Starting phenix.real_space_refine on Wed Jun 18 09:41:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgm_36239/06_2025/8jgm_36239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgm_36239/06_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_36239/06_2025/8jgm_36239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgm_36239/06_2025/8jgm_36239.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgm_36239/06_2025/8jgm_36239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgm_36239/06_2025/8jgm_36239.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.02, per 1000 atoms: 0.62 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: 4.87 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.58 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: 7.97 Time building geometry restraints manager: 5.84 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: 0.03 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: 2.310 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.980 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 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:16.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.085 0.014 TRP F 438 HIS 0.009 0.003 HIS D 503 PHE 0.061 0.008 PHE B 172 TYR 0.081 0.015 TYR E 253 ARG 0.019 0.001 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.22136 ( 817) hydrogen bonds : angle 7.24218 ( 2361) covalent geometry : bond 0.01214 (21708) covalent geometry : angle 1.73339 (29418) *********************** 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 : 2.347 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: 1.7505 time to fit residues: 322.3165 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 : 2.626 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.062035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048228 restraints weight = 67340.635| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.76 r_work: 0.2652 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21708 Z= 0.143 Angle : 0.660 7.952 29418 Z= 0.360 Chirality : 0.046 0.229 3120 Planarity : 0.005 0.036 3786 Dihedral : 5.626 38.577 2882 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.43 % Allowed : 7.71 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2628 helix: 0.29 (0.16), residues: 1014 sheet: 0.47 (0.26), residues: 372 loop : -0.66 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 483 HIS 0.006 0.001 HIS F 367 PHE 0.022 0.002 PHE A 148 TYR 0.013 0.001 TYR C 325 ARG 0.006 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 817) hydrogen bonds : angle 4.68585 ( 2361) covalent geometry : bond 0.00289 (21708) covalent geometry : angle 0.66001 (29418) *********************** 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 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 2.435 Fit side-chains REVERT: A 147 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7901 (tm-30) REVERT: A 280 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: B 169 MET cc_start: 0.7987 (tpp) cc_final: 0.7697 (tpp) REVERT: C 410 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8784 (ptp) REVERT: E 265 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8856 (mm-30) outliers start: 32 outliers final: 4 residues processed: 116 average time/residue: 1.5209 time to fit residues: 199.8460 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 : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 GLU 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 148 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 134 optimal weight: 0.1980 chunk 209 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 155 GLN A 450 ASN A 486 ASN A 503 HIS B 85 HIS B 486 ASN C 486 ASN D 486 ASN F 486 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.045107 restraints weight = 67354.138| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.78 r_work: 0.2548 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21708 Z= 0.159 Angle : 0.594 7.386 29418 Z= 0.319 Chirality : 0.045 0.208 3120 Planarity : 0.005 0.044 3786 Dihedral : 5.035 42.472 2882 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.48 % Allowed : 9.41 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2628 helix: 0.64 (0.16), residues: 1068 sheet: 0.48 (0.26), residues: 372 loop : -0.83 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 483 HIS 0.006 0.001 HIS A 85 PHE 0.015 0.002 PHE F 215 TYR 0.013 0.001 TYR A 93 ARG 0.006 0.001 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 817) hydrogen bonds : angle 4.26844 ( 2361) covalent geometry : bond 0.00364 (21708) covalent geometry : angle 0.59378 (29418) *********************** 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 114 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 2.621 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 117 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8649 (mtp) REVERT: B 169 MET cc_start: 0.8006 (tpp) cc_final: 0.7795 (tpp) REVERT: C 117 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: E 283 ASN cc_start: 0.9116 (t0) cc_final: 0.8846 (t0) REVERT: E 355 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8774 (p90) REVERT: F 486 ASN cc_start: 0.9444 (t0) cc_final: 0.9159 (t0) outliers start: 33 outliers final: 6 residues processed: 106 average time/residue: 1.3862 time to fit residues: 169.2931 Evaluate side-chains 81 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 117 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 117 MET 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 175 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 241 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 186 optimal weight: 0.0270 chunk 129 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 4.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 349 ASN C 85 HIS C 466 ASN D 85 HIS E 85 HIS F 85 HIS F 476 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.042193 restraints weight = 68533.301| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.70 r_work: 0.2459 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 21708 Z= 0.251 Angle : 0.650 8.578 29418 Z= 0.345 Chirality : 0.047 0.208 3120 Planarity : 0.005 0.043 3786 Dihedral : 5.112 51.431 2882 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.42 % Allowed : 8.51 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2628 helix: 0.91 (0.16), residues: 1062 sheet: 0.40 (0.26), residues: 372 loop : -1.01 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 483 HIS 0.010 0.002 HIS E 503 PHE 0.020 0.002 PHE F 148 TYR 0.016 0.001 TYR B 93 ARG 0.007 0.001 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.05802 ( 817) hydrogen bonds : angle 4.28049 ( 2361) covalent geometry : bond 0.00595 (21708) covalent geometry : angle 0.64981 (29418) *********************** 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 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 76 time to evaluate : 2.285 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9113 (mtm) cc_final: 0.8794 (mtp) REVERT: A 147 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 221 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9189 (mp) REVERT: A 280 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8656 (mm-30) REVERT: B 117 MET cc_start: 0.9103 (mtm) cc_final: 0.8892 (mtp) REVERT: E 79 GLU cc_start: 0.8988 (mp0) cc_final: 0.8756 (mp0) REVERT: E 283 ASN cc_start: 0.9080 (t0) cc_final: 0.8790 (t0) REVERT: E 355 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8724 (p90) outliers start: 54 outliers final: 14 residues processed: 121 average time/residue: 1.1302 time to fit residues: 160.2805 Evaluate side-chains 86 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain B residue 77 VAL 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 D residue 209 THR Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 77 VAL 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 176 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 258 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN B 486 ASN D 69 HIS F 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.043918 restraints weight = 67759.301| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.71 r_work: 0.2507 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21708 Z= 0.122 Angle : 0.551 10.995 29418 Z= 0.287 Chirality : 0.043 0.201 3120 Planarity : 0.004 0.040 3786 Dihedral : 4.745 50.683 2882 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.43 % Allowed : 9.77 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2628 helix: 1.01 (0.17), residues: 1062 sheet: 0.51 (0.26), residues: 384 loop : -1.02 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 483 HIS 0.003 0.001 HIS D 69 PHE 0.014 0.001 PHE F 218 TYR 0.007 0.001 TYR A 93 ARG 0.004 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 817) hydrogen bonds : angle 4.04972 ( 2361) covalent geometry : bond 0.00279 (21708) covalent geometry : angle 0.55114 (29418) *********************** 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 110 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 2.547 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9019 (mtm) cc_final: 0.8705 (mtp) REVERT: A 147 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 117 MET cc_start: 0.9022 (mtm) cc_final: 0.8807 (mtp) REVERT: C 84 ASP cc_start: 0.8927 (p0) cc_final: 0.8077 (p0) REVERT: E 283 ASN cc_start: 0.9100 (t0) cc_final: 0.8821 (t0) REVERT: E 355 HIS cc_start: 0.9068 (OUTLIER) cc_final: 0.8578 (p90) outliers start: 32 outliers final: 11 residues processed: 106 average time/residue: 1.2683 time to fit residues: 156.6696 Evaluate side-chains 83 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL 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 327 LEU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 209 THR 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 355 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 116 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN F 349 ASN F 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.057497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.043484 restraints weight = 67585.040| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.69 r_work: 0.2497 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.3482 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= 0.154 Angle : 0.571 16.478 29418 Z= 0.294 Chirality : 0.043 0.200 3120 Planarity : 0.005 0.042 3786 Dihedral : 4.660 52.196 2882 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.70 % Allowed : 10.22 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2628 helix: 1.27 (0.17), residues: 1032 sheet: 0.54 (0.26), residues: 384 loop : -0.83 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 483 HIS 0.004 0.001 HIS D 503 PHE 0.015 0.001 PHE C 218 TYR 0.010 0.001 TYR A 93 ARG 0.003 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 817) hydrogen bonds : angle 4.02243 ( 2361) covalent geometry : bond 0.00363 (21708) covalent geometry : angle 0.57112 (29418) *********************** 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 111 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.9030 (mtm) cc_final: 0.8741 (mtp) REVERT: B 117 MET cc_start: 0.9033 (mtm) cc_final: 0.8817 (mtp) REVERT: C 84 ASP cc_start: 0.8917 (p0) cc_final: 0.8045 (p0) REVERT: E 79 GLU cc_start: 0.8869 (mp0) cc_final: 0.8656 (mp0) REVERT: E 283 ASN cc_start: 0.9087 (t0) cc_final: 0.8819 (t0) REVERT: E 355 HIS cc_start: 0.9040 (OUTLIER) cc_final: 0.8513 (p90) outliers start: 38 outliers final: 16 residues processed: 104 average time/residue: 1.2382 time to fit residues: 150.1320 Evaluate side-chains 87 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL 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 B residue 411 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 355 HIS Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain F residue 148 PHE 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: 6.9990 chunk 8 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 486 ASN 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 = 0.056456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.042442 restraints weight = 67506.756| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.67 r_work: 0.2467 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 21708 Z= 0.215 Angle : 0.603 10.481 29418 Z= 0.312 Chirality : 0.045 0.202 3120 Planarity : 0.005 0.042 3786 Dihedral : 4.779 56.557 2882 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.48 % Allowed : 10.71 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2628 helix: 1.34 (0.17), residues: 1026 sheet: 0.50 (0.26), residues: 384 loop : -0.89 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 483 HIS 0.006 0.001 HIS D 503 PHE 0.017 0.001 PHE F 148 TYR 0.011 0.001 TYR E 93 ARG 0.003 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 817) hydrogen bonds : angle 4.09793 ( 2361) covalent geometry : bond 0.00512 (21708) covalent geometry : angle 0.60274 (29418) *********************** 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: 33 poor density : 71 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9038 (mtm) cc_final: 0.8785 (mtp) REVERT: B 117 MET cc_start: 0.9084 (mtm) cc_final: 0.8879 (mtp) REVERT: C 410 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8483 (mpt) REVERT: E 79 GLU cc_start: 0.8940 (mp0) cc_final: 0.8727 (mp0) REVERT: E 283 ASN cc_start: 0.9086 (t0) cc_final: 0.8817 (t0) REVERT: E 355 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8517 (p90) REVERT: F 79 GLU cc_start: 0.8700 (mp0) cc_final: 0.8481 (pm20) outliers start: 33 outliers final: 17 residues processed: 100 average time/residue: 1.1539 time to fit residues: 135.7099 Evaluate side-chains 89 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 PHE 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 B residue 411 ILE 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 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 E residue 411 ILE Chi-restraints excluded: chain F residue 148 PHE 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 5 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 69 HIS ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN F 486 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.055582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.041562 restraints weight = 68354.881| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 3.68 r_work: 0.2448 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21708 Z= 0.260 Angle : 0.642 16.819 29418 Z= 0.330 Chirality : 0.046 0.207 3120 Planarity : 0.005 0.046 3786 Dihedral : 4.906 56.853 2882 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.30 % Allowed : 11.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2628 helix: 1.29 (0.17), residues: 1026 sheet: 0.44 (0.26), residues: 384 loop : -0.95 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 483 HIS 0.008 0.001 HIS E 367 PHE 0.019 0.002 PHE F 148 TYR 0.011 0.001 TYR B 93 ARG 0.003 0.001 ARG B 498 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 817) hydrogen bonds : angle 4.17260 ( 2361) covalent geometry : bond 0.00619 (21708) covalent geometry : angle 0.64159 (29418) *********************** 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 102 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 2.322 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9091 (mtm) cc_final: 0.8814 (mtp) REVERT: C 169 MET cc_start: 0.8107 (tpp) cc_final: 0.7375 (tmt) REVERT: C 410 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8474 (mpt) REVERT: D 466 ASN cc_start: 0.8493 (t0) cc_final: 0.8209 (t0) REVERT: E 79 GLU cc_start: 0.8965 (mp0) cc_final: 0.8756 (mp0) REVERT: E 283 ASN cc_start: 0.9093 (t0) cc_final: 0.8813 (t0) REVERT: E 355 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8589 (p90) outliers start: 29 outliers final: 17 residues processed: 99 average time/residue: 1.2369 time to fit residues: 144.1071 Evaluate side-chains 89 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 209 THR Chi-restraints excluded: chain C residue 410 MET 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 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 232 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN 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 = 0.3020 r_free = 0.3020 target = 0.056092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.042108 restraints weight = 68177.550| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.68 r_work: 0.2461 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21708 Z= 0.203 Angle : 0.612 13.810 29418 Z= 0.312 Chirality : 0.044 0.202 3120 Planarity : 0.005 0.046 3786 Dihedral : 4.780 52.855 2882 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.12 % Allowed : 11.11 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2628 helix: 1.30 (0.17), residues: 1026 sheet: 0.49 (0.26), residues: 384 loop : -0.96 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 483 HIS 0.006 0.001 HIS E 367 PHE 0.017 0.001 PHE F 148 TYR 0.010 0.001 TYR E 93 ARG 0.003 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 817) hydrogen bonds : angle 4.10357 ( 2361) covalent geometry : bond 0.00484 (21708) covalent geometry : angle 0.61166 (29418) *********************** 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 96 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 2.296 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9055 (mtm) cc_final: 0.8793 (mtp) REVERT: B 329 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8225 (mtm-85) REVERT: C 169 MET cc_start: 0.8146 (tpp) cc_final: 0.7418 (tmt) REVERT: C 410 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8497 (mpt) REVERT: E 283 ASN cc_start: 0.9081 (t0) cc_final: 0.8806 (t0) REVERT: E 355 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8683 (p90) REVERT: F 79 GLU cc_start: 0.8743 (mp0) cc_final: 0.8483 (pm20) outliers start: 25 outliers final: 15 residues processed: 93 average time/residue: 1.2845 time to fit residues: 138.3362 Evaluate side-chains 87 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 77 VAL 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 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 120 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 349 ASN F 503 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.043050 restraints weight = 67530.100| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.69 r_work: 0.2484 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21708 Z= 0.152 Angle : 0.587 13.836 29418 Z= 0.297 Chirality : 0.043 0.200 3120 Planarity : 0.005 0.048 3786 Dihedral : 4.631 50.446 2882 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.94 % Allowed : 11.29 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2628 helix: 1.34 (0.17), residues: 1026 sheet: 0.56 (0.26), residues: 384 loop : -0.92 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 483 HIS 0.005 0.001 HIS E 367 PHE 0.014 0.001 PHE F 148 TYR 0.008 0.001 TYR A 93 ARG 0.002 0.000 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 817) hydrogen bonds : angle 4.02387 ( 2361) covalent geometry : bond 0.00360 (21708) covalent geometry : angle 0.58681 (29418) ********************** 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 93 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 2.324 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9015 (mtm) cc_final: 0.8756 (mtp) REVERT: B 329 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8205 (mtm-85) REVERT: C 169 MET cc_start: 0.8134 (tpp) cc_final: 0.7485 (tmt) REVERT: C 410 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8460 (mpt) REVERT: E 169 MET cc_start: 0.7579 (pmm) cc_final: 0.7322 (pp-130) REVERT: E 283 ASN cc_start: 0.9080 (t0) cc_final: 0.8816 (t0) REVERT: E 355 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8722 (p90) REVERT: F 79 GLU cc_start: 0.8715 (mp0) cc_final: 0.8460 (pm20) outliers start: 21 outliers final: 14 residues processed: 91 average time/residue: 1.3268 time to fit residues: 139.7758 Evaluate side-chains 86 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 209 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 355 HIS 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 13 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 61 optimal weight: 0.0470 chunk 109 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN F 503 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.043916 restraints weight = 67614.299| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.67 r_work: 0.2510 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21708 Z= 0.119 Angle : 0.561 13.323 29418 Z= 0.282 Chirality : 0.042 0.218 3120 Planarity : 0.004 0.043 3786 Dihedral : 4.428 49.817 2882 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.99 % Allowed : 11.16 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2628 helix: 1.41 (0.17), residues: 1020 sheet: 0.64 (0.27), residues: 384 loop : -0.85 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 483 HIS 0.004 0.001 HIS E 367 PHE 0.013 0.001 PHE F 218 TYR 0.006 0.001 TYR A 93 ARG 0.003 0.000 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 817) hydrogen bonds : angle 3.94686 ( 2361) covalent geometry : bond 0.00277 (21708) covalent geometry : angle 0.56147 (29418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10380.57 seconds wall clock time: 178 minutes 27.62 seconds (10707.62 seconds total)