt) REVERT: D 464 ASN cc_start: 0.7468 (t0) cc_final: 0.6801 (t0) REVERT: D 485 MET cc_start: 0.8864 (tpp) cc_final: 0.8637 (tpp) REVERT: D 574 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4544 (mp) REVERT: D 577 MET cc_start: 0.7817 (mtm) cc_final: 0.7542 (ttm) REVERT: D 578 MET cc_start: 0.8408 (mmt) cc_final: 0.8058 (mmt) outliers start: 74 outliers final: 29 residues processed: 493 average time/residue: 0.1352 time to fit residues: 103.6255 Evaluate side-chains 457 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 415 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL 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 342 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 490 LEU 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 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 B residue 577 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 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 402 VAL Chi-restraints excluded: chain C residue 465 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 195 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 340 ILE Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 103 optimal weight: 0.0970 chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 135 optimal weight: 0.0070 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 59 GLN C 128 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.180376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140981 restraints weight = 27472.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145352 restraints weight = 14557.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148223 restraints weight = 9630.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150079 restraints weight = 7388.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151131 restraints weight = 6257.221| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20266 Z= 0.147 Angle : 0.650 10.432 27518 Z= 0.321 Chirality : 0.042 0.176 3110 Planarity : 0.005 0.064 3458 Dihedral : 6.310 43.520 2879 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.05 % Allowed : 19.73 % Favored : 76.22 % 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: -2.46 (0.16), residues: 2440 helix: -0.60 (0.14), residues: 1304 sheet: -2.28 (0.63), residues: 56 loop : -2.95 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.024 0.002 TYR C 623 PHE 0.018 0.001 PHE C 211 TRP 0.016 0.001 TRP B 629 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00352 (20266) covalent geometry : angle 0.65042 (27518) hydrogen bonds : bond 0.03391 ( 696) hydrogen bonds : angle 4.27390 ( 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 528 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 442 time to evaluate : 0.567 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: 0.7737 (m110) cc_final: 0.6885 (t0) REVERT: A 71 LYS cc_start: 0.7465 (mtpt) cc_final: 0.6974 (mmpt) REVERT: A 99 MET cc_start: 0.7755 (mmm) cc_final: 0.7309 (mmm) REVERT: A 144 SER cc_start: 0.8374 (m) cc_final: 0.7736 (p) REVERT: A 153 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7604 (mtt90) REVERT: A 180 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8105 (ttm-80) REVERT: A 239 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: A 268 TRP cc_start: 0.7832 (p-90) cc_final: 0.7476 (p-90) REVERT: A 282 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7955 (mt-10) REVERT: A 300 LYS cc_start: 0.8329 (pmtt) cc_final: 0.7899 (ttmt) REVERT: A 303 GLU cc_start: 0.8423 (tt0) cc_final: 0.8097 (tt0) REVERT: A 315 GLU cc_start: 0.7958 (tp30) cc_final: 0.7528 (mm-30) REVERT: A 378 MET cc_start: 0.7966 (ttm) cc_final: 0.7480 (ttt) REVERT: A 440 MET cc_start: 0.8453 (ttp) cc_final: 0.7563 (tpt) REVERT: A 454 MET cc_start: 0.8310 (tpp) cc_final: 0.8026 (tpt) REVERT: A 489 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7185 (t70) REVERT: A 490 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6779 (tt) REVERT: A 574 LEU cc_start: 0.5306 (OUTLIER) cc_final: 0.4638 (mp) REVERT: A 578 MET cc_start: 0.8227 (mmt) cc_final: 0.7342 (mmt) REVERT: A 637 GLN cc_start: 0.8261 (tp40) cc_final: 0.8000 (tt0) REVERT: B 62 ASN cc_start: 0.7799 (m110) cc_final: 0.7029 (t0) REVERT: B 71 LYS cc_start: 0.7220 (mtpt) cc_final: 0.6840 (mmpt) REVERT: B 99 MET cc_start: 0.7814 (mmm) cc_final: 0.7507 (mmm) REVERT: B 180 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8036 (ttm-80) REVERT: B 211 PHE cc_start: 0.7507 (p90) cc_final: 0.7072 (p90) REVERT: B 239 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: B 250 GLU cc_start: 0.8087 (tp30) cc_final: 0.7860 (mm-30) REVERT: B 268 TRP cc_start: 0.7764 (p-90) cc_final: 0.7394 (p-90) REVERT: B 282 GLU cc_start: 0.8166 (tp30) cc_final: 0.7891 (tp30) REVERT: B 300 LYS cc_start: 0.8342 (pmtt) cc_final: 0.7843 (ttmt) REVERT: B 315 GLU cc_start: 0.7987 (tp30) cc_final: 0.7555 (tp30) REVERT: B 401 LEU cc_start: 0.8545 (mt) cc_final: 0.8252 (tt) REVERT: B 414 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7209 (tpp80) REVERT: B 440 MET cc_start: 0.8413 (ttp) cc_final: 0.7566 (tpt) REVERT: B 454 MET cc_start: 0.8388 (tpp) cc_final: 0.7928 (tpt) REVERT: B 464 ASN cc_start: 0.7651 (t0) cc_final: 0.7176 (t0) REVERT: B 470 ARG cc_start: 0.8602 (ptp-170) cc_final: 0.8179 (ptp-170) REVERT: B 481 MET cc_start: 0.8129 (tpp) cc_final: 0.7567 (tpp) REVERT: B 540 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 542 ASP cc_start: 0.7705 (m-30) cc_final: 0.7374 (m-30) REVERT: B 574 LEU cc_start: 0.5130 (OUTLIER) cc_final: 0.4483 (mp) REVERT: B 577 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7159 (ttm) REVERT: C 99 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6801 (tmm) REVERT: C 180 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8110 (ttm-80) REVERT: C 214 GLN cc_start: 0.8330 (mt0) cc_final: 0.7602 (tm-30) REVERT: C 239 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: C 250 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8206 (tp30) REVERT: C 262 LYS cc_start: 0.8589 (tmtt) cc_final: 0.8251 (tptt) REVERT: C 268 TRP cc_start: 0.8130 (p-90) cc_final: 0.7850 (p-90) REVERT: C 300 LYS cc_start: 0.8332 (pmtt) cc_final: 0.7735 (ttmt) REVERT: C 440 MET cc_start: 0.8617 (ttp) cc_final: 0.7568 (tpt) REVERT: C 464 ASN cc_start: 0.7774 (t0) cc_final: 0.7498 (t0) REVERT: C 536 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7952 (tt) REVERT: C 542 ASP cc_start: 0.7568 (m-30) cc_final: 0.7236 (m-30) REVERT: C 574 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.4870 (mp) REVERT: D 62 ASN cc_start: 0.7846 (m110) cc_final: 0.7001 (t0) REVERT: D 71 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6678 (tttt) REVERT: D 180 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8065 (ttm-80) REVERT: D 211 PHE cc_start: 0.7426 (p90) cc_final: 0.7006 (p90) REVERT: D 239 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: D 268 TRP cc_start: 0.7784 (p-90) cc_final: 0.7230 (p-90) REVERT: D 282 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8034 (mt-10) REVERT: D 294 GLU cc_start: 0.7397 (tt0) cc_final: 0.7063 (tt0) REVERT: D 303 GLU cc_start: 0.8390 (tt0) cc_final: 0.8049 (tt0) REVERT: D 378 MET cc_start: 0.7870 (ttm) cc_final: 0.7275 (ttt) REVERT: D 401 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8404 (mt) REVERT: D 440 MET cc_start: 0.8523 (ttp) cc_final: 0.7510 (tpt) REVERT: D 454 MET cc_start: 0.8256 (tpp) cc_final: 0.7892 (tpt) REVERT: D 464 ASN cc_start: 0.7641 (t0) cc_final: 0.7114 (t0) REVERT: D 574 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4521 (mp) REVERT: D 577 MET cc_start: 0.7781 (mtm) cc_final: 0.7520 (ttm) outliers start: 86 outliers final: 36 residues processed: 491 average time/residue: 0.1322 time to fit residues: 101.9474 Evaluate side-chains 460 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 409 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 540 ILE 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 299 THR Chi-restraints excluded: chain B residue 340 ILE 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 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 634 GLU 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 402 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 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 64 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU 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 299 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 209 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 59 GLN C 128 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139272 restraints weight = 27330.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143135 restraints weight = 15409.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145676 restraints weight = 10504.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147358 restraints weight = 8198.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148290 restraints weight = 6983.185| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20266 Z= 0.135 Angle : 0.638 9.238 27518 Z= 0.313 Chirality : 0.041 0.162 3110 Planarity : 0.004 0.052 3458 Dihedral : 6.125 45.671 2879 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.14 % Allowed : 20.72 % Favored : 75.14 % 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: -2.14 (0.17), residues: 2440 helix: -0.29 (0.14), residues: 1304 sheet: -2.23 (0.64), residues: 56 loop : -2.87 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.022 0.001 TYR A 623 PHE 0.014 0.001 PHE C 211 TRP 0.013 0.001 TRP B 629 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00326 (20266) covalent geometry : angle 0.63803 (27518) hydrogen bonds : bond 0.03154 ( 696) hydrogen bonds : angle 4.12357 ( 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: 88 poor density : 432 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7788 (m110) cc_final: 0.6859 (t0) REVERT: A 71 LYS cc_start: 0.7464 (mtpt) cc_final: 0.7024 (mmpt) REVERT: A 99 MET cc_start: 0.7855 (mmm) cc_final: 0.7511 (mmm) REVERT: A 130 MET cc_start: 0.7755 (mmm) cc_final: 0.7509 (mmm) REVERT: A 144 SER cc_start: 0.8389 (m) cc_final: 0.7730 (p) REVERT: A 180 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8159 (ttm-80) REVERT: A 239 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 268 TRP cc_start: 0.7878 (p-90) cc_final: 0.7479 (p-90) REVERT: A 282 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 300 LYS cc_start: 0.8373 (pmtt) cc_final: 0.7927 (ttmt) REVERT: A 303 GLU cc_start: 0.8364 (tt0) cc_final: 0.8069 (tt0) REVERT: A 315 GLU cc_start: 0.7980 (tp30) cc_final: 0.7564 (mm-30) REVERT: A 378 MET cc_start: 0.7993 (ttm) cc_final: 0.7494 (ttt) REVERT: A 401 LEU cc_start: 0.8563 (mt) cc_final: 0.8135 (tt) REVERT: A 440 MET cc_start: 0.8559 (ttp) cc_final: 0.7622 (tpt) REVERT: A 454 MET cc_start: 0.8518 (tpp) cc_final: 0.8231 (tpt) REVERT: A 470 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8260 (ptp-170) REVERT: A 540 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7985 (tt) REVERT: A 574 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.4861 (mp) REVERT: A 578 MET cc_start: 0.8436 (mmt) cc_final: 0.7825 (mmt) REVERT: B 62 ASN cc_start: 0.7851 (m110) cc_final: 0.7049 (t0) REVERT: B 71 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6821 (mmpt) REVERT: B 99 MET cc_start: 0.7857 (mmm) cc_final: 0.7589 (mmm) REVERT: B 180 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8031 (ttm-80) REVERT: B 211 PHE cc_start: 0.7491 (p90) cc_final: 0.7108 (p90) REVERT: B 239 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: B 282 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: B 294 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7248 (tt0) REVERT: B 300 LYS cc_start: 0.8361 (pmtt) cc_final: 0.7886 (ttmt) REVERT: B 315 GLU cc_start: 0.8001 (tp30) cc_final: 0.7588 (tp30) REVERT: B 401 LEU cc_start: 0.8595 (mt) cc_final: 0.8288 (tt) REVERT: B 414 ARG cc_start: 0.7569 (mmt-90) cc_final: 0.7329 (tpp80) REVERT: B 440 MET cc_start: 0.8437 (ttp) cc_final: 0.7636 (tpt) REVERT: B 454 MET cc_start: 0.8590 (tpp) cc_final: 0.8146 (tpt) REVERT: B 464 ASN cc_start: 0.7611 (t0) cc_final: 0.7218 (t0) REVERT: B 470 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8173 (ptp-170) REVERT: B 481 MET cc_start: 0.8173 (tpp) cc_final: 0.7577 (tpp) REVERT: B 540 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8164 (mt) REVERT: B 542 ASP cc_start: 0.7782 (m-30) cc_final: 0.7454 (m-30) REVERT: B 577 MET cc_start: 0.7581 (mtp) cc_final: 0.7165 (ttm) REVERT: B 629 TRP cc_start: 0.6149 (m-10) cc_final: 0.5931 (m-10) REVERT: C 99 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6872 (tmm) REVERT: C 128 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6524 (tm130) REVERT: C 180 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8157 (ttm-80) REVERT: C 211 PHE cc_start: 0.7458 (p90) cc_final: 0.6940 (p90) REVERT: C 214 GLN cc_start: 0.8269 (mt0) cc_final: 0.7615 (tm-30) REVERT: C 215 MET cc_start: 0.8861 (ttt) cc_final: 0.8628 (ttt) REVERT: C 216 TYR cc_start: 0.9247 (t80) cc_final: 0.8927 (t80) REVERT: C 239 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: C 262 LYS cc_start: 0.8560 (tmtt) cc_final: 0.8314 (tptt) REVERT: C 268 TRP cc_start: 0.8324 (p-90) cc_final: 0.8017 (p-90) REVERT: C 294 GLU cc_start: 0.7156 (tt0) cc_final: 0.6830 (tt0) REVERT: C 300 LYS cc_start: 0.8353 (pmtt) cc_final: 0.7804 (ttmt) REVERT: C 440 MET cc_start: 0.8685 (ttp) cc_final: 0.7560 (tpt) REVERT: C 454 MET cc_start: 0.8585 (tpp) cc_final: 0.8336 (tpt) REVERT: C 464 ASN cc_start: 0.7726 (t0) cc_final: 0.7514 (t0) REVERT: C 536 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (tt) REVERT: C 542 ASP cc_start: 0.7635 (m-30) cc_final: 0.7278 (m-30) REVERT: C 574 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5157 (mp) REVERT: D 62 ASN cc_start: 0.7923 (m110) cc_final: 0.6977 (t0) REVERT: D 180 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.7908 (mtp85) REVERT: D 211 PHE cc_start: 0.7439 (p90) cc_final: 0.7077 (p90) REVERT: D 239 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: D 268 TRP cc_start: 0.7829 (p-90) cc_final: 0.7355 (p-90) REVERT: D 282 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 290 GLN cc_start: 0.6983 (mm110) cc_final: 0.6465 (mm110) REVERT: D 294 GLU cc_start: 0.7345 (tt0) cc_final: 0.6848 (tt0) REVERT: D 303 GLU cc_start: 0.8319 (tt0) cc_final: 0.8033 (tt0) REVERT: D 378 MET cc_start: 0.7917 (ttm) cc_final: 0.7304 (ttt) REVERT: D 401 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8276 (tt) REVERT: D 440 MET cc_start: 0.8585 (ttp) cc_final: 0.7477 (tpt) REVERT: D 454 MET cc_start: 0.8490 (tpp) cc_final: 0.8081 (tpt) REVERT: D 464 ASN cc_start: 0.7794 (t0) cc_final: 0.7269 (t0) REVERT: D 490 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6408 (tt) REVERT: D 574 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.4903 (mp) REVERT: D 577 MET cc_start: 0.7903 (mtm) cc_final: 0.7644 (ttm) outliers start: 88 outliers final: 51 residues processed: 483 average time/residue: 0.1317 time to fit residues: 100.2990 Evaluate side-chains 470 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 404 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 173 VAL 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 298 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 465 VAL 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 105 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 202 ILE 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 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 444 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 540 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 159 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 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 402 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 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 64 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 195 LEU 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 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 465 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 490 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 113 optimal weight: 0.0070 chunk 236 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN C 258 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 HIS ** D 464 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 = 0.4076 r_free = 0.4076 target = 0.184580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148837 restraints weight = 27080.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153137 restraints weight = 14481.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155948 restraints weight = 9526.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157771 restraints weight = 7237.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159015 restraints weight = 6069.029| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4833 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= 0.103 Angle : 0.610 10.438 27518 Z= 0.297 Chirality : 0.040 0.261 3110 Planarity : 0.004 0.052 3458 Dihedral : 5.724 43.187 2879 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.06 % Allowed : 22.18 % Favored : 74.76 % 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: -1.75 (0.17), residues: 2440 helix: 0.13 (0.15), residues: 1300 sheet: -2.10 (0.66), residues: 56 loop : -2.82 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 153 TYR 0.020 0.001 TYR A 623 PHE 0.016 0.001 PHE C 415 TRP 0.009 0.001 TRP B 613 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00230 (20266) covalent geometry : angle 0.61037 (27518) hydrogen bonds : bond 0.02661 ( 696) hydrogen bonds : angle 3.82293 ( 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 506 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 441 time to evaluate : 0.741 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: 0.7820 (m110) cc_final: 0.6940 (t0) REVERT: A 71 LYS cc_start: 0.7385 (mtpt) cc_final: 0.6986 (mmpt) REVERT: A 99 MET cc_start: 0.7802 (mmm) cc_final: 0.7449 (mmm) REVERT: A 180 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8160 (ttm-80) REVERT: A 211 PHE cc_start: 0.7245 (p90) cc_final: 0.7038 (p90) REVERT: A 239 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: A 268 TRP cc_start: 0.7816 (p-90) cc_final: 0.7351 (p-90) REVERT: A 282 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 294 GLU cc_start: 0.7289 (tt0) cc_final: 0.7004 (tt0) REVERT: A 300 LYS cc_start: 0.8368 (pmtt) cc_final: 0.7933 (ttmt) REVERT: A 303 GLU cc_start: 0.8341 (tt0) cc_final: 0.7976 (tt0) REVERT: A 315 GLU cc_start: 0.7954 (tp30) cc_final: 0.7556 (mm-30) REVERT: A 378 MET cc_start: 0.7946 (ttm) cc_final: 0.7421 (ttt) REVERT: A 401 LEU cc_start: 0.8542 (mt) cc_final: 0.8208 (tt) REVERT: A 414 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7365 (tpp80) REVERT: A 438 VAL cc_start: 0.8710 (t) cc_final: 0.8489 (p) REVERT: A 440 MET cc_start: 0.8420 (ttp) cc_final: 0.7513 (tpt) REVERT: A 454 MET cc_start: 0.8482 (tpp) cc_final: 0.8216 (tpt) REVERT: A 470 ARG cc_start: 0.8622 (ptp-170) cc_final: 0.8154 (ptp-170) REVERT: A 574 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4523 (mp) REVERT: A 578 MET cc_start: 0.8239 (mmt) cc_final: 0.7719 (mmt) REVERT: B 62 ASN cc_start: 0.7838 (m110) cc_final: 0.7056 (t0) REVERT: B 71 LYS cc_start: 0.7130 (mtpt) cc_final: 0.6782 (mmpt) REVERT: B 99 MET cc_start: 0.7839 (mmm) cc_final: 0.7559 (mmm) REVERT: B 180 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.7804 (mtp85) REVERT: B 211 PHE cc_start: 0.7264 (p90) cc_final: 0.6995 (p90) REVERT: B 239 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: B 268 TRP cc_start: 0.7793 (p-90) cc_final: 0.7169 (p-90) REVERT: B 282 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: B 294 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7207 (tt0) REVERT: B 300 LYS cc_start: 0.8338 (pmtt) cc_final: 0.7868 (ttmt) REVERT: B 315 GLU cc_start: 0.7954 (tp30) cc_final: 0.7506 (mm-30) REVERT: B 373 LEU cc_start: 0.7703 (mp) cc_final: 0.7223 (tp) REVERT: B 401 LEU cc_start: 0.8538 (mt) cc_final: 0.8219 (tp) REVERT: B 414 ARG cc_start: 0.7528 (mmt-90) cc_final: 0.7301 (tpp80) REVERT: B 440 MET cc_start: 0.8342 (ttp) cc_final: 0.7511 (tpt) REVERT: B 454 MET cc_start: 0.8519 (tpp) cc_final: 0.8092 (tpt) REVERT: B 464 ASN cc_start: 0.7614 (t0) cc_final: 0.7312 (t0) REVERT: B 470 ARG cc_start: 0.8559 (ptp-170) cc_final: 0.8065 (ptp-170) REVERT: B 540 ILE cc_start: 0.8422 (mt) cc_final: 0.7990 (tt) REVERT: B 542 ASP cc_start: 0.7708 (m-30) cc_final: 0.7366 (m-30) REVERT: B 558 THR cc_start: 0.8782 (t) cc_final: 0.8559 (t) REVERT: B 577 MET cc_start: 0.7488 (mtp) cc_final: 0.7165 (ttm) REVERT: C 99 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6822 (tmm) REVERT: C 180 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7779 (mtp85) REVERT: C 214 GLN cc_start: 0.8183 (mt0) cc_final: 0.7540 (tm-30) REVERT: C 215 MET cc_start: 0.8841 (ttt) cc_final: 0.8637 (ttt) REVERT: C 239 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: C 262 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8205 (tptt) REVERT: C 268 TRP cc_start: 0.8223 (p-90) cc_final: 0.7972 (p-90) REVERT: C 294 GLU cc_start: 0.7097 (tt0) cc_final: 0.6773 (tt0) REVERT: C 300 LYS cc_start: 0.8346 (pmtt) cc_final: 0.7488 (tmtt) REVERT: C 440 MET cc_start: 0.8424 (ttp) cc_final: 0.7218 (tpt) REVERT: C 464 ASN cc_start: 0.7785 (t0) cc_final: 0.7583 (t0) REVERT: C 536 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7790 (tt) REVERT: C 542 ASP cc_start: 0.7651 (m-30) cc_final: 0.7324 (m-30) REVERT: C 574 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.5006 (tp) REVERT: C 629 TRP cc_start: 0.6850 (m-10) cc_final: 0.6085 (m-10) REVERT: D 62 ASN cc_start: 0.7937 (m110) cc_final: 0.6983 (t0) REVERT: D 180 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8108 (ttm-80) REVERT: D 211 PHE cc_start: 0.7300 (p90) cc_final: 0.6974 (p90) REVERT: D 239 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: D 268 TRP cc_start: 0.7754 (p-90) cc_final: 0.7242 (p-90) REVERT: D 282 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 290 GLN cc_start: 0.6964 (mm110) cc_final: 0.6473 (mm110) REVERT: D 294 GLU cc_start: 0.7420 (tt0) cc_final: 0.6905 (tt0) REVERT: D 303 GLU cc_start: 0.8344 (tt0) cc_final: 0.8015 (tt0) REVERT: D 378 MET cc_start: 0.7945 (ttm) cc_final: 0.7289 (ttt) REVERT: D 401 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8402 (mt) REVERT: D 414 ARG cc_start: 0.7247 (mmt-90) cc_final: 0.6923 (tpp80) REVERT: D 440 MET cc_start: 0.8514 (ttp) cc_final: 0.7221 (tpt) REVERT: D 454 MET cc_start: 0.8361 (tpp) cc_final: 0.8124 (tpt) REVERT: D 464 ASN cc_start: 0.7597 (t0) cc_final: 0.7268 (t0) REVERT: D 485 MET cc_start: 0.8770 (tpp) cc_final: 0.8479 (tpp) REVERT: D 574 LEU cc_start: 0.5433 (OUTLIER) cc_final: 0.4472 (mt) REVERT: D 577 MET cc_start: 0.7877 (mtm) cc_final: 0.7605 (ttm) REVERT: D 578 MET cc_start: 0.8380 (mmt) cc_final: 0.7840 (mmt) outliers start: 65 outliers final: 30 residues processed: 475 average time/residue: 0.1254 time to fit residues: 93.8401 Evaluate side-chains 448 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 407 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR 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 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 282 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 634 GLU 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 213 CYS 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 448 SER 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 64 LEU Chi-restraints excluded: chain D residue 130 MET 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 401 LEU Chi-restraints excluded: chain D residue 444 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: 3.9990 chunk 172 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 91 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 464 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144964 restraints weight = 27273.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149086 restraints weight = 14677.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151818 restraints weight = 9715.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153625 restraints weight = 7428.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154696 restraints weight = 6242.087| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20266 Z= 0.133 Angle : 0.645 11.313 27518 Z= 0.311 Chirality : 0.041 0.226 3110 Planarity : 0.004 0.044 3458 Dihedral : 5.804 48.210 2879 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.20 % Allowed : 22.69 % Favored : 74.11 % 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: -1.59 (0.17), residues: 2440 helix: 0.28 (0.15), residues: 1288 sheet: -2.16 (0.65), residues: 56 loop : -2.74 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.022 0.001 TYR A 623 PHE 0.020 0.001 PHE D 493 TRP 0.014 0.001 TRP B 629 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00320 (20266) covalent geometry : angle 0.64525 (27518) hydrogen bonds : bond 0.03066 ( 696) hydrogen bonds : angle 3.93351 ( 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 484 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 416 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7811 (m110) cc_final: 0.6946 (t0) REVERT: A 71 LYS cc_start: 0.7366 (mtpt) cc_final: 0.6620 (mmpt) REVERT: A 99 MET cc_start: 0.7807 (mmm) cc_final: 0.7471 (mmm) REVERT: A 144 SER cc_start: 0.8383 (m) cc_final: 0.7762 (p) REVERT: A 180 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8121 (ttm-80) REVERT: A 211 PHE cc_start: 0.7255 (p90) cc_final: 0.6939 (p90) REVERT: A 239 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: A 282 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7946 (mt-10) REVERT: A 294 GLU cc_start: 0.7297 (tt0) cc_final: 0.6979 (tt0) REVERT: A 303 GLU cc_start: 0.8350 (tt0) cc_final: 0.8051 (tt0) REVERT: A 315 GLU cc_start: 0.7895 (tp30) cc_final: 0.7492 (mm-30) REVERT: A 378 MET cc_start: 0.7999 (ttm) cc_final: 0.7525 (ttt) REVERT: A 401 LEU cc_start: 0.8490 (mt) cc_final: 0.8159 (tt) REVERT: A 440 MET cc_start: 0.8471 (ttp) cc_final: 0.7622 (tpp) REVERT: A 454 MET cc_start: 0.8480 (tpp) cc_final: 0.8176 (tpt) REVERT: A 470 ARG cc_start: 0.8671 (ptp-170) cc_final: 0.8160 (ptp-170) REVERT: A 540 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 574 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.4766 (tp) REVERT: A 578 MET cc_start: 0.8299 (mmt) cc_final: 0.7747 (mmt) REVERT: B 62 ASN cc_start: 0.7820 (m110) cc_final: 0.7020 (t0) REVERT: B 71 LYS cc_start: 0.7109 (mtpt) cc_final: 0.6772 (mmpt) REVERT: B 99 MET cc_start: 0.7798 (mmm) cc_final: 0.7543 (mmm) REVERT: B 180 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8078 (ttm-80) REVERT: B 211 PHE cc_start: 0.7313 (p90) cc_final: 0.6959 (p90) REVERT: B 239 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: B 282 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: B 294 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7190 (tt0) REVERT: B 315 GLU cc_start: 0.7996 (tp30) cc_final: 0.7624 (tp30) REVERT: B 401 LEU cc_start: 0.8548 (mt) cc_final: 0.8258 (tt) REVERT: B 414 ARG cc_start: 0.7528 (mmt-90) cc_final: 0.7244 (tpp80) REVERT: B 440 MET cc_start: 0.8461 (ttp) cc_final: 0.7523 (tpt) REVERT: B 454 MET cc_start: 0.8551 (tpp) cc_final: 0.8055 (tpt) REVERT: B 464 ASN cc_start: 0.7775 (t0) cc_final: 0.7452 (t0) REVERT: B 470 ARG cc_start: 0.8634 (ptp-170) cc_final: 0.8103 (ptp-170) REVERT: B 540 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8241 (mt) REVERT: B 542 ASP cc_start: 0.7687 (m-30) cc_final: 0.7244 (m-30) REVERT: B 577 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7382 (ttm) REVERT: C 99 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6886 (tmm) REVERT: C 180 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7811 (mtp85) REVERT: C 211 PHE cc_start: 0.7349 (p90) cc_final: 0.6824 (p90) REVERT: C 214 GLN cc_start: 0.8207 (mt0) cc_final: 0.7591 (tm-30) REVERT: C 217 ASN cc_start: 0.8690 (t0) cc_final: 0.8252 (m-40) REVERT: C 239 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: C 262 LYS cc_start: 0.8593 (tmtt) cc_final: 0.8242 (tptt) REVERT: C 268 TRP cc_start: 0.8255 (p-90) cc_final: 0.7981 (p-90) REVERT: C 294 GLU cc_start: 0.7137 (tt0) cc_final: 0.6817 (tt0) REVERT: C 300 LYS cc_start: 0.8366 (pmtt) cc_final: 0.7499 (tmtt) REVERT: C 414 ARG cc_start: 0.7563 (tpp80) cc_final: 0.7341 (mmm160) REVERT: C 440 MET cc_start: 0.8509 (ttp) cc_final: 0.7213 (tpt) REVERT: C 464 ASN cc_start: 0.7820 (t0) cc_final: 0.7527 (t0) REVERT: C 536 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8045 (tt) REVERT: C 542 ASP cc_start: 0.7628 (m-30) cc_final: 0.7270 (m-30) REVERT: C 629 TRP cc_start: 0.7128 (m-10) cc_final: 0.6441 (m-10) REVERT: C 634 GLU cc_start: 0.8557 (pm20) cc_final: 0.7515 (mp0) REVERT: D 62 ASN cc_start: 0.7989 (m110) cc_final: 0.7053 (t0) REVERT: D 180 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8122 (ttm-80) REVERT: D 211 PHE cc_start: 0.7356 (p90) cc_final: 0.6941 (p90) REVERT: D 239 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: D 282 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8036 (mt-10) REVERT: D 303 GLU cc_start: 0.8339 (tt0) cc_final: 0.8007 (tt0) REVERT: D 378 MET cc_start: 0.7965 (ttm) cc_final: 0.7386 (ttt) REVERT: D 401 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8410 (mt) REVERT: D 414 ARG cc_start: 0.7290 (mmt-90) cc_final: 0.6977 (tpp80) REVERT: D 440 MET cc_start: 0.8568 (ttp) cc_final: 0.7171 (tpt) REVERT: D 454 MET cc_start: 0.8385 (tpp) cc_final: 0.8093 (tpt) REVERT: D 464 ASN cc_start: 0.7818 (t0) cc_final: 0.7402 (t0) REVERT: D 485 MET cc_start: 0.8878 (tpp) cc_final: 0.8491 (tpp) REVERT: D 574 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.4015 (mt) REVERT: D 577 MET cc_start: 0.7945 (mtm) cc_final: 0.7653 (ttm) REVERT: D 578 MET cc_start: 0.8444 (mmt) cc_final: 0.7739 (mmt) outliers start: 68 outliers final: 43 residues processed: 456 average time/residue: 0.1237 time to fit residues: 89.6109 Evaluate side-chains 452 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 396 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 159 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 340 ILE Chi-restraints excluded: chain A residue 465 VAL 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 55 ASP 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 282 GLU 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 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 577 MET 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 195 LEU Chi-restraints excluded: chain C residue 213 CYS 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 404 VAL 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 536 LEU 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 159 LEU Chi-restraints excluded: chain D residue 195 LEU 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 340 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 233 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 229 optimal weight: 0.5980 chunk 150 optimal weight: 0.0370 chunk 36 optimal weight: 0.9990 chunk 137 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.179705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143688 restraints weight = 26969.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147847 restraints weight = 14528.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150606 restraints weight = 9619.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152404 restraints weight = 7343.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153434 restraints weight = 6175.896| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20266 Z= 0.104 Angle : 0.618 12.875 27518 Z= 0.300 Chirality : 0.040 0.166 3110 Planarity : 0.004 0.046 3458 Dihedral : 5.566 45.419 2879 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.40 % Allowed : 23.54 % 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: -1.47 (0.17), residues: 2440 helix: 0.44 (0.15), residues: 1296 sheet: -2.08 (0.66), residues: 56 loop : -2.78 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.021 0.001 TYR A 623 PHE 0.021 0.001 PHE C 415 TRP 0.017 0.001 TRP B 629 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00238 (20266) covalent geometry : angle 0.61828 (27518) hydrogen bonds : bond 0.02681 ( 696) hydrogen bonds : angle 3.74838 ( 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 457 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 406 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7811 (m110) cc_final: 0.6926 (t0) REVERT: A 71 LYS cc_start: 0.7290 (mtpt) cc_final: 0.6574 (mmtt) REVERT: A 99 MET cc_start: 0.7787 (mmm) cc_final: 0.7514 (mmm) REVERT: A 100 GLU cc_start: 0.8411 (tp30) cc_final: 0.8021 (mt-10) REVERT: A 180 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8089 (ttm-80) REVERT: A 239 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: A 268 TRP cc_start: 0.7804 (p-90) cc_final: 0.7272 (p-90) REVERT: A 282 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 294 GLU cc_start: 0.7171 (tt0) cc_final: 0.6884 (tt0) REVERT: A 303 GLU cc_start: 0.8312 (tt0) cc_final: 0.7964 (tt0) REVERT: A 315 GLU cc_start: 0.7876 (tp30) cc_final: 0.7482 (mm-30) REVERT: A 378 MET cc_start: 0.7992 (ttm) cc_final: 0.7468 (ttt) REVERT: A 401 LEU cc_start: 0.8502 (mt) cc_final: 0.8184 (tt) REVERT: A 440 MET cc_start: 0.8382 (ttp) cc_final: 0.7520 (tpp) REVERT: A 454 MET cc_start: 0.8437 (tpp) cc_final: 0.8069 (tpt) REVERT: A 470 ARG cc_start: 0.8645 (ptp-170) cc_final: 0.8140 (ptp-170) REVERT: A 540 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7975 (tt) REVERT: A 578 MET cc_start: 0.8298 (mmt) cc_final: 0.7869 (mmt) REVERT: B 62 ASN cc_start: 0.7822 (m110) cc_final: 0.7095 (t0) REVERT: B 71 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6710 (mmpt) REVERT: B 99 MET cc_start: 0.7759 (mmm) cc_final: 0.7524 (mmm) REVERT: B 180 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7825 (ttm-80) REVERT: B 211 PHE cc_start: 0.7169 (p90) cc_final: 0.6872 (p90) REVERT: B 239 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: B 282 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: B 294 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7221 (tt0) REVERT: B 315 GLU cc_start: 0.7945 (tp30) cc_final: 0.7513 (mm-30) REVERT: B 373 LEU cc_start: 0.7636 (mp) cc_final: 0.7169 (tp) REVERT: B 401 LEU cc_start: 0.8560 (mt) cc_final: 0.8217 (tp) REVERT: B 414 ARG cc_start: 0.7602 (mmt-90) cc_final: 0.7391 (tpp80) REVERT: B 440 MET cc_start: 0.8377 (ttp) cc_final: 0.7390 (tpt) REVERT: B 464 ASN cc_start: 0.7671 (t0) cc_final: 0.7419 (t0) REVERT: B 470 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.8017 (ptp-170) REVERT: B 540 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 542 ASP cc_start: 0.7704 (m-30) cc_final: 0.7207 (m-30) REVERT: B 558 THR cc_start: 0.8766 (t) cc_final: 0.8560 (t) REVERT: B 577 MET cc_start: 0.7631 (mtp) cc_final: 0.7253 (ttm) REVERT: C 55 ASP cc_start: 0.8691 (t0) cc_final: 0.8121 (t70) REVERT: C 99 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6853 (tmm) REVERT: C 180 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.7798 (mtp85) REVERT: C 211 PHE cc_start: 0.7214 (p90) cc_final: 0.6678 (p90) REVERT: C 214 GLN cc_start: 0.8042 (mt0) cc_final: 0.7443 (tm-30) REVERT: C 215 MET cc_start: 0.8734 (ttt) cc_final: 0.8527 (ttt) REVERT: C 217 ASN cc_start: 0.8672 (t0) cc_final: 0.8195 (m-40) REVERT: C 239 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: C 262 LYS cc_start: 0.8560 (tmtt) cc_final: 0.8206 (tptt) REVERT: C 268 TRP cc_start: 0.8242 (p-90) cc_final: 0.7996 (p-90) REVERT: C 294 GLU cc_start: 0.7231 (tt0) cc_final: 0.6935 (tt0) REVERT: C 300 LYS cc_start: 0.8345 (pmtt) cc_final: 0.7472 (tmtt) REVERT: C 440 MET cc_start: 0.8340 (ttp) cc_final: 0.7146 (tpt) REVERT: C 464 ASN cc_start: 0.7780 (t0) cc_final: 0.7457 (t0) REVERT: C 483 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 485 MET cc_start: 0.8419 (tpp) cc_final: 0.7979 (ttm) REVERT: C 536 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7841 (tt) REVERT: C 542 ASP cc_start: 0.7549 (m-30) cc_final: 0.7222 (m-30) REVERT: C 629 TRP cc_start: 0.7267 (m-10) cc_final: 0.6498 (m-10) REVERT: C 634 GLU cc_start: 0.8514 (pm20) cc_final: 0.7530 (mp0) REVERT: D 62 ASN cc_start: 0.7977 (m110) cc_final: 0.7072 (t0) REVERT: D 99 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6406 (tmm) REVERT: D 139 ARG cc_start: 0.7274 (tpp80) cc_final: 0.6829 (mtt90) REVERT: D 180 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8252 (ttm-80) REVERT: D 211 PHE cc_start: 0.7202 (p90) cc_final: 0.6902 (p90) REVERT: D 239 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: D 268 TRP cc_start: 0.7797 (p-90) cc_final: 0.7337 (p-90) REVERT: D 282 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 303 GLU cc_start: 0.8325 (tt0) cc_final: 0.7992 (tt0) REVERT: D 378 MET cc_start: 0.7919 (ttm) cc_final: 0.7435 (ttt) REVERT: D 401 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8399 (mt) REVERT: D 414 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6999 (tpp80) REVERT: D 440 MET cc_start: 0.8507 (ttp) cc_final: 0.7137 (tpt) REVERT: D 454 MET cc_start: 0.8345 (tpp) cc_final: 0.8115 (tpt) REVERT: D 464 ASN cc_start: 0.7709 (t0) cc_final: 0.7353 (t0) REVERT: D 485 MET cc_start: 0.8814 (tpp) cc_final: 0.8522 (tpp) REVERT: D 574 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.3960 (mt) REVERT: D 577 MET cc_start: 0.7941 (mtm) cc_final: 0.7654 (ttm) REVERT: D 578 MET cc_start: 0.8443 (mmt) cc_final: 0.7868 (mmt) outliers start: 51 outliers final: 33 residues processed: 433 average time/residue: 0.1288 time to fit residues: 88.9300 Evaluate side-chains 426 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 381 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 159 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 465 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 554 MET 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 282 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 540 ILE 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 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 282 GLU 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 536 LEU 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 99 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 195 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 401 LEU Chi-restraints excluded: chain D residue 444 LEU 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: 0.0070 chunk 188 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 191 optimal weight: 0.0000 chunk 17 optimal weight: 0.5980 chunk 154 optimal weight: 0.0370 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 59 GLN B 91 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 522 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 = 0.4092 r_free = 0.4092 target = 0.186026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150890 restraints weight = 26985.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155169 restraints weight = 14359.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158003 restraints weight = 9387.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159808 restraints weight = 7104.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161027 restraints weight = 5926.218| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5350 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= 0.103 Angle : 0.624 13.651 27518 Z= 0.304 Chirality : 0.040 0.159 3110 Planarity : 0.004 0.086 3458 Dihedral : 5.365 42.643 2879 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.45 % Allowed : 24.15 % Favored : 73.40 % 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: -1.33 (0.17), residues: 2440 helix: 0.59 (0.15), residues: 1300 sheet: -2.04 (0.65), residues: 56 loop : -2.79 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 615 TYR 0.020 0.001 TYR A 623 PHE 0.025 0.001 PHE A 415 TRP 0.022 0.001 TRP B 629 HIS 0.009 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00228 (20266) covalent geometry : angle 0.62420 (27518) hydrogen bonds : bond 0.02552 ( 696) hydrogen bonds : angle 3.63795 ( 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 461 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 409 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7874 (m110) cc_final: 0.6972 (t0) REVERT: A 99 MET cc_start: 0.7776 (mmm) cc_final: 0.7505 (mmm) REVERT: A 100 GLU cc_start: 0.8447 (tp30) cc_final: 0.8057 (mt-10) REVERT: A 180 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8075 (ttm-80) REVERT: A 239 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: A 250 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7934 (tp30) REVERT: A 268 TRP cc_start: 0.7806 (p-90) cc_final: 0.7330 (p-90) REVERT: A 282 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 290 GLN cc_start: 0.6671 (mm110) cc_final: 0.6456 (mm-40) REVERT: A 303 GLU cc_start: 0.8296 (tt0) cc_final: 0.7927 (tt0) REVERT: A 315 GLU cc_start: 0.7878 (tp30) cc_final: 0.7502 (mm-30) REVERT: A 378 MET cc_start: 0.7921 (ttm) cc_final: 0.7386 (ttt) REVERT: A 440 MET cc_start: 0.8297 (ttp) cc_final: 0.7467 (tpp) REVERT: A 454 MET cc_start: 0.8424 (tpp) cc_final: 0.8093 (tpt) REVERT: A 470 ARG cc_start: 0.8665 (ptp-170) cc_final: 0.8175 (ptp-170) REVERT: A 485 MET cc_start: 0.8413 (tpp) cc_final: 0.7761 (ttm) REVERT: A 540 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8073 (tt) REVERT: B 62 ASN cc_start: 0.7839 (m110) cc_final: 0.7096 (t0) REVERT: B 71 LYS cc_start: 0.7036 (mtpt) cc_final: 0.6616 (mmpt) REVERT: B 99 MET cc_start: 0.7770 (mmm) cc_final: 0.7541 (mmm) REVERT: B 100 GLU cc_start: 0.8434 (tp30) cc_final: 0.8074 (mt-10) REVERT: B 180 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8044 (ttm-80) REVERT: B 239 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: B 294 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7168 (tt0) REVERT: B 315 GLU cc_start: 0.7928 (tp30) cc_final: 0.7496 (tp30) REVERT: B 373 LEU cc_start: 0.7636 (mp) cc_final: 0.7206 (tp) REVERT: B 401 LEU cc_start: 0.8555 (mt) cc_final: 0.8223 (tp) REVERT: B 440 MET cc_start: 0.8351 (ttp) cc_final: 0.7379 (tpt) REVERT: B 464 ASN cc_start: 0.7582 (t0) cc_final: 0.7304 (t0) REVERT: B 470 ARG cc_start: 0.8556 (ptp-170) cc_final: 0.8021 (ptp-170) REVERT: B 540 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8174 (tt) REVERT: B 542 ASP cc_start: 0.7711 (m-30) cc_final: 0.7168 (m-30) REVERT: B 558 THR cc_start: 0.8694 (t) cc_final: 0.8485 (t) REVERT: C 55 ASP cc_start: 0.8633 (t0) cc_final: 0.8037 (t70) REVERT: C 99 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6852 (tmm) REVERT: C 180 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7801 (mtp85) REVERT: C 214 GLN cc_start: 0.7979 (mt0) cc_final: 0.7401 (tm-30) REVERT: C 217 ASN cc_start: 0.8632 (t0) cc_final: 0.8165 (m-40) REVERT: C 239 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: C 262 LYS cc_start: 0.8445 (tmtt) cc_final: 0.8053 (tptt) REVERT: C 268 TRP cc_start: 0.8215 (p-90) cc_final: 0.7937 (p-90) REVERT: C 294 GLU cc_start: 0.7354 (tt0) cc_final: 0.7093 (tt0) REVERT: C 414 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7488 (tpp-160) REVERT: C 440 MET cc_start: 0.8215 (ttp) cc_final: 0.7003 (tpt) REVERT: C 464 ASN cc_start: 0.7811 (t0) cc_final: 0.7536 (t0) REVERT: C 483 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 485 MET cc_start: 0.8196 (tpp) cc_final: 0.7944 (ttm) REVERT: C 536 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7817 (tt) REVERT: C 542 ASP cc_start: 0.7525 (m-30) cc_final: 0.7249 (m-30) REVERT: C 574 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5216 (tp) REVERT: C 634 GLU cc_start: 0.8493 (pm20) cc_final: 0.7498 (mp0) REVERT: D 62 ASN cc_start: 0.8007 (m110) cc_final: 0.7101 (t0) REVERT: D 99 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6213 (tmm) REVERT: D 139 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6791 (mtt90) REVERT: D 180 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8288 (ttm-80) REVERT: D 211 PHE cc_start: 0.7016 (p90) cc_final: 0.6778 (p90) REVERT: D 239 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: D 282 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8057 (mt-10) REVERT: D 303 GLU cc_start: 0.8313 (tt0) cc_final: 0.7985 (tt0) REVERT: D 378 MET cc_start: 0.7912 (ttm) cc_final: 0.7501 (ttt) REVERT: D 401 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8435 (mt) REVERT: D 414 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.6975 (tpp80) REVERT: D 440 MET cc_start: 0.8318 (ttp) cc_final: 0.7048 (tpt) REVERT: D 464 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7332 (t0) REVERT: D 485 MET cc_start: 0.8723 (tpp) cc_final: 0.8498 (tpp) REVERT: D 577 MET cc_start: 0.8044 (mtm) cc_final: 0.7802 (ttm) REVERT: D 578 MET cc_start: 0.8493 (mmt) cc_final: 0.8034 (mmt) outliers start: 52 outliers final: 28 residues processed: 430 average time/residue: 0.1291 time to fit residues: 87.8567 Evaluate side-chains 424 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 384 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 128 GLN Chi-restraints excluded: chain A residue 195 LEU 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 465 VAL Chi-restraints excluded: chain A residue 540 ILE 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 540 ILE Chi-restraints excluded: chain B residue 634 GLU 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 239 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 448 SER 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 64 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 195 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 401 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 464 ASN 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: 5.9990 chunk 23 optimal weight: 6.9990 chunk 124 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 29 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 59 GLN B 91 ASN B 118 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147166 restraints weight = 27085.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151185 restraints weight = 15068.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153828 restraints weight = 10159.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155577 restraints weight = 7863.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156555 restraints weight = 6655.645| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 20266 Z= 0.182 Angle : 0.789 58.946 27518 Z= 0.425 Chirality : 0.048 1.424 3110 Planarity : 0.005 0.120 3458 Dihedral : 5.351 42.637 2879 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.98 % Allowed : 24.62 % Favored : 73.40 % 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: -1.32 (0.17), residues: 2440 helix: 0.60 (0.15), residues: 1300 sheet: -2.04 (0.65), residues: 56 loop : -2.79 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 615 TYR 0.020 0.001 TYR D 324 PHE 0.043 0.001 PHE B 211 TRP 0.049 0.001 TRP C 629 HIS 0.008 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00387 (20266) covalent geometry : angle 0.78948 (27518) hydrogen bonds : bond 0.02555 ( 696) hydrogen bonds : angle 3.63848 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3693.32 seconds wall clock time: 64 minutes 14.40 seconds (3854.40 seconds total)