Starting phenix.real_space_refine on Sun Aug 24 15:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgm_36239/08_2025/8jgm_36239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgm_36239/08_2025/8jgm_36239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgm_36239/08_2025/8jgm_36239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgm_36239/08_2025/8jgm_36239.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgm_36239/08_2025/8jgm_36239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgm_36239/08_2025/8jgm_36239.cif" } resolution = 2.89 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= 0.002 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 13692 2.51 5 N 3540 2.21 5 O 3798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 206 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21120 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3520 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 414} Chain breaks: 1 Chain: "B" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3520 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 414} Chain breaks: 1 Chain: "C" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3520 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 414} Chain breaks: 1 Chain: "D" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3520 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 414} Chain breaks: 1 Chain: "E" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3520 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 414} Chain breaks: 1 Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3520 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 414} Chain breaks: 1 Time building chain proxies: 3.94, per 1000 atoms: 0.19 Number of scatterers: 21120 At special positions: 0 Unit cell: (111.219, 135.84, 141.783, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3798 8.00 N 3540 7.00 C 13692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 674.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 18 sheets defined 48.8% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.525A pdb=" N GLN A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 removed outlier: 3.738A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.625A pdb=" N ILE A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.767A pdb=" N PHE A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 248 through 271 removed outlier: 4.105A pdb=" N GLU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 4.120A pdb=" N ILE A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.608A pdb=" N THR A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.149A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.826A pdb=" N HIS A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 379 through 386 removed outlier: 4.208A pdb=" N ASP A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 393 through 400 removed outlier: 4.021A pdb=" N LYS A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 420 through 424 Proline residue: A 424 - end of helix Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.510A pdb=" N ASP A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.993A pdb=" N ILE A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.710A pdb=" N GLN B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 183 removed outlier: 3.547A pdb=" N VAL B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.532A pdb=" N ILE B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.718A pdb=" N PHE B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 248 through 271 removed outlier: 3.960A pdb=" N GLU B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 4.105A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 removed outlier: 4.062A pdb=" N GLY B 292 " --> pdb=" O GLU B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 302 through 308 removed outlier: 3.527A pdb=" N THR B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.249A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 360 through 366 removed outlier: 4.148A pdb=" N ALA B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.306A pdb=" N ASP B 386 " --> pdb=" O HIS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 420 through 424 Proline residue: B 424 - end of helix Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.752A pdb=" N ILE B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.667A pdb=" N GLN C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.519A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.604A pdb=" N ILE C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.818A pdb=" N PHE C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 248 through 271 removed outlier: 4.199A pdb=" N GLU C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.118A pdb=" N ILE C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 292 removed outlier: 3.703A pdb=" N GLY C 292 " --> pdb=" O GLU C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 302 through 308 removed outlier: 3.678A pdb=" N THR C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.588A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.098A pdb=" N ALA C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 379 through 393 removed outlier: 3.967A pdb=" N ASP C 386 " --> pdb=" O HIS C 382 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 420 through 424 Proline residue: C 424 - end of helix Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.796A pdb=" N GLU C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 509 removed outlier: 3.547A pdb=" N ILE C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 502 " --> pdb=" O ARG C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 removed outlier: 3.590A pdb=" N GLN D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 removed outlier: 3.825A pdb=" N VAL D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.639A pdb=" N ILE D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.649A pdb=" N PHE D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 248 through 271 removed outlier: 3.554A pdb=" N PHE D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 4.112A pdb=" N ILE D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 308 removed outlier: 3.547A pdb=" N THR D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 removed outlier: 4.241A pdb=" N GLY D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 361 through 367 removed outlier: 3.598A pdb=" N LEU D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS D 367 " --> pdb=" O TYR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 379 through 393 removed outlier: 4.133A pdb=" N ASP D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS D 387 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 420 through 424 Proline residue: D 424 - end of helix Processing helix chain 'D' and resid 425 through 434 removed outlier: 3.599A pdb=" N ASP D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'D' and resid 491 through 495 Processing helix chain 'D' and resid 496 through 509 removed outlier: 3.520A pdb=" N ASP D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 removed outlier: 3.543A pdb=" N ARG E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 3.618A pdb=" N VAL E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 202 removed outlier: 3.666A pdb=" N ILE E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.710A pdb=" N PHE E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 removed outlier: 4.621A pdb=" N GLU E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 removed outlier: 4.027A pdb=" N ILE E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 308 removed outlier: 3.710A pdb=" N THR E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 314 removed outlier: 4.128A pdb=" N GLY E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 344 through 354 Processing helix chain 'E' and resid 361 through 367 removed outlier: 3.546A pdb=" N LEU E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS E 367 " --> pdb=" O TYR E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 379 through 386 removed outlier: 4.150A pdb=" N ASP E 386 " --> pdb=" O HIS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 393 Processing helix chain 'E' and resid 393 through 400 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 420 through 424 Proline residue: E 424 - end of helix Processing helix chain 'E' and resid 425 through 435 Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 496 through 509 removed outlier: 4.085A pdb=" N ILE E 500 " --> pdb=" O ALA E 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 502 " --> pdb=" O ARG E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.542A pdb=" N GLN F 142 " --> pdb=" O SER F 138 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 183 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.745A pdb=" N ILE F 190 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 4.104A pdb=" N PHE F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 248 through 271 removed outlier: 3.501A pdb=" N PHE F 257 " --> pdb=" O TYR F 253 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 4.157A pdb=" N ILE F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 292 removed outlier: 3.649A pdb=" N GLY F 292 " --> pdb=" O GLU F 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 289 through 292' Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.608A pdb=" N GLN F 307 " --> pdb=" O PRO F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.837A pdb=" N GLY F 313 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 344 through 353 Processing helix chain 'F' and resid 360 through 366 removed outlier: 4.170A pdb=" N ALA F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 372 Processing helix chain 'F' and resid 379 through 386 removed outlier: 4.109A pdb=" N ASP F 386 " --> pdb=" O HIS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'F' and resid 393 through 400 Processing helix chain 'F' and resid 414 through 419 Processing helix chain 'F' and resid 420 through 424 Proline residue: F 424 - end of helix Processing helix chain 'F' and resid 425 through 435 Processing helix chain 'F' and resid 443 through 448 Processing helix chain 'F' and resid 466 through 474 Processing helix chain 'F' and resid 475 through 477 No H-bonds generated for 'chain 'F' and resid 475 through 477' Processing helix chain 'F' and resid 491 through 495 Processing helix chain 'F' and resid 496 through 509 removed outlier: 4.245A pdb=" N ILE F 500 " --> pdb=" O ALA F 496 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP F 502 " --> pdb=" O ARG F 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.580A pdb=" N PHE A 103 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 122 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 153 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 119 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU A 211 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 121 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN A 213 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 123 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TRP A 208 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 234 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 210 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE A 236 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 212 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ALA A 455 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 234 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA A 457 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 236 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR A 459 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 removed outlier: 4.557A pdb=" N PHE B 103 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 120 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU B 153 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR B 122 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR B 119 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU B 211 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 121 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLN B 213 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 123 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TRP B 208 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 234 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 210 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE B 236 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 212 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N ALA B 455 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 234 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA B 457 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 236 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR B 459 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 71 removed outlier: 4.555A pdb=" N PHE C 103 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 120 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU C 153 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR C 122 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 209 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN C 213 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TRP C 208 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 234 " --> pdb=" O TRP C 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 210 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE C 236 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY C 212 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N ALA C 455 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 234 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA C 457 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 236 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR C 459 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 71 Processing sheet with id=AB2, first strand: chain 'D' and resid 69 through 71 removed outlier: 4.543A pdb=" N PHE D 103 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 120 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 153 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR D 122 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR D 119 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N LEU D 211 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU D 121 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLN D 213 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 123 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TRP D 208 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 234 " --> pdb=" O TRP D 208 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE D 210 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE D 236 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY D 212 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ALA D 455 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL D 234 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ALA D 457 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 236 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N TYR D 459 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 293 through 294 Processing sheet with id=AB4, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AB5, first strand: chain 'E' and resid 69 through 71 removed outlier: 4.619A pdb=" N PHE E 103 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 120 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU E 153 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR E 122 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E 213 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP E 208 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 234 " --> pdb=" O TRP E 208 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E 210 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE E 236 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY E 212 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ALA E 455 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 234 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA E 457 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E 236 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N TYR E 459 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 454 " --> pdb=" O ARG E 481 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TRP E 483 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA E 456 " --> pdb=" O TRP E 483 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR E 485 " --> pdb=" O ALA E 456 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL E 458 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 293 through 294 Processing sheet with id=AB7, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AB8, first strand: chain 'F' and resid 69 through 71 removed outlier: 4.575A pdb=" N PHE F 103 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE F 107 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU F 120 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU F 153 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR F 122 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N TRP F 208 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 234 " --> pdb=" O TRP F 208 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE F 210 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE F 236 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY F 212 " --> pdb=" O ILE F 236 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N ALA F 455 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 234 " --> pdb=" O ALA F 455 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA F 457 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE F 236 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N TYR F 459 " --> pdb=" O ILE F 236 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL F 454 " --> pdb=" O ARG F 481 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TRP F 483 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA F 456 " --> pdb=" O TRP F 483 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR F 485 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL F 458 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 293 through 294 829 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6064 1.34 - 1.46: 3691 1.46 - 1.58: 11809 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 21708 Sorted by residual: bond pdb=" CA PRO B 439 " pdb=" C PRO B 439 " ideal model delta sigma weight residual 1.514 1.539 -0.024 5.50e-03 3.31e+04 1.96e+01 bond pdb=" N ARG F 133 " pdb=" CA ARG F 133 " ideal model delta sigma weight residual 1.458 1.490 -0.032 7.40e-03 1.83e+04 1.89e+01 bond pdb=" CA PRO E 439 " pdb=" C PRO E 439 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.70e+01 bond pdb=" CA PRO F 439 " pdb=" C PRO F 439 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.67e+01 bond pdb=" N ARG C 133 " pdb=" CA ARG C 133 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.62e+01 ... (remaining 21703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 23010 2.07 - 4.15: 5886 4.15 - 6.22: 477 6.22 - 8.30: 35 8.30 - 10.37: 10 Bond angle restraints: 29418 Sorted by residual: angle pdb=" N SER D 168 " pdb=" CA SER D 168 " pdb=" C SER D 168 " ideal model delta sigma weight residual 110.65 100.28 10.37 1.26e+00 6.30e-01 6.78e+01 angle pdb=" N LYS D 173 " pdb=" CA LYS D 173 " pdb=" C LYS D 173 " ideal model delta sigma weight residual 112.54 102.88 9.66 1.22e+00 6.72e-01 6.26e+01 angle pdb=" N ALA C 187 " pdb=" CA ALA C 187 " pdb=" C ALA C 187 " ideal model delta sigma weight residual 111.33 120.81 -9.48 1.21e+00 6.83e-01 6.14e+01 angle pdb=" N ILE D 165 " pdb=" CA ILE D 165 " pdb=" C ILE D 165 " ideal model delta sigma weight residual 108.12 118.39 -10.27 1.44e+00 4.82e-01 5.09e+01 angle pdb=" CA VAL D 77 " pdb=" C VAL D 77 " pdb=" N PRO D 78 " ideal model delta sigma weight residual 116.57 122.89 -6.32 9.80e-01 1.04e+00 4.15e+01 ... (remaining 29413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11981 17.80 - 35.60: 673 35.60 - 53.40: 121 53.40 - 71.20: 50 71.20 - 89.00: 21 Dihedral angle restraints: 12846 sinusoidal: 5214 harmonic: 7632 Sorted by residual: dihedral pdb=" CA SER B 167 " pdb=" C SER B 167 " pdb=" N SER B 168 " pdb=" CA SER B 168 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA SER A 167 " pdb=" C SER A 167 " pdb=" N SER A 168 " pdb=" CA SER A 168 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY B 125 " pdb=" C GLY B 125 " pdb=" N GLY B 126 " pdb=" CA GLY B 126 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 12843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1851 0.075 - 0.150: 981 0.150 - 0.225: 192 0.225 - 0.301: 75 0.301 - 0.376: 21 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA GLU B 79 " pdb=" N GLU B 79 " pdb=" C GLU B 79 " pdb=" CB GLU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA GLU C 79 " pdb=" N GLU C 79 " pdb=" C GLU C 79 " pdb=" CB GLU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA GLU E 79 " pdb=" N GLU E 79 " pdb=" C GLU E 79 " pdb=" CB GLU E 79 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 3117 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 438 " 0.085 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" CG TRP F 438 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP F 438 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 438 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP F 438 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP F 438 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP F 438 " -0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 438 " 0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 438 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP F 438 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 438 " -0.076 2.00e-02 2.50e+03 4.15e-02 4.31e+01 pdb=" CG TRP D 438 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 438 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP D 438 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP D 438 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP D 438 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 438 " 0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 438 " -0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 438 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 438 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 438 " -0.067 2.00e-02 2.50e+03 3.87e-02 3.75e+01 pdb=" CG TRP C 438 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP C 438 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 438 " 0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP C 438 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP C 438 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP C 438 " 0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 438 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 438 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 438 " -0.051 2.00e-02 2.50e+03 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4372 2.82 - 3.34: 19707 3.34 - 3.86: 30946 3.86 - 4.38: 37212 4.38 - 4.90: 65494 Nonbonded interactions: 157731 Sorted by model distance: nonbonded pdb=" OE2 GLU D 409 " pdb=" OH TYR D 464 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU C 106 " pdb=" NH2 ARG C 149 " model vdw 2.348 3.120 nonbonded pdb=" OE2 GLU D 487 " pdb=" NE1 TRP E 483 " model vdw 2.398 3.120 nonbonded pdb=" OG SER F 214 " pdb=" NE2 HIS F 490 " model vdw 2.466 3.120 nonbonded pdb=" OH TYR E 325 " pdb=" O PRO F 134 " model vdw 2.483 3.040 ... (remaining 157726 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.090 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.100 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.046 21708 Z= 0.727 Angle : 1.733 10.373 29418 Z= 1.181 Chirality : 0.096 0.376 3120 Planarity : 0.012 0.124 3786 Dihedral : 12.899 89.000 7962 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.75 (0.15), residues: 2628 helix: -0.72 (0.15), residues: 912 sheet: 0.57 (0.26), residues: 360 loop : -0.53 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 133 TYR 0.081 0.015 TYR E 253 PHE 0.061 0.008 PHE B 172 TRP 0.085 0.014 TRP F 438 HIS 0.009 0.003 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.01214 (21708) covalent geometry : angle 1.73339 (29418) hydrogen bonds : bond 0.22136 ( 817) hydrogen bonds : angle 7.24218 ( 2361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: E 463 MET cc_start: 0.7656 (ttp) cc_final: 0.7190 (ttp) outliers start: 2 outliers final: 1 residues processed: 166 average time/residue: 0.6606 time to fit residues: 121.2621 Evaluate side-chains 88 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 148 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 503 HIS B 486 ASN C 486 ASN D 213 GLN D 466 ASN D 486 ASN E 466 ASN F 448 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.048161 restraints weight = 67265.534| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.75 r_work: 0.2649 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21708 Z= 0.145 Angle : 0.664 7.946 29418 Z= 0.363 Chirality : 0.046 0.231 3120 Planarity : 0.005 0.037 3786 Dihedral : 5.664 38.420 2882 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 7.66 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.24 (0.16), residues: 2628 helix: 0.30 (0.16), residues: 1008 sheet: 0.47 (0.26), residues: 372 loop : -0.66 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 494 TYR 0.012 0.001 TYR C 93 PHE 0.019 0.002 PHE A 148 TRP 0.015 0.001 TRP C 483 HIS 0.007 0.001 HIS F 367 Details of bonding type rmsd covalent geometry : bond 0.00290 (21708) covalent geometry : angle 0.66384 (29418) hydrogen bonds : bond 0.05774 ( 817) hydrogen bonds : angle 4.71865 ( 2361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 169 MET cc_start: 0.7974 (tpp) cc_final: 0.7681 (tpp) REVERT: C 410 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8809 (ptp) REVERT: E 265 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8854 (mm-30) outliers start: 32 outliers final: 5 residues processed: 117 average time/residue: 0.5925 time to fit residues: 77.7351 Evaluate side-chains 82 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 258 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 450 ASN A 486 ASN A 503 HIS B 85 HIS B 486 ASN C 85 HIS D 85 HIS D 486 ASN E 85 HIS F 476 HIS ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.042043 restraints weight = 68589.997| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.74 r_work: 0.2460 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 21708 Z= 0.300 Angle : 0.703 7.248 29418 Z= 0.377 Chirality : 0.049 0.223 3120 Planarity : 0.006 0.056 3786 Dihedral : 5.455 48.049 2882 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 9.32 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2628 helix: 0.56 (0.16), residues: 1050 sheet: 0.35 (0.27), residues: 372 loop : -0.97 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 105 TYR 0.020 0.002 TYR B 93 PHE 0.020 0.002 PHE F 215 TRP 0.016 0.002 TRP C 483 HIS 0.009 0.002 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00720 (21708) covalent geometry : angle 0.70268 (29418) hydrogen bonds : bond 0.06577 ( 817) hydrogen bonds : angle 4.52072 ( 2361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 74 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 466 ASN cc_start: 0.8703 (t0) cc_final: 0.8217 (t0) REVERT: B 117 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8787 (mtp) REVERT: B 169 MET cc_start: 0.8134 (tpp) cc_final: 0.7869 (tpp) REVERT: E 79 GLU cc_start: 0.9011 (mp0) cc_final: 0.8761 (mp0) REVERT: E 283 ASN cc_start: 0.9082 (t0) cc_final: 0.8802 (t0) REVERT: E 355 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8818 (p90) outliers start: 48 outliers final: 11 residues processed: 114 average time/residue: 0.4778 time to fit residues: 62.5573 Evaluate side-chains 82 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain F residue 148 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 148 optimal weight: 0.0060 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 450 ASN B 349 ASN B 486 ASN C 486 ASN F 349 ASN F 486 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.058975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.044922 restraints weight = 67155.312| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.75 r_work: 0.2542 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.113 21708 Z= 0.110 Angle : 0.554 8.390 29418 Z= 0.293 Chirality : 0.043 0.231 3120 Planarity : 0.005 0.052 3786 Dihedral : 4.950 45.954 2882 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.43 % Allowed : 9.86 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2628 helix: 0.75 (0.16), residues: 1068 sheet: 0.46 (0.26), residues: 372 loop : -0.95 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 494 TYR 0.006 0.001 TYR E 223 PHE 0.013 0.001 PHE C 218 TRP 0.015 0.001 TRP A 483 HIS 0.002 0.000 HIS C 490 Details of bonding type rmsd covalent geometry : bond 0.00240 (21708) covalent geometry : angle 0.55406 (29418) hydrogen bonds : bond 0.04157 ( 817) hydrogen bonds : angle 4.08772 ( 2361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 221 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9192 (mp) REVERT: B 117 MET cc_start: 0.8972 (mtm) cc_final: 0.8749 (mtp) REVERT: B 489 MET cc_start: 0.8859 (mmm) cc_final: 0.8607 (mtt) REVERT: C 84 ASP cc_start: 0.8850 (p0) cc_final: 0.8044 (p0) REVERT: E 283 ASN cc_start: 0.9093 (t0) cc_final: 0.8824 (t0) REVERT: E 355 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8646 (p90) outliers start: 32 outliers final: 11 residues processed: 113 average time/residue: 0.4843 time to fit residues: 63.3126 Evaluate side-chains 83 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 355 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 503 HIS B 349 ASN D 69 HIS F 85 HIS F 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.043004 restraints weight = 67552.656| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.68 r_work: 0.2482 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 21708 Z= 0.196 Angle : 0.596 9.900 29418 Z= 0.311 Chirality : 0.045 0.203 3120 Planarity : 0.005 0.051 3786 Dihedral : 4.843 49.903 2882 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.06 % Allowed : 9.63 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.05 (0.16), residues: 2628 helix: 1.01 (0.17), residues: 1068 sheet: 0.47 (0.26), residues: 372 loop : -0.99 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 105 TYR 0.013 0.001 TYR A 93 PHE 0.015 0.001 PHE F 196 TRP 0.016 0.001 TRP A 483 HIS 0.005 0.001 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00463 (21708) covalent geometry : angle 0.59620 (29418) hydrogen bonds : bond 0.05117 ( 817) hydrogen bonds : angle 4.10799 ( 2361) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 75 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9037 (mtm) cc_final: 0.8696 (mtp) REVERT: A 147 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 221 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9180 (mp) REVERT: B 79 GLU cc_start: 0.8591 (mp0) cc_final: 0.8294 (mp0) REVERT: B 117 MET cc_start: 0.9044 (mtm) cc_final: 0.8836 (mtp) REVERT: C 84 ASP cc_start: 0.8892 (p0) cc_final: 0.8083 (p0) REVERT: E 283 ASN cc_start: 0.9092 (t0) cc_final: 0.8824 (t0) REVERT: E 355 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8620 (p90) REVERT: F 147 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8406 (pm20) outliers start: 46 outliers final: 12 residues processed: 113 average time/residue: 0.4436 time to fit residues: 57.7931 Evaluate side-chains 86 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 355 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 159 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 249 optimal weight: 0.3980 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS B 349 ASN F 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.057182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.043135 restraints weight = 67862.087| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.70 r_work: 0.2486 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21708 Z= 0.174 Angle : 0.582 14.562 29418 Z= 0.301 Chirality : 0.044 0.200 3120 Planarity : 0.005 0.043 3786 Dihedral : 4.748 52.063 2882 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.84 % Allowed : 10.53 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.07 (0.16), residues: 2628 helix: 1.06 (0.17), residues: 1062 sheet: 0.48 (0.26), residues: 372 loop : -1.02 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 494 TYR 0.009 0.001 TYR E 93 PHE 0.016 0.001 PHE F 148 TRP 0.018 0.001 TRP A 483 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00411 (21708) covalent geometry : angle 0.58205 (29418) hydrogen bonds : bond 0.04647 ( 817) hydrogen bonds : angle 4.03802 ( 2361) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9044 (mtm) cc_final: 0.8734 (mtp) REVERT: B 117 MET cc_start: 0.9053 (mtm) cc_final: 0.8851 (mtp) REVERT: C 84 ASP cc_start: 0.8868 (p0) cc_final: 0.8060 (p0) REVERT: E 283 ASN cc_start: 0.9100 (t0) cc_final: 0.8831 (t0) REVERT: E 355 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.8574 (p90) REVERT: F 147 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8335 (pm20) outliers start: 41 outliers final: 15 residues processed: 106 average time/residue: 0.4805 time to fit residues: 59.0285 Evaluate side-chains 89 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 355 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 213 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 95 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS B 349 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.042931 restraints weight = 67738.600| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.70 r_work: 0.2481 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21708 Z= 0.183 Angle : 0.585 11.096 29418 Z= 0.301 Chirality : 0.044 0.201 3120 Planarity : 0.005 0.044 3786 Dihedral : 4.715 53.981 2882 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.34 % Allowed : 11.25 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.29 (0.16), residues: 2628 helix: 1.31 (0.17), residues: 1026 sheet: 0.49 (0.27), residues: 372 loop : -0.86 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 494 TYR 0.010 0.001 TYR E 93 PHE 0.016 0.001 PHE F 148 TRP 0.033 0.001 TRP A 483 HIS 0.007 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00434 (21708) covalent geometry : angle 0.58521 (29418) hydrogen bonds : bond 0.04740 ( 817) hydrogen bonds : angle 4.04009 ( 2361) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9022 (mtm) cc_final: 0.8751 (mtp) REVERT: B 329 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8224 (mtm-85) REVERT: C 84 ASP cc_start: 0.8858 (p0) cc_final: 0.8079 (p0) REVERT: C 169 MET cc_start: 0.8135 (tpp) cc_final: 0.7402 (tmt) REVERT: C 410 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8493 (mpt) REVERT: E 283 ASN cc_start: 0.9093 (t0) cc_final: 0.8824 (t0) REVERT: E 355 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8576 (p90) REVERT: F 147 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8319 (pm20) outliers start: 30 outliers final: 17 residues processed: 100 average time/residue: 0.5182 time to fit residues: 59.2264 Evaluate side-chains 91 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 482 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 218 optimal weight: 0.6980 chunk 162 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS B 349 ASN F 349 ASN F 503 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.057094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.043102 restraints weight = 67580.195| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.68 r_work: 0.2490 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21708 Z= 0.157 Angle : 0.572 11.818 29418 Z= 0.293 Chirality : 0.044 0.200 3120 Planarity : 0.005 0.044 3786 Dihedral : 4.639 55.302 2882 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.39 % Allowed : 10.98 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.31 (0.16), residues: 2628 helix: 1.32 (0.17), residues: 1026 sheet: 0.53 (0.27), residues: 372 loop : -0.85 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 494 TYR 0.008 0.001 TYR A 93 PHE 0.014 0.001 PHE F 148 TRP 0.027 0.001 TRP A 483 HIS 0.005 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00370 (21708) covalent geometry : angle 0.57150 (29418) hydrogen bonds : bond 0.04430 ( 817) hydrogen bonds : angle 3.99652 ( 2361) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9004 (mtm) cc_final: 0.8697 (mtp) REVERT: B 79 GLU cc_start: 0.8679 (mp0) cc_final: 0.8463 (mp0) REVERT: B 329 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8184 (mtm-85) REVERT: C 84 ASP cc_start: 0.8832 (p0) cc_final: 0.8049 (p0) REVERT: C 410 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8558 (mpt) REVERT: E 169 MET cc_start: 0.7655 (pmm) cc_final: 0.7422 (pp-130) REVERT: E 283 ASN cc_start: 0.9093 (t0) cc_final: 0.8814 (t0) REVERT: E 355 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8730 (p90) REVERT: F 79 GLU cc_start: 0.8663 (mp0) cc_final: 0.8440 (pm20) REVERT: F 147 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8310 (pm20) outliers start: 31 outliers final: 17 residues processed: 99 average time/residue: 0.4961 time to fit residues: 56.4473 Evaluate side-chains 92 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 113 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN F 486 ASN F 503 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.042455 restraints weight = 67984.987| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 3.68 r_work: 0.2466 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21708 Z= 0.211 Angle : 0.605 11.432 29418 Z= 0.310 Chirality : 0.045 0.200 3120 Planarity : 0.005 0.043 3786 Dihedral : 4.740 59.773 2882 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.52 % Allowed : 10.98 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.33 (0.16), residues: 2628 helix: 1.39 (0.17), residues: 1020 sheet: 0.53 (0.26), residues: 384 loop : -0.89 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.010 0.001 TYR E 93 PHE 0.017 0.001 PHE F 148 TRP 0.030 0.001 TRP A 483 HIS 0.005 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00503 (21708) covalent geometry : angle 0.60504 (29418) hydrogen bonds : bond 0.04946 ( 817) hydrogen bonds : angle 4.06741 ( 2361) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9028 (mtm) cc_final: 0.8747 (mtp) REVERT: B 79 GLU cc_start: 0.8755 (mp0) cc_final: 0.8539 (mp0) REVERT: B 329 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8234 (mtm-85) REVERT: C 169 MET cc_start: 0.7996 (tpp) cc_final: 0.7348 (tmt) REVERT: C 410 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8569 (mpt) REVERT: E 169 MET cc_start: 0.7621 (pmm) cc_final: 0.7415 (pp-130) REVERT: E 283 ASN cc_start: 0.9087 (t0) cc_final: 0.8809 (t0) REVERT: E 355 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8713 (p90) REVERT: F 147 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8316 (pm20) outliers start: 34 outliers final: 18 residues processed: 101 average time/residue: 0.4850 time to fit residues: 56.7392 Evaluate side-chains 93 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 102 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 219 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN F 503 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.058512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.044513 restraints weight = 67585.251| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 3.71 r_work: 0.2524 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21708 Z= 0.103 Angle : 0.562 13.957 29418 Z= 0.282 Chirality : 0.042 0.197 3120 Planarity : 0.004 0.047 3786 Dihedral : 4.453 57.636 2882 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.99 % Allowed : 11.47 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.36 (0.16), residues: 2628 helix: 1.33 (0.17), residues: 1026 sheet: 0.66 (0.26), residues: 384 loop : -0.85 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 186 TYR 0.006 0.001 TYR E 284 PHE 0.016 0.001 PHE A 148 TRP 0.017 0.001 TRP A 483 HIS 0.004 0.001 HIS C 503 Details of bonding type rmsd covalent geometry : bond 0.00232 (21708) covalent geometry : angle 0.56237 (29418) hydrogen bonds : bond 0.03615 ( 817) hydrogen bonds : angle 3.91960 ( 2361) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8972 (mtm) cc_final: 0.8672 (mtp) REVERT: A 169 MET cc_start: 0.5488 (mmm) cc_final: 0.5236 (mmm) REVERT: B 169 MET cc_start: 0.7240 (mmm) cc_final: 0.7024 (mmm) REVERT: B 329 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8159 (mtm-85) REVERT: C 84 ASP cc_start: 0.8912 (p0) cc_final: 0.8047 (p0) REVERT: C 169 MET cc_start: 0.7982 (tpp) cc_final: 0.7433 (tmt) REVERT: C 410 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8549 (mpt) REVERT: E 169 MET cc_start: 0.7755 (pmm) cc_final: 0.7524 (pp-130) REVERT: E 283 ASN cc_start: 0.9093 (t0) cc_final: 0.8813 (t0) REVERT: F 79 GLU cc_start: 0.8661 (mp0) cc_final: 0.8413 (pm20) REVERT: F 147 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: F 169 MET cc_start: 0.8000 (mmm) cc_final: 0.6975 (ppp) outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 0.5582 time to fit residues: 61.6314 Evaluate side-chains 87 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 355 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 213 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 254 optimal weight: 0.3980 chunk 221 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.044077 restraints weight = 67444.967| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.70 r_work: 0.2513 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21708 Z= 0.121 Angle : 0.563 13.853 29418 Z= 0.281 Chirality : 0.042 0.197 3120 Planarity : 0.004 0.044 3786 Dihedral : 4.394 57.897 2882 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.76 % Allowed : 11.92 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.47 (0.16), residues: 2628 helix: 1.44 (0.17), residues: 1020 sheet: 0.72 (0.26), residues: 384 loop : -0.80 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 186 TYR 0.007 0.001 TYR A 93 PHE 0.012 0.001 PHE A 218 TRP 0.021 0.001 TRP A 483 HIS 0.004 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00283 (21708) covalent geometry : angle 0.56254 (29418) hydrogen bonds : bond 0.03877 ( 817) hydrogen bonds : angle 3.89669 ( 2361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3771.45 seconds wall clock time: 65 minutes 22.36 seconds (3922.36 seconds total)