Starting phenix.real_space_refine on Wed Apr 8 13:49:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cm7_30403/04_2026/7cm7_30403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm7_30403/04_2026/7cm7_30403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cm7_30403/04_2026/7cm7_30403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm7_30403/04_2026/7cm7_30403.map" model { file = "/net/cci-nas-00/data/ceres_data/7cm7_30403/04_2026/7cm7_30403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm7_30403/04_2026/7cm7_30403.cif" } resolution = 2.6 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= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 184 5.16 5 C 24744 2.51 5 N 7048 2.21 5 O 7224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39216 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 21, 'TRANS': 598} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 5.73, per 1000 atoms: 0.15 Number of scatterers: 39216 At special positions: 0 Unit cell: (214.165, 214.165, 82.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 16 15.00 O 7224 8.00 N 7048 7.00 C 24744 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9248 Finding SS restraints... Secondary structure from input PDB file: 328 helices and 8 sheets defined 71.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.513A pdb=" N LEU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.702A pdb=" N ARG A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.908A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.547A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.685A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 263 through 278 removed outlier: 4.172A pdb=" N ARG A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.752A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.772A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.579A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.554A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.514A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.624A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.713A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 518' Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.858A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.515A pdb=" N ALA A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.967A pdb=" N ALA A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 removed outlier: 3.607A pdb=" N GLY A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.560A pdb=" N VAL A 675 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.680A pdb=" N THR A 691 " --> pdb=" O TYR A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 86 through 104 removed outlier: 3.514A pdb=" N LEU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.702A pdb=" N ARG B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.909A pdb=" N ASP B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.686A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 263 through 278 removed outlier: 4.172A pdb=" N ARG B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.751A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.771A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 Processing helix chain 'B' and resid 363 through 369 Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.580A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.554A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.513A pdb=" N PHE B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.625A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.713A pdb=" N ARG B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 514 through 518' Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.859A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.515A pdb=" N ALA B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.968A pdb=" N ALA B 600 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 removed outlier: 3.607A pdb=" N GLY B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.560A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 678 " --> pdb=" O VAL B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 removed outlier: 3.681A pdb=" N THR B 691 " --> pdb=" O TYR B 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 82 Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.514A pdb=" N LEU C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.703A pdb=" N ARG C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.910A pdb=" N ASP C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.685A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 237 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 263 through 278 removed outlier: 4.172A pdb=" N ARG C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.752A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.772A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 removed outlier: 4.017A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 359 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.579A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 424 " --> pdb=" O TRP C 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.553A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 453 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.512A pdb=" N PHE C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 3.624A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 500' Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.713A pdb=" N ARG C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 518' Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 545 removed outlier: 3.859A pdb=" N MET C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 3.515A pdb=" N ALA C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 600 removed outlier: 3.967A pdb=" N ALA C 600 " --> pdb=" O LYS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 614 removed outlier: 3.608A pdb=" N GLY C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.559A pdb=" N VAL C 675 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 676 " --> pdb=" O GLN C 673 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 678 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 removed outlier: 3.680A pdb=" N THR C 691 " --> pdb=" O TYR C 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 82 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.513A pdb=" N LEU D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 137 through 150 removed outlier: 3.702A pdb=" N ARG D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.909A pdb=" N ASP D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.685A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 263 through 278 removed outlier: 4.171A pdb=" N ARG D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.752A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 3.771A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'D' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.579A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 424 " --> pdb=" O TRP D 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 425 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 437 removed outlier: 3.553A pdb=" N GLU D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 453 Processing helix chain 'D' and resid 459 through 476 removed outlier: 3.513A pdb=" N PHE D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 3.625A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 497 through 500' Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.714A pdb=" N ARG D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 514 through 518' Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 545 removed outlier: 3.859A pdb=" N MET D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 removed outlier: 3.515A pdb=" N ALA D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 600 removed outlier: 3.967A pdb=" N ALA D 600 " --> pdb=" O LYS D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 614 removed outlier: 3.607A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 650 Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.560A pdb=" N VAL D 675 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 676 " --> pdb=" O GLN D 673 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 678 " --> pdb=" O VAL D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 removed outlier: 3.679A pdb=" N THR D 691 " --> pdb=" O TYR D 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 82 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.513A pdb=" N LEU E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.678A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 137 through 150 removed outlier: 3.703A pdb=" N ARG E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.909A pdb=" N ASP E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.684A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 237 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 263 through 278 removed outlier: 4.171A pdb=" N ARG E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.753A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 312 removed outlier: 3.772A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 359 Processing helix chain 'E' and resid 363 through 369 Processing helix chain 'E' and resid 369 through 380 removed outlier: 4.123A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.579A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 425 " --> pdb=" O LEU E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 437 removed outlier: 3.554A pdb=" N GLU E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 453 Processing helix chain 'E' and resid 459 through 476 removed outlier: 3.513A pdb=" N PHE E 476 " --> pdb=" O GLU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 493 removed outlier: 3.624A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 497 through 500' Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.714A pdb=" N ARG E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 514 through 518' Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 545 removed outlier: 3.859A pdb=" N MET E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 586 removed outlier: 3.516A pdb=" N ALA E 577 " --> pdb=" O GLY E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 600 removed outlier: 3.968A pdb=" N ALA E 600 " --> pdb=" O LYS E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 3.607A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 650 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.559A pdb=" N VAL E 675 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 676 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 678 " --> pdb=" O VAL E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 697 removed outlier: 3.681A pdb=" N THR E 691 " --> pdb=" O TYR E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 82 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 86 through 104 removed outlier: 3.513A pdb=" N LEU F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.703A pdb=" N ARG F 141 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 163 removed outlier: 3.908A pdb=" N ASP F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.685A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 237 Processing helix chain 'F' and resid 238 through 247 Processing helix chain 'F' and resid 254 through 260 Processing helix chain 'F' and resid 263 through 278 removed outlier: 4.171A pdb=" N ARG F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.752A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 312 removed outlier: 3.771A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 359 Processing helix chain 'F' and resid 363 through 369 Processing helix chain 'F' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.579A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 424 " --> pdb=" O TRP F 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 425 " --> pdb=" O LEU F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 437 removed outlier: 3.553A pdb=" N GLU F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 453 Processing helix chain 'F' and resid 459 through 476 removed outlier: 3.513A pdb=" N PHE F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 493 removed outlier: 3.625A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 497 through 500' Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.714A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 514 through 518' Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 545 removed outlier: 3.860A pdb=" N MET F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 586 removed outlier: 3.515A pdb=" N ALA F 577 " --> pdb=" O GLY F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 600 removed outlier: 3.968A pdb=" N ALA F 600 " --> pdb=" O LYS F 597 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 removed outlier: 3.607A pdb=" N GLY F 613 " --> pdb=" O GLN F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 650 Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.560A pdb=" N VAL F 675 " --> pdb=" O MET F 672 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 676 " --> pdb=" O GLN F 673 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE F 678 " --> pdb=" O VAL F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 697 removed outlier: 3.680A pdb=" N THR F 691 " --> pdb=" O TYR F 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 82 Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 86 through 104 removed outlier: 3.513A pdb=" N LEU G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.702A pdb=" N ARG G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 removed outlier: 3.909A pdb=" N ASP G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.685A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 237 Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 254 through 260 Processing helix chain 'G' and resid 263 through 278 removed outlier: 4.171A pdb=" N ARG G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.752A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 removed outlier: 3.772A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 359 Processing helix chain 'G' and resid 363 through 369 Processing helix chain 'G' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 removed outlier: 3.565A pdb=" N SER G 387 " --> pdb=" O ASN G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.579A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE G 424 " --> pdb=" O TRP G 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY G 425 " --> pdb=" O LEU G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 437 removed outlier: 3.554A pdb=" N GLU G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 436 " --> pdb=" O SER G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 453 Processing helix chain 'G' and resid 459 through 476 removed outlier: 3.513A pdb=" N PHE G 476 " --> pdb=" O GLU G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 493 removed outlier: 3.625A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 500 removed outlier: 4.140A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 497 through 500' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.714A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 514 through 518' Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 545 removed outlier: 3.858A pdb=" N MET G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 586 removed outlier: 3.516A pdb=" N ALA G 577 " --> pdb=" O GLY G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 600 removed outlier: 3.968A pdb=" N ALA G 600 " --> pdb=" O LYS G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 614 removed outlier: 3.608A pdb=" N GLY G 613 " --> pdb=" O GLN G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 672 through 678 removed outlier: 3.560A pdb=" N VAL G 675 " --> pdb=" O MET G 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 676 " --> pdb=" O GLN G 673 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE G 678 " --> pdb=" O VAL G 675 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 697 removed outlier: 3.680A pdb=" N THR G 691 " --> pdb=" O TYR G 687 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 82 Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 86 through 104 removed outlier: 3.514A pdb=" N LEU H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.677A pdb=" N VAL H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.702A pdb=" N ARG H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 163 removed outlier: 3.909A pdb=" N ASP H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.540A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 3.546A pdb=" N ALA H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.684A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 237 Processing helix chain 'H' and resid 238 through 247 Processing helix chain 'H' and resid 254 through 260 Processing helix chain 'H' and resid 263 through 278 removed outlier: 4.172A pdb=" N ARG H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 291 Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.752A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 312 removed outlier: 3.772A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 331 removed outlier: 4.016A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 359 Processing helix chain 'H' and resid 363 through 369 Processing helix chain 'H' and resid 369 through 380 removed outlier: 4.122A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 removed outlier: 3.564A pdb=" N SER H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 removed outlier: 3.580A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE H 424 " --> pdb=" O TRP H 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 425 " --> pdb=" O LEU H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 437 removed outlier: 3.553A pdb=" N GLU H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN H 436 " --> pdb=" O SER H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 453 Processing helix chain 'H' and resid 459 through 476 removed outlier: 3.513A pdb=" N PHE H 476 " --> pdb=" O GLU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 493 removed outlier: 3.624A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 500 removed outlier: 4.139A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 497 through 500' Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.714A pdb=" N ARG H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 514 through 518' Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.860A pdb=" N MET H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 586 removed outlier: 3.515A pdb=" N ALA H 577 " --> pdb=" O GLY H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 595 through 600 removed outlier: 3.967A pdb=" N ALA H 600 " --> pdb=" O LYS H 597 " (cutoff:3.500A) Processing helix chain 'H' and resid 606 through 614 removed outlier: 3.607A pdb=" N GLY H 613 " --> pdb=" O GLN H 609 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'H' and resid 672 through 678 removed outlier: 3.559A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 676 " --> pdb=" O GLN H 673 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE H 678 " --> pdb=" O VAL H 675 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 697 removed outlier: 3.680A pdb=" N THR H 691 " --> pdb=" O TYR H 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.664A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE A 681 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.663A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE B 681 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.663A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE C 681 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.664A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE D 681 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.664A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE E 681 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.664A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE F 681 " --> pdb=" O ILE F 653 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.665A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE G 681 " --> pdb=" O ILE G 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.664A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE H 681 " --> pdb=" O ILE H 653 " (cutoff:3.500A) 2008 hydrogen bonds defined for protein. 5904 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: 8.44 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8453 1.33 - 1.45: 8245 1.45 - 1.57: 22918 1.57 - 1.69: 24 1.69 - 1.81: 248 Bond restraints: 39888 Sorted by residual: bond pdb=" C2D NAD C1000 " pdb=" O2D NAD C1000 " ideal model delta sigma weight residual 1.393 1.479 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C2D NAD A1000 " pdb=" O2D NAD A1000 " ideal model delta sigma weight residual 1.393 1.479 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C2D NAD F1000 " pdb=" O2D NAD F1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C2D NAD H1000 " pdb=" O2D NAD H1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C2D NAD G1000 " pdb=" O2D NAD G1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 39883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 53074 2.62 - 5.25: 714 5.25 - 7.87: 126 7.87 - 10.49: 38 10.49 - 13.11: 16 Bond angle restraints: 53968 Sorted by residual: angle pdb=" C SER C 336 " pdb=" N ASN C 337 " pdb=" CA ASN C 337 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C SER H 336 " pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C SER E 336 " pdb=" N ASN E 337 " pdb=" CA ASN E 337 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 ... (remaining 53963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 23628 15.06 - 30.12: 676 30.12 - 45.18: 152 45.18 - 60.24: 13 60.24 - 75.29: 51 Dihedral angle restraints: 24520 sinusoidal: 10264 harmonic: 14256 Sorted by residual: dihedral pdb=" CA TRP D 412 " pdb=" C TRP D 412 " pdb=" N LYS D 413 " pdb=" CA LYS D 413 " ideal model delta harmonic sigma weight residual 180.00 164.62 15.38 0 5.00e+00 4.00e-02 9.46e+00 dihedral pdb=" CA TRP F 412 " pdb=" C TRP F 412 " pdb=" N LYS F 413 " pdb=" CA LYS F 413 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" CA TRP G 412 " pdb=" C TRP G 412 " pdb=" N LYS G 413 " pdb=" CA LYS G 413 " ideal model delta harmonic sigma weight residual 180.00 164.66 15.34 0 5.00e+00 4.00e-02 9.41e+00 ... (remaining 24517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5443 0.069 - 0.139: 660 0.139 - 0.208: 33 0.208 - 0.277: 24 0.277 - 0.347: 8 Chirality restraints: 6168 Sorted by residual: chirality pdb=" C2D NAD G1000 " pdb=" C1D NAD G1000 " pdb=" C3D NAD G1000 " pdb=" O2D NAD G1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C2D NAD B1000 " pdb=" C1D NAD B1000 " pdb=" C3D NAD B1000 " pdb=" O2D NAD B1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C2D NAD C1000 " pdb=" C1D NAD C1000 " pdb=" C3D NAD C1000 " pdb=" O2D NAD C1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 6165 not shown) Planarity restraints: 6944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 283 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C VAL E 283 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL E 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU E 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 283 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C VAL F 283 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL F 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU F 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 283 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C VAL A 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A 284 " 0.014 2.00e-02 2.50e+03 ... (remaining 6941 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 11938 2.84 - 3.35: 34141 3.35 - 3.87: 62517 3.87 - 4.38: 72519 4.38 - 4.90: 125862 Nonbonded interactions: 306977 Sorted by model distance: nonbonded pdb=" OE1 GLN C 436 " pdb=" OG SER D 459 " model vdw 2.319 3.040 nonbonded pdb=" OE1 GLN A 436 " pdb=" OG SER B 459 " model vdw 2.332 3.040 nonbonded pdb=" OE1 GLN E 436 " pdb=" OG SER F 459 " model vdw 2.352 3.040 nonbonded pdb=" OE1 GLN F 436 " pdb=" OG SER G 459 " model vdw 2.391 3.040 nonbonded pdb=" O THR B 475 " pdb=" NH1 ARG B 499 " model vdw 2.399 3.120 ... (remaining 306972 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.170 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 0.004 0.086 39888 Z= 0.218 Angle : 0.837 13.113 53968 Z= 0.449 Chirality : 0.047 0.347 6168 Planarity : 0.006 0.053 6944 Dihedral : 9.039 75.294 15272 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -4.15 (0.09), residues: 4912 helix: -2.87 (0.06), residues: 3248 sheet: -0.42 (0.45), residues: 136 loop : -2.20 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 121 TYR 0.009 0.001 TYR D 568 PHE 0.034 0.002 PHE F 192 TRP 0.014 0.002 TRP F 490 HIS 0.008 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00405 (39888) covalent geometry : angle 0.83720 (53968) hydrogen bonds : bond 0.16070 ( 2008) hydrogen bonds : angle 6.35884 ( 5904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 914 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 LYS cc_start: 0.5779 (mttm) cc_final: 0.5578 (tttp) REVERT: A 672 MET cc_start: 0.3453 (ptm) cc_final: 0.2879 (pp-130) REVERT: B 457 MET cc_start: 0.8407 (ttm) cc_final: 0.7646 (ttm) REVERT: B 643 ILE cc_start: 0.6740 (mt) cc_final: 0.6268 (mt) REVERT: C 118 ASP cc_start: 0.6532 (m-30) cc_final: 0.6280 (m-30) REVERT: C 672 MET cc_start: 0.3261 (ptm) cc_final: 0.2941 (pp-130) REVERT: D 114 GLN cc_start: 0.6258 (mt0) cc_final: 0.5896 (tp-100) REVERT: D 259 PHE cc_start: 0.6182 (t80) cc_final: 0.5964 (t80) REVERT: D 457 MET cc_start: 0.8289 (ttm) cc_final: 0.7513 (ttm) REVERT: D 641 LYS cc_start: 0.5950 (mttm) cc_final: 0.5744 (tttt) REVERT: D 643 ILE cc_start: 0.6712 (mt) cc_final: 0.6291 (mp) REVERT: E 104 LEU cc_start: 0.7710 (mt) cc_final: 0.7496 (mp) REVERT: E 118 ASP cc_start: 0.6556 (m-30) cc_final: 0.6304 (m-30) REVERT: E 672 MET cc_start: 0.3482 (ptm) cc_final: 0.2999 (pp-130) REVERT: F 457 MET cc_start: 0.8336 (ttm) cc_final: 0.7570 (ttm) REVERT: F 641 LYS cc_start: 0.5832 (mttm) cc_final: 0.5572 (tttp) REVERT: F 672 MET cc_start: 0.3429 (ptm) cc_final: 0.3030 (pp-130) REVERT: G 569 ARG cc_start: 0.6425 (tpp-160) cc_final: 0.5810 (mpt180) REVERT: G 672 MET cc_start: 0.3311 (ptm) cc_final: 0.3040 (pp-130) REVERT: H 457 MET cc_start: 0.8451 (ttm) cc_final: 0.7668 (ttm) REVERT: H 641 LYS cc_start: 0.5984 (mttm) cc_final: 0.5698 (tttp) REVERT: H 643 ILE cc_start: 0.6575 (mt) cc_final: 0.6027 (mp) outliers start: 0 outliers final: 0 residues processed: 914 average time/residue: 0.8973 time to fit residues: 957.7296 Evaluate side-chains 416 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 150 GLN A 269 HIS A 337 ASN A 359 GLN A 452 GLN B 114 GLN B 150 GLN B 269 HIS B 337 ASN B 452 GLN B 521 GLN C 143 GLN C 150 GLN C 269 HIS C 337 ASN C 359 GLN C 521 GLN C 652 ASN D 150 GLN D 269 HIS D 337 ASN D 452 GLN D 521 GLN E 143 GLN E 150 GLN E 269 HIS E 337 ASN E 359 GLN E 452 GLN F 150 GLN F 236 HIS F 269 HIS F 337 ASN F 359 GLN F 452 GLN F 587 HIS G 143 GLN G 150 GLN G 269 HIS ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN G 359 GLN G 452 GLN H 114 GLN H 150 GLN H 269 HIS H 337 ASN H 452 GLN H 575 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.192498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126688 restraints weight = 42144.818| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.01 r_work: 0.3156 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 39888 Z= 0.200 Angle : 0.633 8.322 53968 Z= 0.325 Chirality : 0.042 0.161 6168 Planarity : 0.005 0.046 6944 Dihedral : 6.875 55.616 5832 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.28 % Allowed : 9.74 % Favored : 87.98 % 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: -1.58 (0.11), residues: 4912 helix: -0.77 (0.08), residues: 3416 sheet: -1.07 (0.44), residues: 152 loop : -1.35 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 512 TYR 0.021 0.003 TYR E 380 PHE 0.037 0.003 PHE B 433 TRP 0.017 0.002 TRP B 214 HIS 0.010 0.002 HIS G 269 Details of bonding type rmsd covalent geometry : bond 0.00488 (39888) covalent geometry : angle 0.63325 (53968) hydrogen bonds : bond 0.04279 ( 2008) hydrogen bonds : angle 3.98697 ( 5904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 458 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6805 (mmt180) REVERT: A 247 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 259 PHE cc_start: 0.7854 (t80) cc_final: 0.7475 (t80) REVERT: A 307 ARG cc_start: 0.6891 (ttp-110) cc_final: 0.6631 (mtp-110) REVERT: A 328 GLN cc_start: 0.7924 (mt0) cc_final: 0.7676 (mm-40) REVERT: A 385 THR cc_start: 0.8358 (p) cc_final: 0.7896 (m) REVERT: A 630 MET cc_start: 0.3413 (ppp) cc_final: 0.2549 (ptm) REVERT: A 672 MET cc_start: 0.3234 (ptm) cc_final: 0.2743 (pp-130) REVERT: B 247 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: B 259 PHE cc_start: 0.7497 (t80) cc_final: 0.7061 (t80) REVERT: B 363 LYS cc_start: 0.7832 (tppp) cc_final: 0.7406 (tptt) REVERT: B 630 MET cc_start: 0.2930 (OUTLIER) cc_final: 0.2500 (ppp) REVERT: B 672 MET cc_start: 0.4021 (ttp) cc_final: 0.3644 (ttp) REVERT: C 159 ARG cc_start: 0.7766 (tpt170) cc_final: 0.7520 (tpt170) REVERT: C 162 ARG cc_start: 0.7206 (mtt180) cc_final: 0.6776 (mmt180) REVERT: C 259 PHE cc_start: 0.7880 (t80) cc_final: 0.7488 (t80) REVERT: C 285 ARG cc_start: 0.7915 (mpt180) cc_final: 0.7113 (mtm110) REVERT: C 289 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7611 (mtm110) REVERT: C 307 ARG cc_start: 0.6896 (ttp-110) cc_final: 0.6638 (mtp-110) REVERT: C 328 GLN cc_start: 0.7933 (mt0) cc_final: 0.7684 (mm-40) REVERT: C 520 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: C 630 MET cc_start: 0.4392 (ppp) cc_final: 0.3404 (ptm) REVERT: C 672 MET cc_start: 0.3139 (ptm) cc_final: 0.2825 (pp-130) REVERT: D 114 GLN cc_start: 0.6397 (mt0) cc_final: 0.5920 (tp-100) REVERT: D 162 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6857 (mmt180) REVERT: D 259 PHE cc_start: 0.7367 (t80) cc_final: 0.7023 (t80) REVERT: D 363 LYS cc_start: 0.7911 (tppp) cc_final: 0.7312 (tptt) REVERT: D 575 GLN cc_start: 0.6972 (tm-30) cc_final: 0.6638 (tm130) REVERT: D 630 MET cc_start: 0.2670 (OUTLIER) cc_final: 0.2468 (ppp) REVERT: E 147 LEU cc_start: 0.8239 (tp) cc_final: 0.7952 (tp) REVERT: E 247 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7437 (mt-10) REVERT: E 259 PHE cc_start: 0.7935 (t80) cc_final: 0.7542 (t80) REVERT: E 288 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7668 (mt-10) REVERT: E 328 GLN cc_start: 0.7908 (mt0) cc_final: 0.7609 (mm-40) REVERT: E 630 MET cc_start: 0.4136 (ppp) cc_final: 0.3246 (ptm) REVERT: E 672 MET cc_start: 0.3202 (ptm) cc_final: 0.2788 (pp-130) REVERT: F 191 MET cc_start: 0.8887 (mmm) cc_final: 0.8641 (mmm) REVERT: F 247 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: F 286 GLU cc_start: 0.7361 (mp0) cc_final: 0.7084 (mt-10) REVERT: F 328 GLN cc_start: 0.7830 (mt0) cc_final: 0.7610 (mm-40) REVERT: F 521 GLN cc_start: 0.8407 (tp40) cc_final: 0.8080 (tt0) REVERT: F 575 GLN cc_start: 0.6374 (pm20) cc_final: 0.6142 (tm130) REVERT: F 672 MET cc_start: 0.3351 (ptm) cc_final: 0.2959 (pp-130) REVERT: G 147 LEU cc_start: 0.8289 (tp) cc_final: 0.8044 (tp) REVERT: G 259 PHE cc_start: 0.7861 (t80) cc_final: 0.7493 (t80) REVERT: G 307 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6749 (mtp-110) REVERT: G 325 ASP cc_start: 0.7506 (t0) cc_final: 0.7304 (m-30) REVERT: G 403 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7484 (mtm-85) REVERT: G 569 ARG cc_start: 0.6415 (tpp-160) cc_final: 0.5968 (mmp-170) REVERT: G 630 MET cc_start: 0.3793 (ppp) cc_final: 0.2833 (ptm) REVERT: G 672 MET cc_start: 0.3152 (ptm) cc_final: 0.2728 (pp-130) REVERT: H 259 PHE cc_start: 0.7507 (t80) cc_final: 0.7147 (t80) REVERT: H 672 MET cc_start: 0.4195 (ttp) cc_final: 0.3854 (ptm) outliers start: 94 outliers final: 27 residues processed: 519 average time/residue: 0.9632 time to fit residues: 579.6661 Evaluate side-chains 357 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 266 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 434 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 443 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 48 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 337 ASN A 652 ASN B 337 ASN B 587 HIS C 337 ASN D 337 ASN D 587 HIS E 337 ASN E 652 ASN F 337 ASN F 587 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN G 575 GLN G 652 ASN H 337 ASN H 652 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.192180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124677 restraints weight = 42066.453| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.94 r_work: 0.3148 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39888 Z= 0.120 Angle : 0.501 7.180 53968 Z= 0.258 Chirality : 0.038 0.148 6168 Planarity : 0.004 0.033 6944 Dihedral : 6.299 52.817 5832 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.25 % Allowed : 11.87 % Favored : 85.88 % 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: -0.45 (0.12), residues: 4912 helix: 0.10 (0.09), residues: 3432 sheet: -0.77 (0.45), residues: 152 loop : -0.96 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 307 TYR 0.009 0.001 TYR B 429 PHE 0.015 0.001 PHE D 466 TRP 0.009 0.001 TRP A 412 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00286 (39888) covalent geometry : angle 0.50124 (53968) hydrogen bonds : bond 0.03314 ( 2008) hydrogen bonds : angle 3.58461 ( 5904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 359 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7258 (mp) REVERT: A 162 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6800 (mmt180) REVERT: A 217 ARG cc_start: 0.7544 (mmt-90) cc_final: 0.7090 (mmp80) REVERT: A 259 PHE cc_start: 0.7916 (t80) cc_final: 0.7566 (t80) REVERT: A 307 ARG cc_start: 0.6916 (ttp-110) cc_final: 0.6501 (mtp-110) REVERT: A 328 GLN cc_start: 0.7943 (mt0) cc_final: 0.7692 (mm-40) REVERT: A 395 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6413 (mtp180) REVERT: A 414 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: A 672 MET cc_start: 0.3230 (ptm) cc_final: 0.2776 (pp-130) REVERT: B 97 GLN cc_start: 0.7302 (tt0) cc_final: 0.6956 (mp10) REVERT: B 217 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7082 (mmp80) REVERT: B 285 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7060 (mtp-110) REVERT: B 307 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6574 (ttp-110) REVERT: B 363 LYS cc_start: 0.7850 (tppp) cc_final: 0.7527 (tptt) REVERT: B 521 GLN cc_start: 0.8347 (tp40) cc_final: 0.8053 (tt0) REVERT: B 630 MET cc_start: 0.2922 (OUTLIER) cc_final: 0.2494 (ppp) REVERT: B 672 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3721 (ttp) REVERT: C 129 LEU cc_start: 0.7596 (mt) cc_final: 0.7293 (mp) REVERT: C 162 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6849 (mmt180) REVERT: C 259 PHE cc_start: 0.7937 (t80) cc_final: 0.7569 (t80) REVERT: C 285 ARG cc_start: 0.7930 (mpt180) cc_final: 0.7092 (mtm110) REVERT: C 289 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7456 (mtm110) REVERT: C 307 ARG cc_start: 0.6931 (ttp-110) cc_final: 0.6530 (mtp-110) REVERT: C 328 GLN cc_start: 0.7940 (mt0) cc_final: 0.7683 (mm-40) REVERT: C 363 LYS cc_start: 0.7543 (tppp) cc_final: 0.7076 (tptt) REVERT: C 395 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6442 (mtp180) REVERT: C 630 MET cc_start: 0.4110 (ppp) cc_final: 0.3473 (ptm) REVERT: C 672 MET cc_start: 0.3433 (ptm) cc_final: 0.2907 (pp-130) REVERT: D 114 GLN cc_start: 0.6384 (mt0) cc_final: 0.5886 (tp-100) REVERT: D 162 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6832 (mmt180) REVERT: D 217 ARG cc_start: 0.7592 (mmt-90) cc_final: 0.7213 (mmp80) REVERT: D 247 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: D 285 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7061 (mtp-110) REVERT: D 363 LYS cc_start: 0.7815 (tppp) cc_final: 0.7463 (tptt) REVERT: D 520 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: D 521 GLN cc_start: 0.8297 (tp40) cc_final: 0.8042 (tt0) REVERT: D 575 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6744 (tm130) REVERT: D 630 MET cc_start: 0.2641 (OUTLIER) cc_final: 0.2432 (ppp) REVERT: D 672 MET cc_start: 0.4586 (ttp) cc_final: 0.4166 (ttp) REVERT: E 129 LEU cc_start: 0.7390 (mt) cc_final: 0.7024 (mp) REVERT: E 147 LEU cc_start: 0.8247 (tp) cc_final: 0.7996 (tp) REVERT: E 247 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7537 (mt-10) REVERT: E 259 PHE cc_start: 0.7939 (t80) cc_final: 0.7644 (t80) REVERT: E 288 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7637 (mt-10) REVERT: E 328 GLN cc_start: 0.7944 (mt0) cc_final: 0.7664 (mm-40) REVERT: E 363 LYS cc_start: 0.7705 (tppp) cc_final: 0.7262 (tptt) REVERT: E 395 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6399 (mtp180) REVERT: E 414 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: E 568 TYR cc_start: 0.7225 (p90) cc_final: 0.6918 (p90) REVERT: E 569 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6729 (mmp-170) REVERT: E 630 MET cc_start: 0.3993 (ppp) cc_final: 0.3318 (ptm) REVERT: E 672 MET cc_start: 0.3445 (ptm) cc_final: 0.2945 (pp-130) REVERT: F 97 GLN cc_start: 0.7248 (tt0) cc_final: 0.7027 (mp10) REVERT: F 217 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7367 (mmp80) REVERT: F 286 GLU cc_start: 0.7214 (mp0) cc_final: 0.6939 (mt-10) REVERT: F 328 GLN cc_start: 0.7813 (mt0) cc_final: 0.7601 (mm-40) REVERT: F 363 LYS cc_start: 0.7802 (tppp) cc_final: 0.7394 (tptt) REVERT: F 520 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: F 521 GLN cc_start: 0.8337 (tp40) cc_final: 0.8063 (tt0) REVERT: F 587 HIS cc_start: 0.6098 (m90) cc_final: 0.5898 (m-70) REVERT: F 672 MET cc_start: 0.3366 (ptm) cc_final: 0.2847 (pp-130) REVERT: G 162 ARG cc_start: 0.7350 (mtt180) cc_final: 0.6963 (mmt180) REVERT: G 259 PHE cc_start: 0.8080 (t80) cc_final: 0.7764 (t80) REVERT: G 307 ARG cc_start: 0.6862 (ttp-110) cc_final: 0.6577 (mtp-110) REVERT: G 395 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6414 (mtp180) REVERT: G 403 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7403 (mtm-85) REVERT: G 414 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: G 520 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: G 569 ARG cc_start: 0.6472 (tpp-160) cc_final: 0.5993 (mmp-170) REVERT: G 630 MET cc_start: 0.4133 (ppp) cc_final: 0.3885 (mpp) REVERT: G 672 MET cc_start: 0.3075 (ptm) cc_final: 0.2664 (pp-130) REVERT: H 259 PHE cc_start: 0.7641 (t80) cc_final: 0.7343 (t80) REVERT: H 285 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7489 (mpp-170) REVERT: H 520 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: H 521 GLN cc_start: 0.8337 (tp40) cc_final: 0.8076 (tt0) REVERT: H 672 MET cc_start: 0.4277 (ttp) cc_final: 0.3896 (ttp) outliers start: 93 outliers final: 23 residues processed: 425 average time/residue: 0.8662 time to fit residues: 432.3343 Evaluate side-chains 353 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 691 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 520 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 468 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 452 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 274 optimal weight: 0.9980 chunk 466 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 406 optimal weight: 0.2980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 337 ASN B 587 HIS C 156 ASN C 337 ASN C 383 ASN D 337 ASN D 587 HIS E 337 ASN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN G 337 ASN G 575 GLN H 337 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.192536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123949 restraints weight = 42025.966| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.85 r_work: 0.3149 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39888 Z= 0.101 Angle : 0.472 7.418 53968 Z= 0.243 Chirality : 0.038 0.163 6168 Planarity : 0.003 0.032 6944 Dihedral : 5.852 52.902 5832 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.71 % Allowed : 11.89 % Favored : 85.39 % 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: 0.29 (0.12), residues: 4912 helix: 0.63 (0.09), residues: 3432 sheet: -0.44 (0.47), residues: 152 loop : -0.65 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 289 TYR 0.008 0.001 TYR D 429 PHE 0.012 0.001 PHE D 466 TRP 0.006 0.001 TRP F 638 HIS 0.004 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00235 (39888) covalent geometry : angle 0.47180 (53968) hydrogen bonds : bond 0.03031 ( 2008) hydrogen bonds : angle 3.40438 ( 5904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 358 time to evaluate : 1.453 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 129 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7264 (mp) REVERT: A 162 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6769 (mmt180) REVERT: A 217 ARG cc_start: 0.7520 (mmt-90) cc_final: 0.7104 (mmp80) REVERT: A 224 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7645 (mtt180) REVERT: A 259 PHE cc_start: 0.7814 (t80) cc_final: 0.7605 (t80) REVERT: A 307 ARG cc_start: 0.6867 (ttp-110) cc_final: 0.6537 (mtp-110) REVERT: A 363 LYS cc_start: 0.7590 (tppp) cc_final: 0.7167 (tptt) REVERT: A 395 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6479 (mtp180) REVERT: A 403 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7212 (ptt180) REVERT: A 414 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: A 520 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: A 672 MET cc_start: 0.3201 (ptm) cc_final: 0.2760 (pp-130) REVERT: B 97 GLN cc_start: 0.7217 (tt0) cc_final: 0.6711 (mp10) REVERT: B 100 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5703 (mt-10) REVERT: B 217 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7036 (mmp80) REVERT: B 285 ARG cc_start: 0.7971 (mpt180) cc_final: 0.6971 (mtp-110) REVERT: B 307 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6583 (ttp-110) REVERT: B 363 LYS cc_start: 0.7775 (tppp) cc_final: 0.7514 (tptt) REVERT: B 520 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: B 672 MET cc_start: 0.4317 (OUTLIER) cc_final: 0.3803 (ttt) REVERT: C 129 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7263 (mp) REVERT: C 159 ARG cc_start: 0.7630 (tpt170) cc_final: 0.7314 (tpt170) REVERT: C 162 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6821 (mmt180) REVERT: C 224 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7662 (mtt180) REVERT: C 259 PHE cc_start: 0.7919 (t80) cc_final: 0.7688 (t80) REVERT: C 285 ARG cc_start: 0.7916 (mpt180) cc_final: 0.7117 (mtm110) REVERT: C 289 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7445 (mtm110) REVERT: C 307 ARG cc_start: 0.6872 (ttp-110) cc_final: 0.6536 (mtp-110) REVERT: C 328 GLN cc_start: 0.7962 (mt0) cc_final: 0.7693 (mm-40) REVERT: C 395 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6473 (mtp180) REVERT: C 403 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7431 (ttp80) REVERT: C 484 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7970 (ttp-170) REVERT: C 568 TYR cc_start: 0.7180 (p90) cc_final: 0.6821 (p90) REVERT: C 630 MET cc_start: 0.4142 (ppp) cc_final: 0.3466 (ptm) REVERT: C 672 MET cc_start: 0.3400 (ptm) cc_final: 0.2895 (pp-130) REVERT: D 162 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6918 (mmt180) REVERT: D 217 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7241 (mmp80) REVERT: D 285 ARG cc_start: 0.7909 (mpt180) cc_final: 0.6972 (mtp-110) REVERT: D 363 LYS cc_start: 0.7735 (tppp) cc_final: 0.7448 (tptt) REVERT: D 385 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8328 (m) REVERT: D 520 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: D 521 GLN cc_start: 0.8342 (tp40) cc_final: 0.8036 (tt0) REVERT: D 575 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6684 (tm130) REVERT: D 630 MET cc_start: 0.2635 (OUTLIER) cc_final: 0.2434 (ppp) REVERT: D 672 MET cc_start: 0.4687 (ttp) cc_final: 0.4311 (ttp) REVERT: E 104 LEU cc_start: 0.7325 (mt) cc_final: 0.7094 (mp) REVERT: E 288 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 328 GLN cc_start: 0.7947 (mt0) cc_final: 0.7666 (mm-40) REVERT: E 395 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6500 (mtp180) REVERT: E 403 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7311 (ptt180) REVERT: E 414 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: E 520 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: E 568 TYR cc_start: 0.7275 (p90) cc_final: 0.6796 (p90) REVERT: E 630 MET cc_start: 0.3865 (ppp) cc_final: 0.3165 (ptm) REVERT: E 672 MET cc_start: 0.3420 (ptm) cc_final: 0.2936 (pp-130) REVERT: F 97 GLN cc_start: 0.7345 (tt0) cc_final: 0.7111 (mp10) REVERT: F 217 ARG cc_start: 0.7588 (mmt-90) cc_final: 0.7194 (mmp80) REVERT: F 285 ARG cc_start: 0.7968 (mpt180) cc_final: 0.7121 (mtp-110) REVERT: F 328 GLN cc_start: 0.7790 (mt0) cc_final: 0.7558 (mm-40) REVERT: F 363 LYS cc_start: 0.7791 (tppp) cc_final: 0.7507 (ttmm) REVERT: F 520 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: F 521 GLN cc_start: 0.8350 (tp40) cc_final: 0.8049 (tt0) REVERT: F 672 MET cc_start: 0.3402 (ptm) cc_final: 0.2949 (pp-130) REVERT: G 129 LEU cc_start: 0.7525 (mt) cc_final: 0.7238 (mp) REVERT: G 162 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6920 (mmt180) REVERT: G 217 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7134 (mmp80) REVERT: G 259 PHE cc_start: 0.8198 (t80) cc_final: 0.7886 (t80) REVERT: G 307 ARG cc_start: 0.6828 (ttp-110) cc_final: 0.6494 (mtp-110) REVERT: G 395 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6521 (mtp180) REVERT: G 403 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7367 (ptt180) REVERT: G 414 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: G 520 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7923 (tp30) REVERT: G 569 ARG cc_start: 0.6507 (tpp-160) cc_final: 0.6068 (mmp-170) REVERT: G 672 MET cc_start: 0.3059 (ptm) cc_final: 0.2670 (pp-130) REVERT: H 100 GLU cc_start: 0.5843 (mt-10) cc_final: 0.5451 (tp30) REVERT: H 217 ARG cc_start: 0.7660 (mmt-90) cc_final: 0.7245 (mmp80) REVERT: H 259 PHE cc_start: 0.7613 (t80) cc_final: 0.7356 (t80) REVERT: H 285 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7400 (mpp-170) REVERT: H 520 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: H 521 GLN cc_start: 0.8328 (tp40) cc_final: 0.8067 (tt0) REVERT: H 672 MET cc_start: 0.4483 (ttp) cc_final: 0.4072 (ttp) outliers start: 112 outliers final: 27 residues processed: 436 average time/residue: 0.8866 time to fit residues: 452.9873 Evaluate side-chains 368 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 520 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 392 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 490 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 359 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 547 HIS B 337 ASN C 337 ASN C 547 HIS D 337 ASN E 337 ASN E 547 HIS F 337 ASN F 575 GLN F 587 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN G 547 HIS G 575 GLN H 337 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.190667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120143 restraints weight = 41797.029| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.83 r_work: 0.3107 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39888 Z= 0.135 Angle : 0.517 8.345 53968 Z= 0.264 Chirality : 0.039 0.151 6168 Planarity : 0.004 0.044 6944 Dihedral : 6.033 52.454 5832 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.69 % Allowed : 12.23 % Favored : 85.08 % 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: 0.54 (0.12), residues: 4912 helix: 0.81 (0.09), residues: 3440 sheet: -0.41 (0.47), residues: 152 loop : -0.53 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 307 TYR 0.010 0.002 TYR H 380 PHE 0.016 0.002 PHE G 308 TRP 0.006 0.001 TRP D 214 HIS 0.005 0.001 HIS F 587 Details of bonding type rmsd covalent geometry : bond 0.00329 (39888) covalent geometry : angle 0.51742 (53968) hydrogen bonds : bond 0.03467 ( 2008) hydrogen bonds : angle 3.50601 ( 5904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 351 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7296 (mp) REVERT: A 162 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6778 (mmt180) REVERT: A 217 ARG cc_start: 0.7573 (mmt-90) cc_final: 0.7161 (mmp80) REVERT: A 224 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7542 (mmm-85) REVERT: A 307 ARG cc_start: 0.6854 (ttp-110) cc_final: 0.6454 (mtp-110) REVERT: A 414 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: A 520 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: A 672 MET cc_start: 0.3118 (ptm) cc_final: 0.2727 (pp-130) REVERT: B 97 GLN cc_start: 0.7401 (tt0) cc_final: 0.6830 (mp10) REVERT: B 100 GLU cc_start: 0.6050 (mt-10) cc_final: 0.5721 (mt-10) REVERT: B 217 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7158 (mmp80) REVERT: B 282 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: B 285 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6984 (mtp-110) REVERT: B 363 LYS cc_start: 0.7760 (tppp) cc_final: 0.7499 (tptt) REVERT: B 520 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: B 521 GLN cc_start: 0.8324 (tp40) cc_final: 0.8051 (tt0) REVERT: B 575 GLN cc_start: 0.7037 (tm-30) cc_final: 0.6703 (tm130) REVERT: B 672 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.3776 (ttt) REVERT: C 129 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7281 (mp) REVERT: C 159 ARG cc_start: 0.7699 (tpt170) cc_final: 0.7402 (tpt170) REVERT: C 162 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6833 (mmt180) REVERT: C 259 PHE cc_start: 0.8055 (t80) cc_final: 0.7826 (t80) REVERT: C 285 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7083 (mtm110) REVERT: C 289 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7624 (ttm-80) REVERT: C 307 ARG cc_start: 0.6831 (ttp-110) cc_final: 0.6372 (mtp-110) REVERT: C 328 GLN cc_start: 0.7929 (mt0) cc_final: 0.7647 (mm-40) REVERT: C 484 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7999 (ttp-170) REVERT: C 672 MET cc_start: 0.3390 (ptm) cc_final: 0.2899 (pp-130) REVERT: D 114 GLN cc_start: 0.6482 (mt0) cc_final: 0.5928 (tp-100) REVERT: D 162 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6789 (mmt180) REVERT: D 217 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7183 (mmp80) REVERT: D 285 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7003 (mtp-110) REVERT: D 363 LYS cc_start: 0.7743 (tppp) cc_final: 0.7434 (tptt) REVERT: D 520 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: D 521 GLN cc_start: 0.8345 (tp40) cc_final: 0.8050 (tt0) REVERT: D 575 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6748 (tm130) REVERT: D 630 MET cc_start: 0.2649 (OUTLIER) cc_final: 0.2448 (ppp) REVERT: D 672 MET cc_start: 0.4648 (ttp) cc_final: 0.4307 (ttp) REVERT: E 129 LEU cc_start: 0.7502 (mt) cc_final: 0.7179 (mp) REVERT: E 288 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 328 GLN cc_start: 0.7930 (mt0) cc_final: 0.7646 (mm-40) REVERT: E 403 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7416 (ptt180) REVERT: E 414 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: E 520 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: E 569 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6832 (mmp-170) REVERT: E 630 MET cc_start: 0.3921 (ppp) cc_final: 0.3206 (ptm) REVERT: E 672 MET cc_start: 0.3438 (ptm) cc_final: 0.2949 (pp-130) REVERT: F 97 GLN cc_start: 0.7413 (tt0) cc_final: 0.7003 (mp10) REVERT: F 100 GLU cc_start: 0.6255 (mt-10) cc_final: 0.5668 (mt-10) REVERT: F 114 GLN cc_start: 0.6526 (mt0) cc_final: 0.6019 (tp-100) REVERT: F 149 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7153 (tp30) REVERT: F 155 GLU cc_start: 0.7306 (mp0) cc_final: 0.6656 (mp0) REVERT: F 217 ARG cc_start: 0.7611 (mmt-90) cc_final: 0.7326 (mmp80) REVERT: F 285 ARG cc_start: 0.7944 (mpt180) cc_final: 0.7129 (mtp-110) REVERT: F 328 GLN cc_start: 0.7876 (mt0) cc_final: 0.7528 (mm-40) REVERT: F 363 LYS cc_start: 0.7790 (tppp) cc_final: 0.7540 (ttmm) REVERT: F 520 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: F 521 GLN cc_start: 0.8372 (tp40) cc_final: 0.8056 (tt0) REVERT: F 672 MET cc_start: 0.3381 (ptm) cc_final: 0.2968 (pp-130) REVERT: G 259 PHE cc_start: 0.8230 (t80) cc_final: 0.7948 (t80) REVERT: G 307 ARG cc_start: 0.6920 (ttp-110) cc_final: 0.6623 (mtp-110) REVERT: G 361 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7488 (ptmt) REVERT: G 403 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7296 (ptt180) REVERT: G 414 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: G 520 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: G 569 ARG cc_start: 0.6518 (tpp-160) cc_final: 0.6194 (tpp-160) REVERT: G 672 MET cc_start: 0.3174 (ptm) cc_final: 0.2778 (pp-130) REVERT: H 100 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5639 (tp30) REVERT: H 217 ARG cc_start: 0.7590 (mmt-90) cc_final: 0.7183 (mmp80) REVERT: H 259 PHE cc_start: 0.7859 (t80) cc_final: 0.7649 (t80) REVERT: H 282 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: H 285 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7412 (mpp-170) REVERT: H 520 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: H 521 GLN cc_start: 0.8358 (tp40) cc_final: 0.8068 (tt0) REVERT: H 672 MET cc_start: 0.4515 (ttp) cc_final: 0.4067 (ttp) outliers start: 111 outliers final: 33 residues processed: 432 average time/residue: 0.8652 time to fit residues: 437.6201 Evaluate side-chains 385 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 329 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 520 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 192 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 345 optimal weight: 0.0770 chunk 176 optimal weight: 4.9990 chunk 402 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 334 optimal weight: 0.0030 chunk 140 optimal weight: 0.8980 chunk 423 optimal weight: 0.8980 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 337 ASN F 337 ASN F 587 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN G 575 GLN H 337 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124818 restraints weight = 42310.079| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.03 r_work: 0.3143 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 39888 Z= 0.089 Angle : 0.454 7.770 53968 Z= 0.231 Chirality : 0.037 0.140 6168 Planarity : 0.003 0.036 6944 Dihedral : 5.498 51.357 5832 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.03 % Allowed : 13.11 % Favored : 84.86 % 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: 1.02 (0.12), residues: 4912 helix: 1.19 (0.09), residues: 3416 sheet: -0.21 (0.47), residues: 152 loop : -0.37 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 289 TYR 0.006 0.001 TYR E 503 PHE 0.019 0.001 PHE E 259 TRP 0.006 0.001 TRP A 638 HIS 0.005 0.001 HIS F 587 Details of bonding type rmsd covalent geometry : bond 0.00198 (39888) covalent geometry : angle 0.45358 (53968) hydrogen bonds : bond 0.02798 ( 2008) hydrogen bonds : angle 3.34077 ( 5904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 351 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 162 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6775 (mmt180) REVERT: A 217 ARG cc_start: 0.7452 (mmt-90) cc_final: 0.7109 (mmp80) REVERT: A 224 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7622 (mtt180) REVERT: A 307 ARG cc_start: 0.6811 (ttp-110) cc_final: 0.6449 (mtp-110) REVERT: A 395 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6262 (mtp180) REVERT: A 403 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7111 (ptt180) REVERT: A 414 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: A 569 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6319 (mmp-170) REVERT: A 672 MET cc_start: 0.3244 (ptm) cc_final: 0.2816 (pp-130) REVERT: B 97 GLN cc_start: 0.7295 (tt0) cc_final: 0.6775 (mp10) REVERT: B 100 GLU cc_start: 0.6045 (mt-10) cc_final: 0.5699 (mt-10) REVERT: B 217 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.6889 (mmp80) REVERT: B 249 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8121 (mmt90) REVERT: B 285 ARG cc_start: 0.7885 (mpt180) cc_final: 0.6958 (mtp-110) REVERT: B 363 LYS cc_start: 0.7731 (tppp) cc_final: 0.7498 (tptt) REVERT: B 520 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: B 521 GLN cc_start: 0.8357 (tp40) cc_final: 0.8071 (tt0) REVERT: B 575 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6572 (tm130) REVERT: B 672 MET cc_start: 0.4305 (OUTLIER) cc_final: 0.3840 (ttt) REVERT: C 129 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7332 (mp) REVERT: C 162 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6818 (mmt180) REVERT: C 217 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.7034 (mmp80) REVERT: C 224 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7624 (mtt180) REVERT: C 259 PHE cc_start: 0.8002 (t80) cc_final: 0.7709 (t80) REVERT: C 289 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7488 (ttm-80) REVERT: C 395 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: C 403 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7243 (ptt180) REVERT: C 414 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: C 672 MET cc_start: 0.3374 (ptm) cc_final: 0.2887 (pp-130) REVERT: D 114 GLN cc_start: 0.6383 (mt0) cc_final: 0.5885 (tp-100) REVERT: D 162 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6880 (mmt180) REVERT: D 217 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.7233 (mmp80) REVERT: D 249 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8112 (mmt90) REVERT: D 285 ARG cc_start: 0.7906 (mpt180) cc_final: 0.7028 (mtp-110) REVERT: D 307 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6798 (ttp-110) REVERT: D 363 LYS cc_start: 0.7766 (tppp) cc_final: 0.7477 (tptt) REVERT: D 385 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8277 (m) REVERT: D 520 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: D 521 GLN cc_start: 0.8366 (tp40) cc_final: 0.8048 (tt0) REVERT: D 575 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6619 (tm130) REVERT: D 672 MET cc_start: 0.4739 (ttp) cc_final: 0.4394 (ttp) REVERT: E 104 LEU cc_start: 0.7254 (mt) cc_final: 0.7014 (mp) REVERT: E 129 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7211 (mp) REVERT: E 288 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7734 (mt-10) REVERT: E 395 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6280 (mtp180) REVERT: E 403 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7301 (ptt180) REVERT: E 414 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: E 568 TYR cc_start: 0.7209 (p90) cc_final: 0.6815 (p90) REVERT: E 569 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6433 (mmp-170) REVERT: E 672 MET cc_start: 0.3416 (ptm) cc_final: 0.2927 (pp-130) REVERT: F 97 GLN cc_start: 0.7419 (tt0) cc_final: 0.7167 (mp10) REVERT: F 111 GLU cc_start: 0.6341 (mp0) cc_final: 0.5846 (mt-10) REVERT: F 114 GLN cc_start: 0.6506 (mt0) cc_final: 0.5932 (tp-100) REVERT: F 155 GLU cc_start: 0.7340 (mp0) cc_final: 0.6680 (mp0) REVERT: F 217 ARG cc_start: 0.7573 (mmt-90) cc_final: 0.7197 (mmp80) REVERT: F 249 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8095 (mmt90) REVERT: F 285 ARG cc_start: 0.7918 (mpt180) cc_final: 0.7106 (mtp-110) REVERT: F 328 GLN cc_start: 0.7845 (mt0) cc_final: 0.7586 (mm-40) REVERT: F 363 LYS cc_start: 0.7697 (tppp) cc_final: 0.7434 (tptt) REVERT: F 520 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: F 521 GLN cc_start: 0.8358 (tp40) cc_final: 0.8044 (tt0) REVERT: F 672 MET cc_start: 0.3447 (ptm) cc_final: 0.3000 (pp-130) REVERT: G 129 LEU cc_start: 0.7446 (mt) cc_final: 0.7231 (mp) REVERT: G 162 ARG cc_start: 0.7338 (mtt180) cc_final: 0.6803 (mmt180) REVERT: G 217 ARG cc_start: 0.7939 (mmt-90) cc_final: 0.7137 (mmp80) REVERT: G 224 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7616 (mtt180) REVERT: G 259 PHE cc_start: 0.8136 (t80) cc_final: 0.7892 (t80) REVERT: G 361 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7443 (ptmt) REVERT: G 395 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6224 (mtp180) REVERT: G 403 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7269 (ptt180) REVERT: G 414 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: G 545 MET cc_start: 0.5838 (ptt) cc_final: 0.5546 (ppp) REVERT: G 569 ARG cc_start: 0.6512 (tpp-160) cc_final: 0.6133 (mmm160) REVERT: G 672 MET cc_start: 0.3065 (ptm) cc_final: 0.2679 (pp-130) REVERT: H 97 GLN cc_start: 0.6668 (mp10) cc_final: 0.6129 (mp10) REVERT: H 100 GLU cc_start: 0.5904 (mt-10) cc_final: 0.5627 (mt-10) REVERT: H 217 ARG cc_start: 0.7670 (mmt-90) cc_final: 0.7156 (mmp80) REVERT: H 249 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7998 (mmt90) REVERT: H 285 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7455 (mpp-170) REVERT: H 520 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: H 521 GLN cc_start: 0.8338 (tp40) cc_final: 0.8062 (tt0) REVERT: H 672 MET cc_start: 0.4455 (ttp) cc_final: 0.4079 (ttp) outliers start: 84 outliers final: 28 residues processed: 414 average time/residue: 0.8984 time to fit residues: 435.9921 Evaluate side-chains 383 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 366 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 415 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 425 optimal weight: 10.0000 chunk 355 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 255 optimal weight: 1.9990 chunk 382 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 486 ASN B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN E 97 GLN E 486 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 ASN G 486 ASN G 575 GLN H 337 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.190938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119804 restraints weight = 41880.835| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.81 r_work: 0.3117 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39888 Z= 0.118 Angle : 0.501 8.563 53968 Z= 0.254 Chirality : 0.038 0.150 6168 Planarity : 0.003 0.038 6944 Dihedral : 5.657 51.905 5832 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.23 % Allowed : 12.96 % Favored : 84.81 % 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: 1.05 (0.12), residues: 4912 helix: 1.17 (0.09), residues: 3448 sheet: -0.20 (0.47), residues: 152 loop : -0.26 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 289 TYR 0.009 0.001 TYR E 429 PHE 0.022 0.001 PHE E 259 TRP 0.005 0.001 TRP G 253 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00281 (39888) covalent geometry : angle 0.50101 (53968) hydrogen bonds : bond 0.03247 ( 2008) hydrogen bonds : angle 3.43988 ( 5904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 341 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7279 (mp) REVERT: A 162 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6769 (mmt180) REVERT: A 217 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.7079 (mmp80) REVERT: A 224 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7395 (mmm-85) REVERT: A 307 ARG cc_start: 0.6778 (ttp-110) cc_final: 0.6491 (mtp-110) REVERT: A 395 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6254 (mtp180) REVERT: A 403 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7169 (ptt180) REVERT: A 414 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: A 520 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: A 569 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6339 (mmp-170) REVERT: A 672 MET cc_start: 0.3061 (ptm) cc_final: 0.2693 (pp-130) REVERT: B 97 GLN cc_start: 0.7316 (tt0) cc_final: 0.6779 (mp10) REVERT: B 100 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5680 (mt-10) REVERT: B 217 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.6911 (mmp80) REVERT: B 249 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.8152 (mmt90) REVERT: B 285 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6999 (mtp-110) REVERT: B 288 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 363 LYS cc_start: 0.7758 (tppp) cc_final: 0.7518 (tptt) REVERT: B 520 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: B 521 GLN cc_start: 0.8310 (tp40) cc_final: 0.8025 (tt0) REVERT: B 569 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.6095 (mmp-170) REVERT: B 575 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6666 (tm130) REVERT: B 672 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.3801 (ttt) REVERT: C 129 LEU cc_start: 0.7572 (mt) cc_final: 0.7306 (mp) REVERT: C 162 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6794 (mmt180) REVERT: C 259 PHE cc_start: 0.8112 (t80) cc_final: 0.7901 (t80) REVERT: C 289 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7605 (ttm-80) REVERT: C 395 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6236 (mtp180) REVERT: C 403 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7210 (ptt180) REVERT: C 414 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: C 484 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7983 (ttp-170) REVERT: C 630 MET cc_start: 0.3677 (OUTLIER) cc_final: 0.3060 (ppp) REVERT: C 672 MET cc_start: 0.3381 (ptm) cc_final: 0.2884 (pp-130) REVERT: D 114 GLN cc_start: 0.6430 (mt0) cc_final: 0.5869 (tp-100) REVERT: D 162 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6787 (mmt180) REVERT: D 217 ARG cc_start: 0.7638 (mmt-90) cc_final: 0.7256 (mmp80) REVERT: D 249 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8173 (mmt90) REVERT: D 285 ARG cc_start: 0.7904 (mpt180) cc_final: 0.7041 (mtp-110) REVERT: D 288 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7426 (mt-10) REVERT: D 307 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7132 (mtp-110) REVERT: D 363 LYS cc_start: 0.7762 (tppp) cc_final: 0.7466 (tptt) REVERT: D 385 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8321 (m) REVERT: D 520 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: D 521 GLN cc_start: 0.8353 (tp40) cc_final: 0.8012 (tt0) REVERT: D 575 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6757 (tm130) REVERT: D 672 MET cc_start: 0.4739 (ttp) cc_final: 0.4363 (ttp) REVERT: E 97 GLN cc_start: 0.6515 (mp-120) cc_final: 0.6296 (mp10) REVERT: E 100 GLU cc_start: 0.6036 (tp30) cc_final: 0.5836 (tp30) REVERT: E 129 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7168 (mp) REVERT: E 162 ARG cc_start: 0.6360 (mmt180) cc_final: 0.6052 (mmt180) REVERT: E 288 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7802 (mt-10) REVERT: E 395 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6211 (mtp180) REVERT: E 403 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7341 (ptt180) REVERT: E 414 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: E 568 TYR cc_start: 0.7277 (p90) cc_final: 0.6983 (p90) REVERT: E 569 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6483 (mmp-170) REVERT: E 589 PHE cc_start: 0.7129 (m-10) cc_final: 0.6906 (m-10) REVERT: E 672 MET cc_start: 0.3407 (ptm) cc_final: 0.2914 (pp-130) REVERT: F 97 GLN cc_start: 0.7406 (tt0) cc_final: 0.7155 (mp10) REVERT: F 114 GLN cc_start: 0.6478 (mt0) cc_final: 0.5920 (tp-100) REVERT: F 155 GLU cc_start: 0.7347 (mp0) cc_final: 0.6660 (mp0) REVERT: F 159 ARG cc_start: 0.7876 (tpt170) cc_final: 0.7629 (tpt170) REVERT: F 217 ARG cc_start: 0.7545 (mmt-90) cc_final: 0.7174 (mmp80) REVERT: F 249 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.8179 (mmt90) REVERT: F 285 ARG cc_start: 0.7980 (mpt180) cc_final: 0.7124 (mtp-110) REVERT: F 288 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7385 (mt-10) REVERT: F 328 GLN cc_start: 0.7870 (mt0) cc_final: 0.7526 (mm-40) REVERT: F 363 LYS cc_start: 0.7680 (tppp) cc_final: 0.7410 (tptt) REVERT: F 520 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: F 521 GLN cc_start: 0.8386 (tp40) cc_final: 0.8046 (tt0) REVERT: F 672 MET cc_start: 0.3431 (ptm) cc_final: 0.2980 (pp-130) REVERT: G 162 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6779 (mmt180) REVERT: G 217 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7106 (mmp80) REVERT: G 259 PHE cc_start: 0.8190 (t80) cc_final: 0.7958 (t80) REVERT: G 361 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7506 (ptmt) REVERT: G 395 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6281 (mtp180) REVERT: G 403 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7283 (ptt180) REVERT: G 414 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: G 545 MET cc_start: 0.5880 (ptt) cc_final: 0.5582 (ppp) REVERT: G 569 ARG cc_start: 0.6528 (tpp-160) cc_final: 0.6161 (mmm160) REVERT: G 672 MET cc_start: 0.3053 (ptm) cc_final: 0.2667 (pp-130) REVERT: H 97 GLN cc_start: 0.6680 (mp10) cc_final: 0.6144 (mp10) REVERT: H 217 ARG cc_start: 0.7512 (mmt-90) cc_final: 0.7095 (mmp80) REVERT: H 249 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7986 (mmt90) REVERT: H 259 PHE cc_start: 0.8011 (t80) cc_final: 0.7752 (t80) REVERT: H 282 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: H 285 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7426 (mpp-170) REVERT: H 288 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7258 (mt-10) REVERT: H 520 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7915 (tp30) REVERT: H 521 GLN cc_start: 0.8359 (tp40) cc_final: 0.8049 (tt0) REVERT: H 672 MET cc_start: 0.4597 (ttp) cc_final: 0.4065 (ttt) outliers start: 92 outliers final: 38 residues processed: 413 average time/residue: 0.8919 time to fit residues: 431.5250 Evaluate side-chains 392 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 463 optimal weight: 0.3980 chunk 483 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 453 optimal weight: 1.9990 chunk 437 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN D 337 ASN E 337 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN H 337 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.191789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120653 restraints weight = 41918.488| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.79 r_work: 0.3144 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39888 Z= 0.100 Angle : 0.483 14.288 53968 Z= 0.243 Chirality : 0.038 0.161 6168 Planarity : 0.003 0.044 6944 Dihedral : 5.441 51.390 5832 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.06 % Allowed : 13.11 % Favored : 84.84 % 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: 1.25 (0.12), residues: 4912 helix: 1.32 (0.09), residues: 3432 sheet: -0.13 (0.47), residues: 152 loop : -0.16 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 289 TYR 0.007 0.001 TYR G 429 PHE 0.032 0.001 PHE E 259 TRP 0.006 0.001 TRP A 638 HIS 0.002 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00230 (39888) covalent geometry : angle 0.48350 (53968) hydrogen bonds : bond 0.02981 ( 2008) hydrogen bonds : angle 3.39370 ( 5904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 341 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 162 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6750 (mmt180) REVERT: A 217 ARG cc_start: 0.7480 (mmt-90) cc_final: 0.7143 (mmp80) REVERT: A 307 ARG cc_start: 0.6814 (ttp-110) cc_final: 0.6563 (mtp-110) REVERT: A 395 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6294 (mtp180) REVERT: A 403 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7089 (ptt180) REVERT: A 414 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: A 520 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: A 545 MET cc_start: 0.5873 (ptt) cc_final: 0.5596 (ppp) REVERT: A 569 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6314 (mmp-170) REVERT: A 630 MET cc_start: 0.2854 (ppp) cc_final: 0.2071 (ttp) REVERT: A 672 MET cc_start: 0.3037 (ptm) cc_final: 0.2574 (pp-130) REVERT: B 97 GLN cc_start: 0.7299 (tt0) cc_final: 0.6769 (mp10) REVERT: B 217 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.6831 (mmp80) REVERT: B 249 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8172 (mmt90) REVERT: B 285 ARG cc_start: 0.7889 (mpt180) cc_final: 0.7008 (mtp-110) REVERT: B 363 LYS cc_start: 0.7782 (tppp) cc_final: 0.7569 (tptt) REVERT: B 520 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: B 521 GLN cc_start: 0.8346 (tp40) cc_final: 0.8051 (tt0) REVERT: B 569 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.6037 (mmp-170) REVERT: B 575 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6502 (tm130) REVERT: B 672 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.3739 (ttt) REVERT: C 159 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7132 (tpp80) REVERT: C 162 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6771 (mmt180) REVERT: C 217 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7004 (mmp80) REVERT: C 289 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7512 (ttm-80) REVERT: C 307 ARG cc_start: 0.6952 (mtp-110) cc_final: 0.6276 (mtm110) REVERT: C 395 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6246 (mtp180) REVERT: C 400 GLU cc_start: 0.6878 (pm20) cc_final: 0.6676 (pp20) REVERT: C 403 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7177 (ptt180) REVERT: C 414 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: C 545 MET cc_start: 0.5849 (ptt) cc_final: 0.5539 (ppp) REVERT: C 672 MET cc_start: 0.3347 (ptm) cc_final: 0.2881 (pp-130) REVERT: D 114 GLN cc_start: 0.6378 (mt0) cc_final: 0.5843 (tp-100) REVERT: D 162 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6766 (mmt180) REVERT: D 217 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.7239 (mmp80) REVERT: D 249 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8172 (mmt90) REVERT: D 285 ARG cc_start: 0.7931 (mpt180) cc_final: 0.7050 (mtp-110) REVERT: D 307 ARG cc_start: 0.7362 (mtm110) cc_final: 0.7122 (mtp-110) REVERT: D 363 LYS cc_start: 0.7779 (tppp) cc_final: 0.7516 (tptt) REVERT: D 385 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8324 (m) REVERT: D 520 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: D 521 GLN cc_start: 0.8296 (tp40) cc_final: 0.7987 (tt0) REVERT: D 575 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6701 (tm130) REVERT: D 672 MET cc_start: 0.4651 (ttp) cc_final: 0.4292 (ttp) REVERT: E 100 GLU cc_start: 0.6044 (tp30) cc_final: 0.5821 (tp30) REVERT: E 129 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7111 (mp) REVERT: E 288 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7737 (mt-10) REVERT: E 395 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6286 (mtp180) REVERT: E 403 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7300 (ptt180) REVERT: E 414 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: E 545 MET cc_start: 0.5875 (ptt) cc_final: 0.5569 (ppp) REVERT: E 568 TYR cc_start: 0.7226 (p90) cc_final: 0.6905 (p90) REVERT: E 569 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6449 (mmp-170) REVERT: E 672 MET cc_start: 0.3376 (ptm) cc_final: 0.2895 (pp-130) REVERT: F 97 GLN cc_start: 0.7381 (tt0) cc_final: 0.7130 (mp10) REVERT: F 100 GLU cc_start: 0.6192 (tp30) cc_final: 0.5980 (tp30) REVERT: F 111 GLU cc_start: 0.6291 (mp0) cc_final: 0.5816 (mt-10) REVERT: F 114 GLN cc_start: 0.6395 (mt0) cc_final: 0.5892 (tp-100) REVERT: F 155 GLU cc_start: 0.7322 (mp0) cc_final: 0.6610 (mp0) REVERT: F 217 ARG cc_start: 0.7528 (mmt-90) cc_final: 0.7226 (mmp80) REVERT: F 249 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.8113 (mmt90) REVERT: F 328 GLN cc_start: 0.7813 (mt0) cc_final: 0.7495 (mm-40) REVERT: F 363 LYS cc_start: 0.7698 (tppp) cc_final: 0.7436 (tptt) REVERT: F 520 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: F 521 GLN cc_start: 0.8360 (tp40) cc_final: 0.8033 (tt0) REVERT: F 672 MET cc_start: 0.3425 (ptm) cc_final: 0.2992 (pp-130) REVERT: G 104 LEU cc_start: 0.7331 (mt) cc_final: 0.7079 (mp) REVERT: G 162 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6758 (mmt180) REVERT: G 217 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7097 (mmp80) REVERT: G 259 PHE cc_start: 0.8192 (t80) cc_final: 0.7900 (t80) REVERT: G 361 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7457 (ptmt) REVERT: G 395 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6225 (mtp180) REVERT: G 403 ARG cc_start: 0.7754 (mtp-110) cc_final: 0.7194 (ptt180) REVERT: G 414 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: G 545 MET cc_start: 0.5901 (ptt) cc_final: 0.5614 (ppp) REVERT: G 569 ARG cc_start: 0.6515 (tpp-160) cc_final: 0.6137 (mmm160) REVERT: G 672 MET cc_start: 0.3020 (ptm) cc_final: 0.2646 (pp-130) REVERT: H 217 ARG cc_start: 0.7500 (mmt-90) cc_final: 0.7086 (mmp80) REVERT: H 249 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7978 (mmt90) REVERT: H 285 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7132 (mtm110) REVERT: H 520 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: H 521 GLN cc_start: 0.8335 (tp40) cc_final: 0.8039 (tt0) REVERT: H 672 MET cc_start: 0.4628 (ttp) cc_final: 0.4275 (ttp) outliers start: 85 outliers final: 38 residues processed: 411 average time/residue: 0.8634 time to fit residues: 417.2865 Evaluate side-chains 383 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 323 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 569 ARG Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 204 optimal weight: 0.0000 chunk 189 optimal weight: 0.9990 chunk 333 optimal weight: 4.9990 chunk 221 optimal weight: 0.0010 chunk 477 optimal weight: 2.9990 chunk 323 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 383 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN F 337 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 337 ASN G 575 GLN H 337 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.192752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122842 restraints weight = 42252.849| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.82 r_work: 0.3154 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 0.037 39888 Z= 0.091 Angle : 0.473 11.267 53968 Z= 0.238 Chirality : 0.037 0.385 6168 Planarity : 0.003 0.054 6944 Dihedral : 5.158 50.693 5832 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.72 % Allowed : 13.88 % Favored : 84.40 % 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: 1.40 (0.13), residues: 4912 helix: 1.42 (0.09), residues: 3432 sheet: -0.00 (0.47), residues: 152 loop : -0.10 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 307 TYR 0.006 0.001 TYR E 429 PHE 0.032 0.001 PHE E 259 TRP 0.007 0.001 TRP A 253 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00203 (39888) covalent geometry : angle 0.47284 (53968) hydrogen bonds : bond 0.02793 ( 2008) hydrogen bonds : angle 3.37043 ( 5904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 344 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7226 (mp) REVERT: A 162 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6736 (mmt180) REVERT: A 217 ARG cc_start: 0.7384 (mmt-90) cc_final: 0.7092 (mmp80) REVERT: A 395 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6265 (mtp180) REVERT: A 403 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7113 (ptt180) REVERT: A 414 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: A 520 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: A 545 MET cc_start: 0.5831 (ptt) cc_final: 0.5581 (ppp) REVERT: A 569 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6292 (mmp-170) REVERT: A 630 MET cc_start: 0.2864 (ppp) cc_final: 0.2036 (ttp) REVERT: A 672 MET cc_start: 0.3217 (ptm) cc_final: 0.2706 (pp-130) REVERT: B 97 GLN cc_start: 0.7109 (tt0) cc_final: 0.6746 (mp10) REVERT: B 133 LEU cc_start: 0.7768 (mt) cc_final: 0.7474 (tp) REVERT: B 217 ARG cc_start: 0.7715 (mmt-90) cc_final: 0.6866 (mmp80) REVERT: B 285 ARG cc_start: 0.7854 (mpt180) cc_final: 0.6815 (mtp-110) REVERT: B 289 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7342 (mtt90) REVERT: B 520 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: B 521 GLN cc_start: 0.8359 (tp40) cc_final: 0.8066 (tt0) REVERT: B 569 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5945 (mmp-170) REVERT: B 575 GLN cc_start: 0.6804 (tm-30) cc_final: 0.6456 (tm130) REVERT: B 672 MET cc_start: 0.4258 (OUTLIER) cc_final: 0.3787 (ttt) REVERT: C 162 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6779 (mmt180) REVERT: C 217 ARG cc_start: 0.7848 (mmt-90) cc_final: 0.7003 (mmp80) REVERT: C 289 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7532 (ttm-80) REVERT: C 307 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6572 (mtm110) REVERT: C 395 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6295 (mtp180) REVERT: C 403 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7127 (ptt180) REVERT: C 414 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: C 545 MET cc_start: 0.5788 (ptt) cc_final: 0.5525 (ppp) REVERT: C 672 MET cc_start: 0.3361 (ptm) cc_final: 0.2878 (pp-130) REVERT: D 133 LEU cc_start: 0.7755 (mt) cc_final: 0.7511 (tp) REVERT: D 162 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6768 (mmt180) REVERT: D 217 ARG cc_start: 0.7633 (mmt-90) cc_final: 0.7236 (mmp80) REVERT: D 285 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7203 (mtp-110) REVERT: D 307 ARG cc_start: 0.7404 (mtm110) cc_final: 0.7151 (mtp-110) REVERT: D 385 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8314 (m) REVERT: D 520 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: D 521 GLN cc_start: 0.8366 (tp40) cc_final: 0.8033 (tt0) REVERT: D 575 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6685 (tm130) REVERT: D 672 MET cc_start: 0.4636 (ttp) cc_final: 0.4263 (ttp) REVERT: E 97 GLN cc_start: 0.7148 (tp-100) cc_final: 0.6801 (mp10) REVERT: E 100 GLU cc_start: 0.6059 (tp30) cc_final: 0.5537 (tp30) REVERT: E 104 LEU cc_start: 0.7363 (mt) cc_final: 0.6987 (mp) REVERT: E 217 ARG cc_start: 0.7876 (mmt-90) cc_final: 0.7034 (mmp80) REVERT: E 395 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6217 (mtp180) REVERT: E 403 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7275 (ptt180) REVERT: E 414 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: E 545 MET cc_start: 0.5811 (ptt) cc_final: 0.5529 (ppp) REVERT: E 568 TYR cc_start: 0.7255 (p90) cc_final: 0.6832 (p90) REVERT: E 672 MET cc_start: 0.3379 (ptm) cc_final: 0.2897 (pp-130) REVERT: F 97 GLN cc_start: 0.7370 (tt0) cc_final: 0.7128 (mp10) REVERT: F 100 GLU cc_start: 0.6137 (tp30) cc_final: 0.5896 (tp30) REVERT: F 111 GLU cc_start: 0.6199 (mp0) cc_final: 0.5789 (mt-10) REVERT: F 114 GLN cc_start: 0.6389 (mt0) cc_final: 0.5855 (tp-100) REVERT: F 155 GLU cc_start: 0.7347 (mp0) cc_final: 0.6656 (mp0) REVERT: F 217 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7303 (mmp80) REVERT: F 285 ARG cc_start: 0.7893 (mpt180) cc_final: 0.7135 (mtp-110) REVERT: F 328 GLN cc_start: 0.7806 (mt0) cc_final: 0.7552 (mm-40) REVERT: F 363 LYS cc_start: 0.7730 (tppp) cc_final: 0.7509 (tptt) REVERT: F 520 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: F 521 GLN cc_start: 0.8377 (tp40) cc_final: 0.8039 (tt0) REVERT: F 672 MET cc_start: 0.3431 (ptm) cc_final: 0.3002 (pp-130) REVERT: G 104 LEU cc_start: 0.7308 (mt) cc_final: 0.7072 (mp) REVERT: G 162 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6720 (mmt180) REVERT: G 217 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7104 (mmp80) REVERT: G 259 PHE cc_start: 0.8119 (t80) cc_final: 0.7903 (t80) REVERT: G 307 ARG cc_start: 0.7017 (mtp-110) cc_final: 0.6382 (mtm110) REVERT: G 361 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7435 (ptmt) REVERT: G 395 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6228 (mtp180) REVERT: G 403 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7213 (ptt180) REVERT: G 414 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: G 545 MET cc_start: 0.5928 (ptt) cc_final: 0.5658 (ppp) REVERT: G 569 ARG cc_start: 0.6538 (tpp-160) cc_final: 0.6169 (mmm160) REVERT: G 672 MET cc_start: 0.3019 (ptm) cc_final: 0.2652 (pp-130) REVERT: H 133 LEU cc_start: 0.7769 (mt) cc_final: 0.7544 (tp) REVERT: H 217 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.7153 (mmp80) REVERT: H 288 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7300 (mt-10) REVERT: H 363 LYS cc_start: 0.7811 (tptt) cc_final: 0.7570 (tppt) REVERT: H 520 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: H 521 GLN cc_start: 0.8355 (tp40) cc_final: 0.8054 (tt0) REVERT: H 672 MET cc_start: 0.4518 (ttp) cc_final: 0.3928 (pp-130) outliers start: 71 outliers final: 32 residues processed: 402 average time/residue: 0.8702 time to fit residues: 409.9543 Evaluate side-chains 365 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 307 optimal weight: 0.0980 chunk 375 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 422 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 490 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN H 236 HIS ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.188105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117152 restraints weight = 41897.500| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.64 r_work: 0.3079 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 39888 Z= 0.213 Angle : 0.640 12.977 53968 Z= 0.322 Chirality : 0.044 0.201 6168 Planarity : 0.005 0.054 6944 Dihedral : 6.390 54.715 5832 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.77 % Allowed : 13.74 % Favored : 84.50 % 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: 0.77 (0.12), residues: 4912 helix: 0.89 (0.09), residues: 3496 sheet: -0.20 (0.48), residues: 152 loop : -0.19 (0.19), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 307 TYR 0.014 0.002 TYR D 429 PHE 0.031 0.002 PHE E 259 TRP 0.009 0.002 TRP F 662 HIS 0.006 0.002 HIS H 225 Details of bonding type rmsd covalent geometry : bond 0.00525 (39888) covalent geometry : angle 0.63959 (53968) hydrogen bonds : bond 0.04226 ( 2008) hydrogen bonds : angle 3.73601 ( 5904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9824 Ramachandran restraints generated. 4912 Oldfield, 0 Emsley, 4912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 345 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7350 (mp) REVERT: A 162 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6886 (mmt180) REVERT: A 217 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.7134 (mmp80) REVERT: A 395 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6267 (mtp180) REVERT: A 414 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: A 520 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: A 563 ASP cc_start: 0.5613 (m-30) cc_final: 0.5050 (p0) REVERT: A 672 MET cc_start: 0.3442 (ptm) cc_final: 0.2931 (pp-130) REVERT: B 97 GLN cc_start: 0.7171 (tt0) cc_final: 0.6606 (mp10) REVERT: B 217 ARG cc_start: 0.7667 (mmt-90) cc_final: 0.7236 (mmp80) REVERT: B 285 ARG cc_start: 0.7931 (mpt180) cc_final: 0.7089 (mtp-110) REVERT: B 520 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: B 521 GLN cc_start: 0.8339 (tp40) cc_final: 0.8063 (tt0) REVERT: B 575 GLN cc_start: 0.7245 (tm-30) cc_final: 0.6920 (tm130) REVERT: B 672 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.3792 (ttt) REVERT: C 162 ARG cc_start: 0.7455 (mtt180) cc_final: 0.6963 (mmt180) REVERT: C 224 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (mtt180) REVERT: C 289 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7674 (ttm-80) REVERT: C 395 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6247 (mtp180) REVERT: C 414 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: C 484 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7999 (ttp-170) REVERT: C 630 MET cc_start: 0.3395 (OUTLIER) cc_final: 0.2847 (ppp) REVERT: C 672 MET cc_start: 0.3139 (ptm) cc_final: 0.2741 (pp-130) REVERT: D 114 GLN cc_start: 0.6574 (mt0) cc_final: 0.5997 (tp-100) REVERT: D 162 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6866 (mmt180) REVERT: D 217 ARG cc_start: 0.7588 (mmt-90) cc_final: 0.7301 (mmp80) REVERT: D 285 ARG cc_start: 0.7909 (mpt180) cc_final: 0.7109 (mtm-85) REVERT: D 307 ARG cc_start: 0.7296 (mtm110) cc_final: 0.7092 (mtp-110) REVERT: D 520 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: D 521 GLN cc_start: 0.8351 (tp40) cc_final: 0.8058 (tt0) REVERT: D 575 GLN cc_start: 0.7400 (tm-30) cc_final: 0.7132 (tm130) REVERT: D 672 MET cc_start: 0.4658 (ttp) cc_final: 0.4252 (ttp) REVERT: E 97 GLN cc_start: 0.7203 (tp-100) cc_final: 0.6933 (mp10) REVERT: E 100 GLU cc_start: 0.6085 (tp30) cc_final: 0.5776 (tp30) REVERT: E 129 LEU cc_start: 0.7617 (mp) cc_final: 0.7330 (mp) REVERT: E 224 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7607 (mtt180) REVERT: E 395 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6277 (mtp180) REVERT: E 414 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: E 672 MET cc_start: 0.3173 (ptm) cc_final: 0.2771 (pp-130) REVERT: F 97 GLN cc_start: 0.7280 (tt0) cc_final: 0.7031 (mp10) REVERT: F 100 GLU cc_start: 0.6228 (tp30) cc_final: 0.6012 (tp30) REVERT: F 111 GLU cc_start: 0.6323 (mp0) cc_final: 0.5866 (mt-10) REVERT: F 114 GLN cc_start: 0.6581 (mt0) cc_final: 0.6071 (tp-100) REVERT: F 217 ARG cc_start: 0.7580 (mmt-90) cc_final: 0.7306 (mmp80) REVERT: F 285 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7219 (mtm-85) REVERT: F 328 GLN cc_start: 0.8052 (mt0) cc_final: 0.7468 (mm-40) REVERT: F 520 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: F 521 GLN cc_start: 0.8353 (tp40) cc_final: 0.8045 (tt0) REVERT: F 672 MET cc_start: 0.3418 (ptm) cc_final: 0.2887 (pp-130) REVERT: G 159 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.7131 (tpp80) REVERT: G 162 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6889 (mmt180) REVERT: G 224 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7592 (mtt180) REVERT: G 259 PHE cc_start: 0.8344 (t80) cc_final: 0.8131 (t80) REVERT: G 361 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7567 (ptmt) REVERT: G 395 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: G 403 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7334 (ptt180) REVERT: G 414 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: G 569 ARG cc_start: 0.6672 (tpp-160) cc_final: 0.6309 (mmm160) REVERT: G 672 MET cc_start: 0.3412 (ptm) cc_final: 0.2957 (pp-130) REVERT: H 217 ARG cc_start: 0.7442 (mmt-90) cc_final: 0.7197 (mmp80) REVERT: H 520 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: H 521 GLN cc_start: 0.8304 (tp40) cc_final: 0.8042 (tt0) REVERT: H 672 MET cc_start: 0.4592 (ttp) cc_final: 0.4276 (ttp) outliers start: 73 outliers final: 36 residues processed: 410 average time/residue: 0.8686 time to fit residues: 417.7133 Evaluate side-chains 381 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 653 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain H residue 520 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 64 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 437 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN E 337 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN H 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.190827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120108 restraints weight = 42166.657| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.94 r_work: 0.3110 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39888 Z= 0.110 Angle : 0.516 9.947 53968 Z= 0.262 Chirality : 0.039 0.380 6168 Planarity : 0.004 0.061 6944 Dihedral : 5.801 52.646 5832 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.41 % Allowed : 14.58 % Favored : 84.01 % 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: 1.26 (0.13), residues: 4912 helix: 1.27 (0.09), residues: 3400 sheet: -0.09 (0.48), residues: 152 loop : 0.04 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 307 TYR 0.008 0.001 TYR E 429 PHE 0.030 0.001 PHE E 259 TRP 0.007 0.001 TRP B 638 HIS 0.003 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00258 (39888) covalent geometry : angle 0.51636 (53968) hydrogen bonds : bond 0.03126 ( 2008) hydrogen bonds : angle 3.53649 ( 5904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19227.90 seconds wall clock time: 326 minutes 11.87 seconds (19571.87 seconds total)