Starting phenix.real_space_refine on Mon Jul 6 20:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cm7_30403/07_2026/7cm7_30403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm7_30403/07_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_30403/07_2026/7cm7_30403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm7_30403/07_2026/7cm7_30403.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cm7_30403/07_2026/7cm7_30403.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cm7_30403/07_2026/7cm7_30403.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cm7_30403/07_2026/7cm7_30403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm7_30403/07_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.08, per 1000 atoms: 0.16 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 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: 1.33 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: 8.84 Time building geometry restraints manager: 4.77 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: 23352 15.06 - 30.12: 608 30.12 - 45.18: 136 45.18 - 60.24: 8 60.24 - 75.29: 16 Dihedral angle restraints: 24120 sinusoidal: 9864 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 24117 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: 0.15 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: 3.990 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: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.140 Process input model: 34.820 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 8.327 75.294 14872 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/Z covalent geometry : bond 0.00405 / 0.22 (39888) covalent geometry : angle 0.83720 / 0.45 (53968) hydrogen bonds : bond 0.16070 / 10.37 ( 2008) hydrogen bonds : angle 6.35884 / 4.43 ( 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 : 1.271 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: 0.8470 time to fit residues: 910.8280 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 : 1.397 ------------------------------------------------------------------------------- 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... A 143 GLN A 150 GLN 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 337 ASN D 452 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 337 ASN F 359 GLN F 452 GLN F 587 HIS G 143 GLN G 150 GLN G 269 HIS 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.192718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122247 restraints weight = 42159.940| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.75 r_work: 0.3156 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 39888 Z= 0.199 Angle : 0.620 8.130 53968 Z= 0.320 Chirality : 0.042 0.157 6168 Planarity : 0.005 0.048 6944 Dihedral : 5.063 37.721 5432 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 10.08 % Favored : 87.86 % 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: -1.60 (0.11), residues: 4912 helix: -0.79 (0.08), residues: 3416 sheet: -1.01 (0.44), residues: 152 loop : -1.35 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 569 TYR 0.020 0.003 TYR C 380 PHE 0.037 0.003 PHE H 433 TRP 0.017 0.002 TRP H 490 HIS 0.009 0.002 HIS C 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (39888) covalent geometry : angle 0.62003 / 0.32 (53968) hydrogen bonds : bond 0.04245 / 2.86 ( 2008) hydrogen bonds : angle 4.00246 / 2.83 ( 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 542 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 457 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6785 (mmt180) REVERT: A 224 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7519 (mmm-85) REVERT: A 259 PHE cc_start: 0.7902 (t80) cc_final: 0.7406 (t80) REVERT: A 288 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 307 ARG cc_start: 0.6852 (ttp-110) cc_final: 0.6579 (mtp-110) REVERT: A 328 GLN cc_start: 0.7871 (mt0) cc_final: 0.7645 (mm-40) REVERT: A 630 MET cc_start: 0.3731 (ppp) cc_final: 0.2738 (ptm) REVERT: A 672 MET cc_start: 0.3276 (ptm) cc_final: 0.2781 (pp-130) REVERT: B 259 PHE cc_start: 0.7429 (t80) cc_final: 0.6974 (t80) REVERT: B 363 LYS cc_start: 0.7808 (tppp) cc_final: 0.7391 (tptt) REVERT: B 569 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6659 (mmp-170) REVERT: B 630 MET cc_start: 0.2934 (OUTLIER) cc_final: 0.2505 (ppp) REVERT: B 672 MET cc_start: 0.4019 (ttp) cc_final: 0.3640 (ttp) REVERT: C 159 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7507 (tpt170) REVERT: C 224 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7638 (mmm-85) REVERT: C 259 PHE cc_start: 0.7808 (t80) cc_final: 0.7403 (t80) REVERT: C 285 ARG cc_start: 0.7909 (mpt180) cc_final: 0.7038 (mtm110) REVERT: C 288 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7581 (mt-10) REVERT: C 289 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7512 (mtm110) REVERT: C 307 ARG cc_start: 0.6891 (ttp-110) cc_final: 0.6626 (mtp-110) REVERT: C 325 ASP cc_start: 0.7702 (t0) cc_final: 0.7482 (m-30) REVERT: C 328 GLN cc_start: 0.7891 (mt0) cc_final: 0.7670 (mm-40) REVERT: C 414 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: C 630 MET cc_start: 0.4379 (ppp) cc_final: 0.3360 (ptm) REVERT: C 672 MET cc_start: 0.3132 (ptm) cc_final: 0.2818 (pp-130) REVERT: D 114 GLN cc_start: 0.6398 (mt0) cc_final: 0.5907 (tp-100) REVERT: D 162 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6842 (mmt180) REVERT: D 259 PHE cc_start: 0.7465 (t80) cc_final: 0.7121 (t80) REVERT: D 363 LYS cc_start: 0.7886 (tppp) cc_final: 0.7280 (tptt) REVERT: D 575 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6674 (tm-30) REVERT: E 147 LEU cc_start: 0.8222 (tp) cc_final: 0.7959 (tp) REVERT: E 247 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7285 (mt-10) REVERT: E 259 PHE cc_start: 0.7852 (t80) cc_final: 0.7434 (t80) REVERT: E 288 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7646 (mt-10) REVERT: E 307 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6650 (mtp-110) REVERT: E 325 ASP cc_start: 0.7724 (t0) cc_final: 0.7493 (m-30) REVERT: E 328 GLN cc_start: 0.7873 (mt0) cc_final: 0.7595 (mm-40) REVERT: E 630 MET cc_start: 0.4071 (ppp) cc_final: 0.3188 (ptm) REVERT: E 672 MET cc_start: 0.3240 (ptm) cc_final: 0.2819 (pp-130) REVERT: F 286 GLU cc_start: 0.7345 (mp0) cc_final: 0.7055 (mt-10) REVERT: F 328 GLN cc_start: 0.7791 (mt0) cc_final: 0.7555 (mm-40) REVERT: F 521 GLN cc_start: 0.8354 (tp40) cc_final: 0.8045 (tt0) REVERT: F 575 GLN cc_start: 0.6363 (pm20) cc_final: 0.6115 (tm130) REVERT: F 672 MET cc_start: 0.3409 (ptm) cc_final: 0.2961 (pp-130) REVERT: G 147 LEU cc_start: 0.8279 (tp) cc_final: 0.8024 (tp) REVERT: G 259 PHE cc_start: 0.7805 (t80) cc_final: 0.7414 (t80) REVERT: G 288 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7558 (mt-10) REVERT: G 307 ARG cc_start: 0.7043 (ttp-110) cc_final: 0.6723 (mtp-110) REVERT: G 325 ASP cc_start: 0.7493 (t0) cc_final: 0.7276 (m-30) REVERT: G 403 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7463 (mtm-85) REVERT: G 569 ARG cc_start: 0.6406 (tpp-160) cc_final: 0.5966 (mmp-170) REVERT: G 630 MET cc_start: 0.3980 (ppp) cc_final: 0.3003 (ptm) REVERT: G 672 MET cc_start: 0.3112 (ptm) cc_final: 0.2698 (pp-130) REVERT: H 259 PHE cc_start: 0.7434 (t80) cc_final: 0.7070 (t80) outliers start: 85 outliers final: 28 residues processed: 510 average time/residue: 0.9196 time to fit residues: 548.5624 Evaluate side-chains 355 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 569 ARG 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 414 GLU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 167 VAL 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 167 VAL 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 G residue 586 LEU 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: 1.9990 chunk 193 optimal weight: 0.0020 chunk 434 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 303 optimal weight: 8.9990 chunk 443 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 269 HIS A 337 ASN A 652 ASN B 337 ASN B 587 HIS C 337 ASN D 269 HIS D 337 ASN D 587 HIS E 337 ASN E 652 ASN F 269 HIS 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.192941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122537 restraints weight = 42164.425| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.84 r_work: 0.3156 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39888 Z= 0.108 Angle : 0.487 7.411 53968 Z= 0.250 Chirality : 0.038 0.147 6168 Planarity : 0.004 0.038 6944 Dihedral : 4.536 33.428 5432 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.96 % Allowed : 12.14 % Favored : 85.90 % 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: -0.44 (0.12), residues: 4912 helix: 0.08 (0.09), residues: 3432 sheet: -0.61 (0.45), residues: 152 loop : -0.93 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 307 TYR 0.009 0.001 TYR E 503 PHE 0.013 0.001 PHE B 592 TRP 0.009 0.001 TRP C 412 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (39888) covalent geometry : angle 0.48686 / 0.25 (53968) hydrogen bonds : bond 0.03156 / 2.13 ( 2008) hydrogen bonds : angle 3.55560 / 2.51 ( 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 453 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7168 (mtt180) cc_final: 0.6776 (mmt180) REVERT: A 259 PHE cc_start: 0.7831 (t80) cc_final: 0.7459 (t80) REVERT: A 328 GLN cc_start: 0.7843 (mt0) cc_final: 0.7629 (mm-40) REVERT: A 395 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6383 (mtp180) REVERT: A 414 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: A 630 MET cc_start: 0.4253 (ppp) cc_final: 0.3250 (ptm) REVERT: A 672 MET cc_start: 0.3212 (ptm) cc_final: 0.2770 (pp-130) REVERT: B 97 GLN cc_start: 0.7252 (tt0) cc_final: 0.6917 (mp10) REVERT: B 217 ARG cc_start: 0.7610 (mmt-90) cc_final: 0.7045 (mmp80) REVERT: B 259 PHE cc_start: 0.7623 (t80) cc_final: 0.7366 (t80) REVERT: B 285 ARG cc_start: 0.8071 (mpt180) cc_final: 0.7100 (mtp-110) REVERT: B 363 LYS cc_start: 0.7812 (tppp) cc_final: 0.7549 (tptt) REVERT: B 521 GLN cc_start: 0.8289 (tp40) cc_final: 0.8031 (tt0) REVERT: B 630 MET cc_start: 0.2911 (OUTLIER) cc_final: 0.2482 (ppp) REVERT: B 672 MET cc_start: 0.4087 (OUTLIER) cc_final: 0.3720 (ttp) REVERT: C 129 LEU cc_start: 0.7548 (mt) cc_final: 0.7248 (mp) REVERT: C 162 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6823 (mmt180) REVERT: C 245 MET cc_start: 0.8854 (mtp) cc_final: 0.8596 (mtp) REVERT: C 259 PHE cc_start: 0.7803 (t80) cc_final: 0.7428 (t80) REVERT: C 285 ARG cc_start: 0.7884 (mpt180) cc_final: 0.6972 (mtm110) REVERT: C 288 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 289 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7417 (mtm110) REVERT: C 325 ASP cc_start: 0.7541 (t0) cc_final: 0.7315 (m-30) REVERT: C 328 GLN cc_start: 0.7847 (mt0) cc_final: 0.7591 (mm-40) REVERT: C 363 LYS cc_start: 0.7521 (tppp) cc_final: 0.7062 (tptt) REVERT: C 395 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6443 (mtp180) REVERT: C 520 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: C 630 MET cc_start: 0.4141 (ppp) cc_final: 0.3452 (ptm) REVERT: C 672 MET cc_start: 0.3383 (ptm) cc_final: 0.2923 (pp-130) REVERT: D 114 GLN cc_start: 0.6385 (mt0) cc_final: 0.5836 (tp-100) REVERT: D 162 ARG cc_start: 0.7329 (mtt180) cc_final: 0.6816 (mmt180) REVERT: D 217 ARG cc_start: 0.7577 (mmt-90) cc_final: 0.7197 (mmp80) REVERT: D 247 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: D 282 GLU cc_start: 0.8231 (pt0) cc_final: 0.8021 (tt0) REVERT: D 285 ARG cc_start: 0.8018 (mpt180) cc_final: 0.7115 (mtp-110) REVERT: D 363 LYS cc_start: 0.7716 (tppp) cc_final: 0.7392 (tptt) REVERT: D 396 LEU cc_start: 0.8257 (mt) cc_final: 0.8048 (mp) REVERT: D 575 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6701 (tm130) REVERT: D 672 MET cc_start: 0.4622 (ttp) cc_final: 0.4344 (ttp) REVERT: E 129 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6992 (mp) REVERT: E 147 LEU cc_start: 0.8245 (tp) cc_final: 0.8005 (tp) REVERT: E 217 ARG cc_start: 0.7477 (mmt-90) cc_final: 0.7187 (mmp80) REVERT: E 245 MET cc_start: 0.8752 (mtp) cc_final: 0.8536 (mtp) REVERT: E 247 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7569 (mt-10) REVERT: E 259 PHE cc_start: 0.7848 (t80) cc_final: 0.7562 (t80) REVERT: E 288 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7648 (mt-10) REVERT: E 328 GLN cc_start: 0.7830 (mt0) cc_final: 0.7539 (mm-40) REVERT: E 363 LYS cc_start: 0.7633 (tppp) cc_final: 0.7188 (tptt) REVERT: E 395 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6386 (mtp180) REVERT: E 414 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: E 630 MET cc_start: 0.4194 (ppp) cc_final: 0.3292 (ptm) REVERT: E 672 MET cc_start: 0.3411 (ptm) cc_final: 0.2927 (pp-130) REVERT: F 97 GLN cc_start: 0.7342 (tt0) cc_final: 0.7035 (mp10) REVERT: F 155 GLU cc_start: 0.7363 (mp0) cc_final: 0.6956 (mp0) REVERT: F 217 ARG cc_start: 0.7736 (mmt-90) cc_final: 0.7361 (mmp80) REVERT: F 247 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: F 286 GLU cc_start: 0.7184 (mp0) cc_final: 0.6910 (mt-10) REVERT: F 363 LYS cc_start: 0.7770 (tppp) cc_final: 0.7323 (tptt) REVERT: F 396 LEU cc_start: 0.8255 (mt) cc_final: 0.8037 (mp) REVERT: F 520 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: F 521 GLN cc_start: 0.8338 (tp40) cc_final: 0.8053 (tt0) REVERT: F 575 GLN cc_start: 0.6304 (pm20) cc_final: 0.6091 (tm130) REVERT: F 672 MET cc_start: 0.3332 (ptm) cc_final: 0.2842 (pp-130) REVERT: G 162 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6918 (mmt180) REVERT: G 259 PHE cc_start: 0.7948 (t80) cc_final: 0.7593 (t80) REVERT: G 325 ASP cc_start: 0.7500 (t0) cc_final: 0.7300 (m-30) REVERT: G 395 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6426 (mtp180) REVERT: G 403 ARG cc_start: 0.7895 (mtp-110) cc_final: 0.7390 (mtm-85) REVERT: G 414 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: G 520 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: G 569 ARG cc_start: 0.6370 (tpp-160) cc_final: 0.5883 (mmp-170) REVERT: G 630 MET cc_start: 0.4143 (ppp) cc_final: 0.3017 (ptm) REVERT: G 672 MET cc_start: 0.3175 (ptm) cc_final: 0.2723 (pp-130) REVERT: H 259 PHE cc_start: 0.7345 (t80) cc_final: 0.7082 (t80) REVERT: H 520 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: H 521 GLN cc_start: 0.8332 (tp40) cc_final: 0.8059 (tt0) REVERT: H 672 MET cc_start: 0.4552 (ttp) cc_final: 0.4211 (ttp) outliers start: 81 outliers final: 17 residues processed: 430 average time/residue: 0.8799 time to fit residues: 447.2849 Evaluate side-chains 343 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 167 VAL 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 520 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 247 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 E residue 129 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 414 GLU 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 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 408 SER Chi-restraints excluded: chain H residue 414 GLU 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: 3.9990 chunk 452 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 295 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 466 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 406 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 547 HIS B 337 ASN B 587 HIS C 156 ASN C 547 HIS D 337 ASN D 587 HIS E 337 ASN E 547 HIS F 337 ASN F 587 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN G 328 GLN G 337 ASN G 547 HIS G 575 GLN H 337 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.189867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119910 restraints weight = 41738.557| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.79 r_work: 0.3096 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39888 Z= 0.172 Angle : 0.572 7.911 53968 Z= 0.292 Chirality : 0.041 0.162 6168 Planarity : 0.004 0.035 6944 Dihedral : 4.723 30.937 5432 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.17 % Allowed : 11.68 % Favored : 85.15 % 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: 0.04 (0.12), residues: 4912 helix: 0.43 (0.09), residues: 3440 sheet: -0.59 (0.46), residues: 152 loop : -0.68 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 307 TYR 0.014 0.002 TYR E 429 PHE 0.019 0.002 PHE G 466 TRP 0.009 0.001 TRP F 214 HIS 0.006 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (39888) covalent geometry : angle 0.57217 / 0.29 (53968) hydrogen bonds : bond 0.03871 / 2.61 ( 2008) hydrogen bonds : angle 3.62764 / 2.57 ( 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 488 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 357 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6868 (mmt180) REVERT: A 259 PHE cc_start: 0.8115 (t80) cc_final: 0.7858 (t80) REVERT: A 307 ARG cc_start: 0.7259 (mtp-110) cc_final: 0.6776 (mtp-110) REVERT: A 328 GLN cc_start: 0.8026 (mt0) cc_final: 0.7734 (mm-40) REVERT: A 363 LYS cc_start: 0.7593 (tppp) cc_final: 0.7220 (tptt) REVERT: A 395 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6386 (mtp180) REVERT: A 414 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: A 520 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: A 672 MET cc_start: 0.3252 (ptm) cc_final: 0.2832 (pp-130) REVERT: B 97 GLN cc_start: 0.7354 (tt0) cc_final: 0.7067 (mp10) REVERT: B 100 GLU cc_start: 0.6281 (mt-10) cc_final: 0.6010 (tp30) REVERT: B 217 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7153 (mmp80) REVERT: B 259 PHE cc_start: 0.8069 (t80) cc_final: 0.7853 (t80) REVERT: B 285 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6989 (mtp-110) REVERT: B 363 LYS cc_start: 0.7942 (tppp) cc_final: 0.7662 (ttmm) REVERT: B 521 GLN cc_start: 0.8357 (tp40) cc_final: 0.8055 (tt0) REVERT: B 575 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6764 (tm130) REVERT: B 630 MET cc_start: 0.2984 (OUTLIER) cc_final: 0.2539 (ppp) REVERT: B 672 MET cc_start: 0.4136 (OUTLIER) cc_final: 0.3713 (ttp) REVERT: C 129 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7325 (mp) REVERT: C 159 ARG cc_start: 0.7663 (tpt170) cc_final: 0.7456 (tpt170) REVERT: C 162 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6885 (mmt180) REVERT: C 259 PHE cc_start: 0.8145 (t80) cc_final: 0.7819 (t80) REVERT: C 285 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7043 (mtm110) REVERT: C 288 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 289 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7619 (mtm110) REVERT: C 325 ASP cc_start: 0.7532 (t0) cc_final: 0.7309 (m-30) REVERT: C 328 GLN cc_start: 0.7984 (mt0) cc_final: 0.7662 (mm-40) REVERT: C 395 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6404 (mtp180) REVERT: C 484 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8020 (ttp-170) REVERT: C 520 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: C 630 MET cc_start: 0.4197 (ppp) cc_final: 0.3443 (ptm) REVERT: C 672 MET cc_start: 0.3377 (ptm) cc_final: 0.2962 (pp-130) REVERT: D 114 GLN cc_start: 0.6480 (mt0) cc_final: 0.5966 (tp-100) REVERT: D 162 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6871 (mmt180) REVERT: D 217 ARG cc_start: 0.7659 (mmt-90) cc_final: 0.7274 (mmp80) REVERT: D 259 PHE cc_start: 0.8146 (t80) cc_final: 0.7866 (t80) REVERT: D 285 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7023 (mtp-110) REVERT: D 307 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7225 (mtp-110) REVERT: D 363 LYS cc_start: 0.7857 (tppp) cc_final: 0.7512 (tptt) REVERT: D 672 MET cc_start: 0.4582 (ttp) cc_final: 0.4278 (ttp) REVERT: E 129 LEU cc_start: 0.7508 (mt) cc_final: 0.7208 (mp) REVERT: E 217 ARG cc_start: 0.7533 (mmt-90) cc_final: 0.7041 (mmp80) REVERT: E 288 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7960 (mt-10) REVERT: E 328 GLN cc_start: 0.8025 (mt0) cc_final: 0.7669 (mm-40) REVERT: E 395 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6402 (mtp180) REVERT: E 414 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: E 520 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: E 569 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6863 (mmp-170) REVERT: E 630 MET cc_start: 0.3900 (ppp) cc_final: 0.3184 (ptm) REVERT: E 672 MET cc_start: 0.3220 (ptm) cc_final: 0.2861 (pp-130) REVERT: F 97 GLN cc_start: 0.7393 (tt0) cc_final: 0.7178 (mp10) REVERT: F 100 GLU cc_start: 0.6401 (mt-10) cc_final: 0.6164 (tp30) REVERT: F 114 GLN cc_start: 0.6528 (mt0) cc_final: 0.6014 (tp-100) REVERT: F 217 ARG cc_start: 0.7716 (mmt-90) cc_final: 0.7419 (mmp80) REVERT: F 286 GLU cc_start: 0.7182 (mp0) cc_final: 0.6898 (mt-10) REVERT: F 363 LYS cc_start: 0.7872 (tppp) cc_final: 0.7568 (ttmm) REVERT: F 520 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: F 521 GLN cc_start: 0.8330 (tp40) cc_final: 0.8018 (tt0) REVERT: F 575 GLN cc_start: 0.6504 (pm20) cc_final: 0.6173 (tm130) REVERT: F 672 MET cc_start: 0.3419 (ptm) cc_final: 0.3005 (pp-130) REVERT: G 129 LEU cc_start: 0.7617 (mt) cc_final: 0.7350 (mp) REVERT: G 162 ARG cc_start: 0.7359 (mtt180) cc_final: 0.6970 (mmt180) REVERT: G 259 PHE cc_start: 0.8272 (t80) cc_final: 0.7995 (t80) REVERT: G 307 ARG cc_start: 0.7129 (mtp-110) cc_final: 0.6658 (mtp-110) REVERT: G 325 ASP cc_start: 0.7628 (t0) cc_final: 0.7415 (m-30) REVERT: G 395 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6226 (mtp180) REVERT: G 403 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7471 (mtm-85) REVERT: G 414 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: G 520 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: G 569 ARG cc_start: 0.6515 (tpp-160) cc_final: 0.6062 (mmp-170) REVERT: G 630 MET cc_start: 0.3667 (ppp) cc_final: 0.3422 (mtt) REVERT: G 672 MET cc_start: 0.3238 (ptm) cc_final: 0.2819 (pp-130) REVERT: H 100 GLU cc_start: 0.6078 (mt-10) cc_final: 0.5685 (tp30) REVERT: H 217 ARG cc_start: 0.7707 (mmt-90) cc_final: 0.7359 (mmp80) REVERT: H 259 PHE cc_start: 0.7951 (t80) cc_final: 0.7749 (t80) REVERT: H 520 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: H 521 GLN cc_start: 0.8299 (tp40) cc_final: 0.8015 (tt0) REVERT: H 672 MET cc_start: 0.4588 (ttp) cc_final: 0.4208 (ttp) outliers start: 131 outliers final: 32 residues processed: 455 average time/residue: 0.8725 time to fit residues: 468.1282 Evaluate side-chains 375 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 THR 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 167 VAL Chi-restraints excluded: chain B residue 179 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 630 MET 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 385 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain C residue 520 GLU 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 E residue 123 ASP 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 E residue 520 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 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 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 520 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 179 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 53 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 392 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 490 optimal weight: 3.9990 chunk 284 optimal weight: 0.5980 chunk 359 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN B 337 ASN B 587 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN D 587 HIS 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.190123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123817 restraints weight = 41697.439| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.92 r_work: 0.3099 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4755 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 : 0.519 7.476 53968 Z= 0.266 Chirality : 0.039 0.158 6168 Planarity : 0.004 0.030 6944 Dihedral : 4.511 29.991 5432 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.88 % Allowed : 11.80 % Favored : 85.32 % 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: 0.47 (0.12), residues: 4912 helix: 0.75 (0.09), residues: 3440 sheet: -0.50 (0.47), residues: 152 loop : -0.51 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 289 TYR 0.011 0.001 TYR E 429 PHE 0.015 0.002 PHE G 308 TRP 0.007 0.001 TRP F 638 HIS 0.006 0.001 HIS F 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (39888) covalent geometry : angle 0.51871 / 0.27 (53968) hydrogen bonds : bond 0.03454 / 2.33 ( 2008) hydrogen bonds : angle 3.54927 / 2.51 ( 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: 119 poor density : 343 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6834 (mmt180) REVERT: A 224 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7663 (mtt180) REVERT: A 307 ARG cc_start: 0.7204 (mtp-110) cc_final: 0.6730 (mtp-110) REVERT: A 414 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: A 520 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: A 672 MET cc_start: 0.3213 (ptm) cc_final: 0.2810 (pp-130) REVERT: B 97 GLN cc_start: 0.7422 (tt0) cc_final: 0.6841 (mp10) REVERT: B 100 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5774 (mt-10) REVERT: B 217 ARG cc_start: 0.7768 (mmt-90) cc_final: 0.7305 (mmp80) REVERT: B 285 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7024 (mtp-110) REVERT: B 307 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6645 (ttp-110) REVERT: B 363 LYS cc_start: 0.7916 (tppp) cc_final: 0.7658 (ttmm) REVERT: B 520 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: B 575 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6742 (tm130) REVERT: B 672 MET cc_start: 0.4286 (OUTLIER) cc_final: 0.3901 (ttp) REVERT: C 100 GLU cc_start: 0.6098 (tp30) cc_final: 0.5861 (tp30) REVERT: C 129 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7350 (mp) REVERT: C 159 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7469 (tpt170) REVERT: C 162 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6867 (mmt180) REVERT: C 224 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7720 (mtt180) REVERT: C 259 PHE cc_start: 0.8106 (t80) cc_final: 0.7894 (t80) REVERT: C 285 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7100 (mtm110) REVERT: C 288 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 289 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7679 (mtm110) REVERT: C 328 GLN cc_start: 0.8023 (mt0) cc_final: 0.7626 (mm-40) REVERT: C 414 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: C 484 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8019 (ttp-170) REVERT: C 520 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: C 672 MET cc_start: 0.3426 (ptm) cc_final: 0.2938 (pp-130) REVERT: D 114 GLN cc_start: 0.6499 (mt0) cc_final: 0.5948 (tp-100) REVERT: D 162 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6851 (mmt180) REVERT: D 217 ARG cc_start: 0.7719 (mmt-90) cc_final: 0.7306 (mmp80) REVERT: D 259 PHE cc_start: 0.8096 (t80) cc_final: 0.7875 (t80) REVERT: D 285 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7046 (mtp-110) REVERT: D 307 ARG cc_start: 0.7344 (mtm110) cc_final: 0.7086 (mtp-110) REVERT: D 363 LYS cc_start: 0.7825 (tppp) cc_final: 0.7485 (tptt) REVERT: D 520 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: D 575 GLN cc_start: 0.7223 (tm-30) cc_final: 0.6753 (tm130) REVERT: D 672 MET cc_start: 0.4674 (ttp) cc_final: 0.4318 (ttp) REVERT: E 129 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7232 (mp) REVERT: E 217 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7293 (mmp80) REVERT: E 288 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7875 (mt-10) REVERT: E 328 GLN cc_start: 0.8013 (mt0) cc_final: 0.7619 (mm-40) REVERT: E 403 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7423 (ptt180) REVERT: E 414 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: E 520 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: E 569 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6870 (mmp-170) REVERT: E 672 MET cc_start: 0.3253 (ptm) cc_final: 0.2818 (pp-130) REVERT: F 97 GLN cc_start: 0.7388 (tt0) cc_final: 0.7155 (mp10) REVERT: F 100 GLU cc_start: 0.6387 (mt-10) cc_final: 0.6150 (tp30) REVERT: F 114 GLN cc_start: 0.6498 (mt0) cc_final: 0.5971 (tp-100) REVERT: F 171 LEU cc_start: 0.7739 (mt) cc_final: 0.7530 (tp) REVERT: F 217 ARG cc_start: 0.7635 (mmt-90) cc_final: 0.7382 (mmp80) REVERT: F 249 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.8109 (mmt90) REVERT: F 259 PHE cc_start: 0.8533 (t80) cc_final: 0.8310 (t80) REVERT: F 286 GLU cc_start: 0.7180 (mp0) cc_final: 0.6881 (mt-10) REVERT: F 307 ARG cc_start: 0.7463 (mtm110) cc_final: 0.7248 (mtp-110) REVERT: F 363 LYS cc_start: 0.7851 (tppp) cc_final: 0.7570 (ttmm) REVERT: F 520 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: F 521 GLN cc_start: 0.8388 (tp40) cc_final: 0.8074 (tt0) REVERT: F 575 GLN cc_start: 0.6525 (pm20) cc_final: 0.6206 (tm130) REVERT: F 672 MET cc_start: 0.3349 (ptm) cc_final: 0.2780 (pp-130) REVERT: G 162 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6929 (mmt180) REVERT: G 224 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7422 (mmm-85) REVERT: G 259 PHE cc_start: 0.8248 (t80) cc_final: 0.8039 (t80) REVERT: G 307 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.6623 (mtp-110) REVERT: G 325 ASP cc_start: 0.7708 (t0) cc_final: 0.7456 (m-30) REVERT: G 403 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7342 (ptt180) REVERT: G 414 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: G 520 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: G 569 ARG cc_start: 0.6536 (tpp-160) cc_final: 0.6145 (mmm160) REVERT: G 589 PHE cc_start: 0.7241 (m-10) cc_final: 0.7011 (m-10) REVERT: G 672 MET cc_start: 0.3201 (ptm) cc_final: 0.2796 (pp-130) REVERT: H 217 ARG cc_start: 0.7617 (mmt-90) cc_final: 0.7252 (mmp80) REVERT: H 259 PHE cc_start: 0.8060 (t80) cc_final: 0.7850 (t80) REVERT: H 520 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: H 521 GLN cc_start: 0.8360 (tp40) cc_final: 0.8079 (tt0) REVERT: H 672 MET cc_start: 0.4653 (ttp) cc_final: 0.4277 (ttp) outliers start: 119 outliers final: 38 residues processed: 428 average time/residue: 0.8856 time to fit residues: 445.2491 Evaluate side-chains 379 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 320 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 385 THR 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 285 ARG 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 129 LEU 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 295 LEU Chi-restraints excluded: chain C residue 385 THR 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 520 GLU Chi-restraints excluded: chain D residue 167 VAL 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 123 ASP 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 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 167 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 F residue 593 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 295 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 192 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 345 optimal weight: 0.0870 chunk 176 optimal weight: 0.9990 chunk 402 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 334 optimal weight: 0.0670 chunk 140 optimal weight: 0.9990 chunk 423 optimal weight: 0.7980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.4212 r_free = 0.4212 target = 0.192002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125530 restraints weight = 42279.749| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.96 r_work: 0.3143 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 39888 Z= 0.091 Angle : 0.461 7.281 53968 Z= 0.235 Chirality : 0.037 0.154 6168 Planarity : 0.003 0.035 6944 Dihedral : 4.168 28.842 5432 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.84 % Allowed : 13.01 % Favored : 85.15 % 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: 1.01 (0.12), residues: 4912 helix: 1.16 (0.09), residues: 3424 sheet: -0.27 (0.47), residues: 152 loop : -0.31 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 289 TYR 0.006 0.001 TYR E 429 PHE 0.010 0.001 PHE D 592 TRP 0.007 0.001 TRP D 638 HIS 0.005 0.001 HIS F 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (39888) covalent geometry : angle 0.46055 / 0.24 (53968) hydrogen bonds : bond 0.02830 / 1.91 ( 2008) hydrogen bonds : angle 3.37259 / 2.39 ( 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 450 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 374 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ARG cc_start: 0.7608 (tpt170) cc_final: 0.7256 (tpp80) REVERT: A 162 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6816 (mmt180) REVERT: A 217 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7277 (mmp80) REVERT: A 307 ARG cc_start: 0.7036 (mtp-110) cc_final: 0.6571 (mtp-110) REVERT: A 395 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6244 (mtp180) REVERT: A 403 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7190 (ptt180) REVERT: A 414 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: A 569 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6372 (mmp-170) REVERT: A 672 MET cc_start: 0.3071 (ptm) cc_final: 0.2692 (pp-130) REVERT: B 97 GLN cc_start: 0.7344 (tt0) cc_final: 0.6795 (mp10) REVERT: B 100 GLU cc_start: 0.6046 (mt-10) cc_final: 0.5695 (mt-10) REVERT: B 114 GLN cc_start: 0.6393 (tp40) cc_final: 0.6192 (tp-100) REVERT: B 217 ARG cc_start: 0.7668 (mmt-90) cc_final: 0.6876 (mmp80) REVERT: B 249 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8067 (mmt90) REVERT: B 259 PHE cc_start: 0.8001 (t80) cc_final: 0.7799 (t80) REVERT: B 285 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7008 (mtp-110) REVERT: B 307 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6684 (ttp-110) REVERT: B 363 LYS cc_start: 0.7805 (tppp) cc_final: 0.7550 (tptt) REVERT: B 521 GLN cc_start: 0.8356 (tp40) cc_final: 0.8070 (tt0) REVERT: B 575 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6558 (tm130) REVERT: B 672 MET cc_start: 0.4344 (OUTLIER) cc_final: 0.3837 (ttt) REVERT: C 100 GLU cc_start: 0.6075 (tp30) cc_final: 0.5828 (tp30) REVERT: C 159 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7358 (tpt170) REVERT: C 162 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6811 (mmt180) REVERT: C 217 ARG cc_start: 0.7818 (mmt-90) cc_final: 0.7002 (mmp80) REVERT: C 259 PHE cc_start: 0.8003 (t80) cc_final: 0.7736 (t80) REVERT: C 289 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7508 (mtm110) REVERT: C 395 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6274 (mtp180) REVERT: C 400 GLU cc_start: 0.6943 (pm20) cc_final: 0.6734 (pp20) REVERT: C 403 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7255 (ptt180) REVERT: C 414 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: C 568 TYR cc_start: 0.7309 (p90) cc_final: 0.6865 (p90) REVERT: C 672 MET cc_start: 0.3348 (ptm) cc_final: 0.2860 (pp-130) REVERT: D 114 GLN cc_start: 0.6472 (mt0) cc_final: 0.5920 (tp-100) REVERT: D 162 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6818 (mmt180) REVERT: D 217 ARG cc_start: 0.7646 (mmt-90) cc_final: 0.7284 (mmp80) REVERT: D 285 ARG cc_start: 0.7922 (mpt180) cc_final: 0.7031 (mtp-110) REVERT: D 307 ARG cc_start: 0.7255 (mtm110) cc_final: 0.6721 (ttp-110) REVERT: D 363 LYS cc_start: 0.7744 (tppp) cc_final: 0.7449 (tptt) REVERT: D 520 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: D 575 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6622 (tm130) REVERT: D 672 MET cc_start: 0.4754 (ttp) cc_final: 0.4436 (ttp) REVERT: E 100 GLU cc_start: 0.6082 (tp30) cc_final: 0.5658 (tp30) REVERT: E 104 LEU cc_start: 0.7295 (mt) cc_final: 0.6938 (mp) REVERT: E 129 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7174 (mp) REVERT: E 217 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7099 (mmp80) REVERT: E 288 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7730 (mt-10) REVERT: E 395 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6245 (mtp180) REVERT: E 403 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7282 (ptt180) REVERT: E 414 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: E 568 TYR cc_start: 0.7190 (p90) cc_final: 0.6773 (p90) REVERT: E 569 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6597 (mmp-170) REVERT: E 672 MET cc_start: 0.3255 (ptm) cc_final: 0.2828 (pp-130) REVERT: F 97 GLN cc_start: 0.7362 (tt0) cc_final: 0.7106 (mp-120) REVERT: F 100 GLU cc_start: 0.6207 (mt-10) cc_final: 0.5987 (tp30) REVERT: F 111 GLU cc_start: 0.6372 (mp0) cc_final: 0.5923 (mt-10) REVERT: F 114 GLN cc_start: 0.6485 (mt0) cc_final: 0.5911 (tp-100) REVERT: F 217 ARG cc_start: 0.7619 (mmt-90) cc_final: 0.7384 (mmp80) REVERT: F 249 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8142 (mmt90) REVERT: F 259 PHE cc_start: 0.8412 (t80) cc_final: 0.8141 (t80) REVERT: F 286 GLU cc_start: 0.7061 (mp0) cc_final: 0.6813 (mm-30) REVERT: F 307 ARG cc_start: 0.7388 (mtm110) cc_final: 0.7182 (mtp-110) REVERT: F 363 LYS cc_start: 0.7768 (tppp) cc_final: 0.7526 (ttmm) REVERT: F 520 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: F 521 GLN cc_start: 0.8363 (tp40) cc_final: 0.8046 (tt0) REVERT: F 575 GLN cc_start: 0.6307 (pm20) cc_final: 0.6088 (tm130) REVERT: F 672 MET cc_start: 0.3384 (ptm) cc_final: 0.2867 (pp-130) REVERT: G 104 LEU cc_start: 0.7391 (mt) cc_final: 0.7124 (mp) REVERT: G 129 LEU cc_start: 0.7516 (mt) cc_final: 0.7312 (mp) REVERT: G 162 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6871 (mmt180) REVERT: G 217 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.7098 (mmp80) REVERT: G 259 PHE cc_start: 0.8126 (t80) cc_final: 0.7911 (t80) REVERT: G 307 ARG cc_start: 0.7056 (mtp-110) cc_final: 0.6599 (mtp-110) REVERT: G 361 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7555 (ptmt) REVERT: G 395 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6225 (mtp180) REVERT: G 403 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7267 (ptt180) REVERT: G 414 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: G 569 ARG cc_start: 0.6516 (tpp-160) cc_final: 0.6118 (mmm160) REVERT: G 589 PHE cc_start: 0.7214 (m-10) cc_final: 0.7005 (m-10) REVERT: G 672 MET cc_start: 0.3129 (ptm) cc_final: 0.2768 (pp-130) REVERT: H 100 GLU cc_start: 0.5898 (tp30) cc_final: 0.5668 (tp30) REVERT: H 217 ARG cc_start: 0.7677 (mmt-90) cc_final: 0.7299 (mmp80) REVERT: H 249 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8014 (mmt90) REVERT: H 259 PHE cc_start: 0.7930 (t80) cc_final: 0.7691 (t80) REVERT: H 520 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: H 521 GLN cc_start: 0.8344 (tp40) cc_final: 0.8058 (tt0) REVERT: H 672 MET cc_start: 0.4634 (ttp) cc_final: 0.4295 (ttp) outliers start: 76 outliers final: 18 residues processed: 429 average time/residue: 0.8940 time to fit residues: 450.3844 Evaluate side-chains 371 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 385 THR 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 408 SER Chi-restraints excluded: chain B residue 506 VAL 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 C residue 414 GLU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain E residue 129 LEU 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 E residue 569 ARG Chi-restraints excluded: chain F residue 283 VAL 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 G residue 295 LEU Chi-restraints excluded: chain G residue 361 LYS 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 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: 0.8980 chunk 415 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 425 optimal weight: 10.0000 chunk 355 optimal weight: 0.9980 chunk 311 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 255 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN E 486 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 ASN G 97 GLN G 337 ASN G 575 GLN ** 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 = 0.4199 r_free = 0.4199 target = 0.190868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121754 restraints weight = 41915.439| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.96 r_work: 0.3112 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39888 Z= 0.108 Angle : 0.487 8.001 53968 Z= 0.247 Chirality : 0.038 0.155 6168 Planarity : 0.003 0.036 6944 Dihedral : 4.198 28.899 5432 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.35 % Allowed : 12.98 % Favored : 84.67 % 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: 1.12 (0.12), residues: 4912 helix: 1.21 (0.09), residues: 3448 sheet: -0.18 (0.47), residues: 152 loop : -0.19 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 289 TYR 0.008 0.001 TYR E 429 PHE 0.015 0.001 PHE B 592 TRP 0.006 0.001 TRP G 253 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (39888) covalent geometry : angle 0.48660 / 0.25 (53968) hydrogen bonds : bond 0.03145 / 2.11 ( 2008) hydrogen bonds : angle 3.41354 / 2.42 ( 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 445 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 348 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6795 (mmt180) REVERT: A 217 ARG cc_start: 0.8014 (mmt-90) cc_final: 0.7287 (mmp80) REVERT: A 224 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7620 (mtt180) REVERT: A 307 ARG cc_start: 0.7061 (mtp-110) cc_final: 0.6599 (mtp-110) REVERT: A 395 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6199 (mtp180) REVERT: A 403 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7078 (ptt180) REVERT: A 414 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: A 520 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: A 569 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6386 (mmp-170) REVERT: A 672 MET cc_start: 0.3063 (ptm) cc_final: 0.2689 (pp-130) REVERT: B 97 GLN cc_start: 0.7322 (tt0) cc_final: 0.6779 (mp10) REVERT: B 217 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.6866 (mmp80) REVERT: B 249 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8134 (mmt90) REVERT: B 285 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7043 (mtp-110) REVERT: B 288 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7409 (mt-10) REVERT: B 363 LYS cc_start: 0.7795 (tppp) cc_final: 0.7550 (tptt) REVERT: B 521 GLN cc_start: 0.8319 (tp40) cc_final: 0.8041 (tt0) REVERT: B 575 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6690 (tm130) REVERT: B 672 MET cc_start: 0.4473 (OUTLIER) cc_final: 0.3850 (ttt) REVERT: C 100 GLU cc_start: 0.6075 (tp30) cc_final: 0.5865 (tp30) REVERT: C 159 ARG cc_start: 0.7644 (tpt170) cc_final: 0.7366 (tpt170) REVERT: C 162 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6828 (mmt180) REVERT: C 217 ARG cc_start: 0.7844 (mmt-90) cc_final: 0.7018 (mmp80) REVERT: C 259 PHE cc_start: 0.8072 (t80) cc_final: 0.7782 (t80) REVERT: C 289 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7553 (ttm-80) REVERT: C 395 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6284 (mtp180) REVERT: C 403 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7208 (ptt180) REVERT: C 414 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: C 484 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7938 (ttp-170) REVERT: C 630 MET cc_start: 0.3687 (OUTLIER) cc_final: 0.3059 (ppp) REVERT: C 672 MET cc_start: 0.3385 (ptm) cc_final: 0.2897 (pp-130) REVERT: D 114 GLN cc_start: 0.6442 (mt0) cc_final: 0.5888 (tp-100) REVERT: D 162 ARG cc_start: 0.7319 (mtt180) cc_final: 0.6785 (mmt180) REVERT: D 217 ARG cc_start: 0.7672 (mmt-90) cc_final: 0.7326 (mmp80) REVERT: D 285 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7059 (mtp-110) REVERT: D 288 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7439 (mt-10) REVERT: D 363 LYS cc_start: 0.7739 (tppp) cc_final: 0.7441 (tptt) REVERT: D 520 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: D 575 GLN cc_start: 0.7159 (tm-30) cc_final: 0.6801 (tm130) REVERT: D 672 MET cc_start: 0.4711 (ttp) cc_final: 0.4342 (ttp) REVERT: E 129 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7173 (mp) REVERT: E 162 ARG cc_start: 0.6350 (mmt180) cc_final: 0.6117 (mmt180) REVERT: E 217 ARG cc_start: 0.7510 (mmt-90) cc_final: 0.7101 (mmp80) REVERT: E 288 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7795 (mt-10) REVERT: E 395 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6177 (mtp180) REVERT: E 403 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7292 (ptt180) REVERT: E 414 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: E 545 MET cc_start: 0.5825 (ptt) cc_final: 0.5558 (ppp) REVERT: E 568 TYR cc_start: 0.7271 (p90) cc_final: 0.6996 (p90) REVERT: E 569 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6690 (mmp-170) REVERT: E 630 MET cc_start: 0.3651 (OUTLIER) cc_final: 0.3083 (ppp) REVERT: E 672 MET cc_start: 0.3290 (ptm) cc_final: 0.2850 (pp-130) REVERT: F 97 GLN cc_start: 0.7231 (tt0) cc_final: 0.6986 (mp10) REVERT: F 100 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5994 (tp30) REVERT: F 114 GLN cc_start: 0.6521 (mt0) cc_final: 0.5987 (tp-100) REVERT: F 155 GLU cc_start: 0.7328 (mp0) cc_final: 0.6698 (mp0) REVERT: F 217 ARG cc_start: 0.7634 (mmt-90) cc_final: 0.7377 (mmp80) REVERT: F 249 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.8172 (mmt90) REVERT: F 307 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7221 (mtp-110) REVERT: F 363 LYS cc_start: 0.7679 (tppp) cc_final: 0.7408 (tptt) REVERT: F 520 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: F 521 GLN cc_start: 0.8369 (tp40) cc_final: 0.8050 (tt0) REVERT: F 672 MET cc_start: 0.3402 (ptm) cc_final: 0.2991 (pp-130) REVERT: G 104 LEU cc_start: 0.7411 (mt) cc_final: 0.7151 (mp) REVERT: G 217 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7120 (mmp80) REVERT: G 259 PHE cc_start: 0.8217 (t80) cc_final: 0.8006 (t80) REVERT: G 307 ARG cc_start: 0.7092 (mtp-110) cc_final: 0.6635 (mtp-110) REVERT: G 361 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7482 (ptmt) REVERT: G 395 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6175 (mtp180) REVERT: G 403 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7267 (ptt180) REVERT: G 414 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: G 569 ARG cc_start: 0.6556 (tpp-160) cc_final: 0.6182 (mmm160) REVERT: G 672 MET cc_start: 0.3161 (ptm) cc_final: 0.2779 (pp-130) REVERT: H 217 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7152 (mmp80) REVERT: H 249 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7984 (mmt90) REVERT: H 259 PHE cc_start: 0.7939 (t80) cc_final: 0.7723 (t80) REVERT: H 288 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7355 (mt-10) REVERT: H 520 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: H 521 GLN cc_start: 0.8334 (tp40) cc_final: 0.8050 (tt0) REVERT: H 672 MET cc_start: 0.4533 (ttp) cc_final: 0.4197 (ttp) outliers start: 97 outliers final: 41 residues processed: 423 average time/residue: 0.8557 time to fit residues: 425.8515 Evaluate side-chains 395 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 385 THR 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 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 C residue 653 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 285 ARG 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 97 GLN Chi-restraints excluded: chain E residue 129 LEU 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 E residue 630 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU 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 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 283 VAL Chi-restraints excluded: chain H residue 295 LEU 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: 3.9990 chunk 199 optimal weight: 0.0670 chunk 463 optimal weight: 2.9990 chunk 483 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 453 optimal weight: 2.9990 chunk 437 optimal weight: 4.9990 chunk 362 optimal weight: 10.0000 chunk 66 optimal weight: 0.0470 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 486 ASN B 337 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 337 ASN G 575 GLN H 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120399 restraints weight = 41879.737| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.80 r_work: 0.3135 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4891 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= 0.101 Angle : 0.483 14.615 53968 Z= 0.244 Chirality : 0.038 0.157 6168 Planarity : 0.003 0.044 6944 Dihedral : 4.120 28.802 5432 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.08 % Allowed : 13.37 % Favored : 84.54 % 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 (0.13), residues: 4912 helix: 1.29 (0.09), residues: 3448 sheet: -0.08 (0.47), residues: 152 loop : -0.13 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 289 TYR 0.007 0.001 TYR G 429 PHE 0.020 0.001 PHE D 259 TRP 0.006 0.001 TRP G 253 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (39888) covalent geometry : angle 0.48314 / 0.24 (53968) hydrogen bonds : bond 0.03014 / 2.02 ( 2008) hydrogen bonds : angle 3.39355 / 2.41 ( 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 429 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.6234 (mp-120) cc_final: 0.6018 (mm-40) REVERT: A 162 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6752 (mmt180) REVERT: A 307 ARG cc_start: 0.7029 (mtp-110) cc_final: 0.6563 (mtp-110) REVERT: A 395 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6211 (mtp180) REVERT: A 403 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7057 (ptt180) REVERT: A 414 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: A 520 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: A 545 MET cc_start: 0.5881 (ptt) cc_final: 0.5610 (ppp) REVERT: A 569 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6372 (mmp-170) REVERT: A 630 MET cc_start: 0.2857 (ppp) cc_final: 0.2075 (ttp) REVERT: A 672 MET cc_start: 0.3050 (ptm) cc_final: 0.2573 (pp-130) REVERT: B 97 GLN cc_start: 0.6956 (tt0) cc_final: 0.6584 (mp10) REVERT: B 100 GLU cc_start: 0.6228 (mt-10) cc_final: 0.5918 (mt-10) REVERT: B 217 ARG cc_start: 0.7681 (mmt-90) cc_final: 0.6856 (mmp80) REVERT: B 249 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.8123 (mmt90) REVERT: B 285 ARG cc_start: 0.7839 (mpt180) cc_final: 0.7019 (mtp-110) REVERT: B 363 LYS cc_start: 0.7741 (tppp) cc_final: 0.7499 (tptt) REVERT: B 521 GLN cc_start: 0.8312 (tp40) cc_final: 0.8025 (tt0) REVERT: B 575 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6609 (tm130) REVERT: B 672 MET cc_start: 0.4488 (OUTLIER) cc_final: 0.3844 (ttt) REVERT: C 97 GLN cc_start: 0.6274 (mp-120) cc_final: 0.5979 (mm-40) REVERT: C 100 GLU cc_start: 0.6042 (tp30) cc_final: 0.5837 (tp30) REVERT: C 159 ARG cc_start: 0.7601 (tpt170) cc_final: 0.7312 (tpt170) REVERT: C 162 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6786 (mmt180) REVERT: C 217 ARG cc_start: 0.7811 (mmt-90) cc_final: 0.6980 (mmp80) REVERT: C 259 PHE cc_start: 0.8027 (t80) cc_final: 0.7731 (t80) REVERT: C 289 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7494 (ttm-80) REVERT: C 395 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6278 (mtp180) REVERT: C 403 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7086 (ptt180) REVERT: C 414 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: C 484 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7901 (ttp-170) REVERT: C 545 MET cc_start: 0.5882 (ptt) cc_final: 0.5605 (ppp) REVERT: C 630 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.3037 (ppp) REVERT: C 672 MET cc_start: 0.3363 (ptm) cc_final: 0.2875 (pp-130) REVERT: D 162 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6748 (mmt180) REVERT: D 217 ARG cc_start: 0.7601 (mmt-90) cc_final: 0.7250 (mmp80) REVERT: D 249 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8104 (mmt90) REVERT: D 285 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7076 (mtp-110) REVERT: D 363 LYS cc_start: 0.7726 (tppp) cc_final: 0.7465 (tptt) REVERT: D 520 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: D 575 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6725 (tm130) REVERT: D 672 MET cc_start: 0.4550 (ttp) cc_final: 0.4178 (ttp) REVERT: E 100 GLU cc_start: 0.5922 (tp30) cc_final: 0.5549 (tp30) REVERT: E 129 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7086 (mp) REVERT: E 217 ARG cc_start: 0.7495 (mmt-90) cc_final: 0.7088 (mmp80) REVERT: E 288 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7720 (mt-10) REVERT: E 395 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6246 (mtp180) REVERT: E 403 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7316 (ptt180) REVERT: E 414 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: E 545 MET cc_start: 0.5837 (ptt) cc_final: 0.5576 (ppp) REVERT: E 568 TYR cc_start: 0.7283 (p90) cc_final: 0.6925 (p90) REVERT: E 672 MET cc_start: 0.3260 (ptm) cc_final: 0.2834 (pp-130) REVERT: F 97 GLN cc_start: 0.7210 (tt0) cc_final: 0.6958 (mp10) REVERT: F 100 GLU cc_start: 0.6213 (mt-10) cc_final: 0.5955 (tp30) REVERT: F 111 GLU cc_start: 0.6190 (mp0) cc_final: 0.5769 (mt-10) REVERT: F 114 GLN cc_start: 0.6474 (mt0) cc_final: 0.5898 (tp-100) REVERT: F 155 GLU cc_start: 0.7284 (mp0) cc_final: 0.6642 (mp0) REVERT: F 217 ARG cc_start: 0.7566 (mmt-90) cc_final: 0.7311 (mmp80) REVERT: F 249 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.8135 (mmt90) REVERT: F 285 ARG cc_start: 0.7908 (mpt180) cc_final: 0.7184 (mtp-110) REVERT: F 307 ARG cc_start: 0.7400 (mtm110) cc_final: 0.7170 (mtp-110) REVERT: F 363 LYS cc_start: 0.7667 (tppp) cc_final: 0.7398 (tptt) REVERT: F 520 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: F 521 GLN cc_start: 0.8356 (tp40) cc_final: 0.8032 (tt0) REVERT: F 672 MET cc_start: 0.3382 (ptm) cc_final: 0.2981 (pp-130) REVERT: G 104 LEU cc_start: 0.7356 (mt) cc_final: 0.7098 (mp) REVERT: G 162 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6824 (mmt180) REVERT: G 217 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7102 (mmp80) REVERT: G 224 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7510 (ttm170) REVERT: G 259 PHE cc_start: 0.8206 (t80) cc_final: 0.7990 (t80) REVERT: G 307 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.6547 (mtp-110) REVERT: G 361 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7442 (ptmt) REVERT: G 395 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6180 (mtp180) REVERT: G 403 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7159 (ptt180) REVERT: G 414 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: G 545 MET cc_start: 0.5823 (ptt) cc_final: 0.5577 (ppp) REVERT: G 569 ARG cc_start: 0.6552 (tpp-160) cc_final: 0.6167 (mmm160) REVERT: G 672 MET cc_start: 0.3143 (ptm) cc_final: 0.2767 (pp-130) REVERT: H 100 GLU cc_start: 0.6111 (tp30) cc_final: 0.5896 (tp30) REVERT: H 217 ARG cc_start: 0.7464 (mmt-90) cc_final: 0.7151 (mmp80) REVERT: H 249 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7967 (mmt90) REVERT: H 259 PHE cc_start: 0.7829 (t80) cc_final: 0.7595 (t80) REVERT: H 520 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: H 521 GLN cc_start: 0.8331 (tp40) cc_final: 0.8036 (tt0) REVERT: H 672 MET cc_start: 0.4625 (ttp) cc_final: 0.4230 (ttp) outliers start: 86 outliers final: 42 residues processed: 412 average time/residue: 0.8867 time to fit residues: 430.7809 Evaluate side-chains 389 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 385 THR 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 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 C residue 653 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 285 ARG 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 97 GLN Chi-restraints excluded: chain E residue 129 LEU 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 F residue 163 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 385 THR 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 224 ARG 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.0319 > 50: distance: 4 - 34: 30.220 distance: 14 - 43: 11.895 distance: 23 - 52: 28.326 distance: 29 - 34: 27.315 distance: 30 - 57: 25.328 distance: 34 - 35: 29.201 distance: 35 - 36: 24.961 distance: 35 - 38: 24.789 distance: 36 - 37: 11.941 distance: 36 - 43: 18.938 distance: 38 - 39: 21.342 distance: 39 - 40: 11.189 distance: 40 - 41: 6.697 distance: 40 - 42: 25.647 distance: 43 - 44: 25.336 distance: 44 - 45: 20.459 distance: 44 - 47: 6.879 distance: 45 - 46: 27.256 distance: 45 - 52: 17.940 distance: 47 - 48: 20.334 distance: 48 - 49: 15.254 distance: 49 - 50: 13.338 distance: 49 - 51: 17.473 distance: 52 - 53: 25.772 distance: 53 - 54: 17.562 distance: 53 - 56: 33.908 distance: 54 - 55: 24.141 distance: 54 - 57: 20.637 distance: 57 - 58: 12.639 distance: 58 - 59: 25.523 distance: 58 - 61: 7.479 distance: 59 - 60: 49.738 distance: 59 - 71: 20.515 distance: 61 - 62: 9.700 distance: 62 - 63: 7.454 distance: 62 - 64: 25.068 distance: 63 - 65: 19.319 distance: 64 - 66: 47.675 distance: 64 - 67: 31.491 distance: 65 - 66: 39.179 distance: 66 - 68: 33.772 distance: 67 - 69: 7.142 distance: 68 - 70: 15.728 distance: 69 - 70: 8.680 distance: 71 - 72: 28.485 distance: 72 - 73: 10.136 distance: 72 - 75: 45.967 distance: 73 - 74: 16.859 distance: 73 - 79: 40.030 distance: 75 - 76: 27.364 distance: 76 - 77: 22.125 distance: 76 - 78: 30.308 distance: 79 - 80: 36.270 distance: 80 - 81: 31.259 distance: 80 - 83: 12.929 distance: 81 - 82: 27.074 distance: 81 - 87: 32.659 distance: 83 - 84: 41.747 distance: 84 - 85: 35.522 distance: 84 - 86: 48.957 distance: 87 - 88: 30.063 distance: 87 - 93: 22.163 distance: 88 - 89: 26.114 distance: 88 - 91: 19.911 distance: 89 - 90: 22.115 distance: 89 - 94: 52.569 distance: 91 - 92: 21.924 distance: 92 - 93: 27.617 distance: 94 - 95: 32.803 distance: 95 - 96: 22.688 distance: 95 - 98: 16.425 distance: 96 - 97: 46.367 distance: 96 - 99: 12.180 distance: 99 - 100: 30.424 distance: 100 - 101: 9.168 distance: 100 - 103: 7.950 distance: 101 - 102: 15.544 distance: 101 - 106: 21.111 distance: 103 - 104: 15.217 distance: 103 - 105: 29.854 distance: 106 - 107: 6.534 distance: 107 - 108: 17.793 distance: 108 - 109: 13.073 distance: 108 - 110: 24.551 distance: 109 - 131: 29.330