Starting phenix.real_space_refine on Wed Nov 20 07:27:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u39_41854/11_2024/8u39_41854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u39_41854/11_2024/8u39_41854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u39_41854/11_2024/8u39_41854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u39_41854/11_2024/8u39_41854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u39_41854/11_2024/8u39_41854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u39_41854/11_2024/8u39_41854.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 17164 2.51 5 N 4669 2.21 5 O 5439 1.98 5 H 28630 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 56000 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 8000 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 508} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 24.74, per 1000 atoms: 0.44 Number of scatterers: 56000 At special positions: 0 Unit cell: (161.419, 160.35, 94.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 5439 8.00 N 4669 7.00 C 17164 6.00 H 28630 1.00 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: 13.85 Conformation dependent library (CDL) restraints added in 4.4 seconds 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 28 sheets defined 59.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'G' and resid 7 through 27 Processing helix chain 'G' and resid 50 through 57 removed outlier: 3.577A pdb=" N VAL G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 78 removed outlier: 4.167A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 107 Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.591A pdb=" N PHE G 202 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE G 203 " --> pdb=" O PRO G 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 199 through 203' Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.514A pdb=" N LYS G 210 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 241 removed outlier: 4.213A pdb=" N ILE G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Proline residue: G 233 - end of helix removed outlier: 3.666A pdb=" N ILE G 237 " --> pdb=" O PRO G 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 238 " --> pdb=" O ALA G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 268 removed outlier: 3.694A pdb=" N LYS G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 295 removed outlier: 3.613A pdb=" N LYS G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 316 removed outlier: 3.591A pdb=" N LEU G 316 " --> pdb=" O PRO G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 354 removed outlier: 4.201A pdb=" N LYS G 343 " --> pdb=" O ALA G 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 344 " --> pdb=" O GLN G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 373 Processing helix chain 'G' and resid 384 through 408 Processing helix chain 'G' and resid 415 through 420 removed outlier: 3.649A pdb=" N LEU G 419 " --> pdb=" O GLY G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 426 removed outlier: 4.232A pdb=" N ASP G 426 " --> pdb=" O PRO G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 446 Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 461 through 471 Processing helix chain 'G' and resid 496 through 516 Processing helix chain 'A' and resid 7 through 27 Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.577A pdb=" N VAL A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 78 removed outlier: 4.166A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 107 Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.589A pdb=" N PHE A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.513A pdb=" N LYS A 210 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 4.214A pdb=" N ILE A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Proline residue: A 233 - end of helix removed outlier: 3.668A pdb=" N ILE A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.696A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.613A pdb=" N LYS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.591A pdb=" N LEU A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 4.201A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 344 " --> pdb=" O GLN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 384 through 408 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.650A pdb=" N LEU A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 4.231A pdb=" N ASP A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 496 through 516 Processing helix chain 'B' and resid 7 through 27 Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.576A pdb=" N VAL B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 78 removed outlier: 4.165A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.590A pdb=" N PHE B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 203 " --> pdb=" O PRO B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.514A pdb=" N LYS B 210 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 4.214A pdb=" N ILE B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 3.667A pdb=" N ILE B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.695A pdb=" N LYS B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.613A pdb=" N LYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.590A pdb=" N LEU B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 4.200A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 344 " --> pdb=" O GLN B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 Processing helix chain 'B' and resid 384 through 408 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.650A pdb=" N LEU B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.231A pdb=" N ASP B 426 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 496 through 516 Processing helix chain 'C' and resid 7 through 27 Processing helix chain 'C' and resid 50 through 57 removed outlier: 3.577A pdb=" N VAL C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 78 removed outlier: 4.165A pdb=" N VAL C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 107 Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.590A pdb=" N PHE C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.513A pdb=" N LYS C 210 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 4.214A pdb=" N ILE C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Proline residue: C 233 - end of helix removed outlier: 3.666A pdb=" N ILE C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 removed outlier: 3.694A pdb=" N LYS C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.614A pdb=" N LYS C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.591A pdb=" N LEU C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 354 removed outlier: 4.201A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 344 " --> pdb=" O GLN C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 384 through 408 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.649A pdb=" N LEU C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 removed outlier: 4.232A pdb=" N ASP C 426 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 496 through 516 Processing helix chain 'D' and resid 7 through 27 Processing helix chain 'D' and resid 50 through 57 removed outlier: 3.576A pdb=" N VAL D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 78 removed outlier: 4.166A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 107 Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.590A pdb=" N PHE D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 203 " --> pdb=" O PRO D 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 199 through 203' Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.514A pdb=" N LYS D 210 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.213A pdb=" N ILE D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 3.668A pdb=" N ILE D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 removed outlier: 3.695A pdb=" N LYS D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.614A pdb=" N LYS D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.591A pdb=" N LEU D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 354 removed outlier: 4.200A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 344 " --> pdb=" O GLN D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 408 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.649A pdb=" N LEU D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 removed outlier: 4.232A pdb=" N ASP D 426 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 496 through 516 Processing helix chain 'E' and resid 7 through 27 Processing helix chain 'E' and resid 50 through 57 removed outlier: 3.576A pdb=" N VAL E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 78 removed outlier: 4.166A pdb=" N VAL E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 107 Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.590A pdb=" N PHE E 202 " --> pdb=" O SER E 199 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE E 203 " --> pdb=" O PRO E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'E' and resid 206 through 210 removed outlier: 3.515A pdb=" N LYS E 210 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 241 removed outlier: 4.213A pdb=" N ILE E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Proline residue: E 233 - end of helix removed outlier: 3.667A pdb=" N ILE E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 268 removed outlier: 3.695A pdb=" N LYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.614A pdb=" N LYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.591A pdb=" N LEU E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 354 removed outlier: 4.201A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 344 " --> pdb=" O GLN E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 373 Processing helix chain 'E' and resid 384 through 408 Processing helix chain 'E' and resid 415 through 420 removed outlier: 3.649A pdb=" N LEU E 419 " --> pdb=" O GLY E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 removed outlier: 4.231A pdb=" N ASP E 426 " --> pdb=" O PRO E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 461 through 471 Processing helix chain 'E' and resid 496 through 516 Processing helix chain 'F' and resid 7 through 27 Processing helix chain 'F' and resid 50 through 57 removed outlier: 3.576A pdb=" N VAL F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 78 removed outlier: 4.166A pdb=" N VAL F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 76 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.752A pdb=" N GLY F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.590A pdb=" N PHE F 202 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE F 203 " --> pdb=" O PRO F 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 199 through 203' Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.514A pdb=" N LYS F 210 " --> pdb=" O LYS F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 4.213A pdb=" N ILE F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Proline residue: F 233 - end of helix removed outlier: 3.667A pdb=" N ILE F 237 " --> pdb=" O PRO F 233 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 removed outlier: 3.696A pdb=" N LYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.614A pdb=" N LYS F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 removed outlier: 3.591A pdb=" N LEU F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 354 removed outlier: 4.201A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 344 " --> pdb=" O GLN F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 373 Processing helix chain 'F' and resid 384 through 408 Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.649A pdb=" N LEU F 419 " --> pdb=" O GLY F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 removed outlier: 4.233A pdb=" N ASP F 426 " --> pdb=" O PRO F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'F' and resid 496 through 516 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 removed outlier: 5.924A pdb=" N VAL G 518 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.304A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 191 through 193 removed outlier: 6.734A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE G 213 " --> pdb=" O VAL G 322 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL G 272 " --> pdb=" O LEU G 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 3 through 6 removed outlier: 5.924A pdb=" N VAL A 518 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.305A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 191 through 193 removed outlier: 6.733A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 213 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 272 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6 removed outlier: 5.924A pdb=" N VAL B 518 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.304A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS B 176 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 191 through 193 removed outlier: 6.733A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 213 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 272 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.924A pdb=" N VAL C 518 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.305A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 191 through 193 removed outlier: 6.733A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 213 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 272 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'D' and resid 3 through 6 removed outlier: 5.924A pdb=" N VAL D 518 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.305A pdb=" N THR D 174 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL D 380 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS D 176 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 191 through 193 removed outlier: 6.734A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 213 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 272 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 removed outlier: 5.924A pdb=" N VAL E 518 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.304A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 191 through 193 removed outlier: 6.733A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 213 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL E 272 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AC8, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.304A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 191 through 193 removed outlier: 6.733A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE F 213 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL F 272 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 410 through 412 1675 hydrogen bonds defined for protein. 4773 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: 25.55 Time building geometry restraints manager: 16.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28609 1.03 - 1.23: 175 1.23 - 1.42: 10052 1.42 - 1.62: 17213 1.62 - 1.81: 175 Bond restraints: 56224 Sorted by residual: bond pdb=" N ILE D 58 " pdb=" CA ILE D 58 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.46e+01 bond pdb=" N ILE E 58 " pdb=" CA ILE E 58 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" N ILE G 58 " pdb=" CA ILE G 58 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.43e+01 bond pdb=" N ILE C 58 " pdb=" CA ILE C 58 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.43e+01 ... (remaining 56219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 100601 2.52 - 5.04: 2117 5.04 - 7.56: 63 7.56 - 10.09: 7 10.09 - 12.61: 7 Bond angle restraints: 102795 Sorted by residual: angle pdb=" N ASP F 337 " pdb=" CA ASP F 337 " pdb=" C ASP F 337 " ideal model delta sigma weight residual 113.21 105.53 7.68 1.15e+00 7.56e-01 4.46e+01 angle pdb=" N ASP C 337 " pdb=" CA ASP C 337 " pdb=" C ASP C 337 " ideal model delta sigma weight residual 113.21 105.53 7.68 1.15e+00 7.56e-01 4.46e+01 angle pdb=" N ASP E 337 " pdb=" CA ASP E 337 " pdb=" C ASP E 337 " ideal model delta sigma weight residual 113.21 105.55 7.66 1.15e+00 7.56e-01 4.44e+01 angle pdb=" N ASP B 337 " pdb=" CA ASP B 337 " pdb=" C ASP B 337 " ideal model delta sigma weight residual 113.21 105.55 7.66 1.15e+00 7.56e-01 4.43e+01 angle pdb=" N ASP G 337 " pdb=" CA ASP G 337 " pdb=" C ASP G 337 " ideal model delta sigma weight residual 113.21 105.56 7.65 1.15e+00 7.56e-01 4.43e+01 ... (remaining 102790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 23204 17.01 - 34.02: 1729 34.02 - 51.04: 554 51.04 - 68.05: 245 68.05 - 85.06: 35 Dihedral angle restraints: 25767 sinusoidal: 14840 harmonic: 10927 Sorted by residual: dihedral pdb=" CA CYS D 211 " pdb=" CB CYS D 211 " pdb=" SG CYS D 211 " pdb=" HG CYS D 211 " ideal model delta sinusoidal sigma weight residual 180.00 123.96 56.04 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA CYS E 211 " pdb=" CB CYS E 211 " pdb=" SG CYS E 211 " pdb=" HG CYS E 211 " ideal model delta sinusoidal sigma weight residual 180.00 123.96 56.04 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA CYS G 211 " pdb=" CB CYS G 211 " pdb=" SG CYS G 211 " pdb=" HG CYS G 211 " ideal model delta sinusoidal sigma weight residual 180.00 123.99 56.01 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 25764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2878 0.045 - 0.090: 865 0.090 - 0.135: 622 0.135 - 0.180: 131 0.180 - 0.226: 61 Chirality restraints: 4557 Sorted by residual: chirality pdb=" CA VAL C 54 " pdb=" N VAL C 54 " pdb=" C VAL C 54 " pdb=" CB VAL C 54 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL F 54 " pdb=" N VAL F 54 " pdb=" C VAL F 54 " pdb=" CB VAL F 54 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4554 not shown) Planarity restraints: 8358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 110 " -0.186 2.00e-02 2.50e+03 4.18e-01 2.62e+03 pdb=" CG ASN E 110 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN E 110 " 0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN E 110 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 110 " -0.708 2.00e-02 2.50e+03 pdb="HD22 ASN E 110 " 0.694 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 110 " 0.186 2.00e-02 2.50e+03 4.18e-01 2.62e+03 pdb=" CG ASN G 110 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN G 110 " -0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN G 110 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN G 110 " 0.707 2.00e-02 2.50e+03 pdb="HD22 ASN G 110 " -0.693 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 110 " -0.186 2.00e-02 2.50e+03 4.18e-01 2.62e+03 pdb=" CG ASN D 110 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN D 110 " 0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN D 110 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 110 " -0.707 2.00e-02 2.50e+03 pdb="HD22 ASN D 110 " 0.693 2.00e-02 2.50e+03 ... (remaining 8355 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.78: 105 1.78 - 2.49: 40404 2.49 - 3.19: 178565 3.19 - 3.90: 213613 3.90 - 4.60: 345380 Nonbonded interactions: 778067 Sorted by model distance: nonbonded pdb=" HB VAL A 518 " pdb="HG23 VAL B 36 " model vdw 1.076 2.440 nonbonded pdb=" HB VAL D 518 " pdb="HG23 VAL E 36 " model vdw 1.076 2.440 nonbonded pdb=" HB VAL C 518 " pdb="HG23 VAL D 36 " model vdw 1.076 2.440 nonbonded pdb=" HB VAL B 518 " pdb="HG23 VAL C 36 " model vdw 1.076 2.440 nonbonded pdb=" HB VAL E 518 " pdb="HG23 VAL F 36 " model vdw 1.076 2.440 ... (remaining 778062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.010 Extract box with map and model: 1.960 Check model and map are aligned: 0.380 Set scattering table: 0.520 Process input model: 111.640 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.130 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4881 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 : 0.007 0.045 27594 Z= 0.486 Angle : 1.088 7.683 37233 Z= 0.810 Chirality : 0.063 0.226 4557 Planarity : 0.004 0.042 4802 Dihedral : 11.864 82.897 10514 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.14), residues: 3654 helix: 1.16 (0.12), residues: 1918 sheet: -0.86 (0.21), residues: 567 loop : -1.76 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 42 HIS 0.002 0.001 HIS B 241 PHE 0.019 0.002 PHE D 193 TYR 0.004 0.001 TYR C 197 ARG 0.003 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 211 CYS cc_start: 0.7089 (t) cc_final: 0.6664 (t) REVERT: G 284 LYS cc_start: 0.7942 (tmtt) cc_final: 0.7134 (mmtp) REVERT: A 126 ILE cc_start: 0.6734 (mm) cc_final: 0.6291 (mt) REVERT: B 186 GLU cc_start: 0.4044 (pt0) cc_final: 0.3765 (pt0) REVERT: B 358 GLU cc_start: 0.6527 (tm-30) cc_final: 0.5896 (tm-30) REVERT: B 487 MET cc_start: 0.5660 (mmm) cc_final: 0.4522 (mmt) REVERT: B 512 LEU cc_start: 0.6339 (tp) cc_final: 0.5009 (mp) REVERT: C 359 TYR cc_start: 0.7559 (t80) cc_final: 0.6817 (t80) REVERT: D 164 MET cc_start: 0.6508 (mmm) cc_final: 0.6186 (mtt) REVERT: D 452 THR cc_start: 0.4475 (p) cc_final: 0.4117 (p) REVERT: E 136 VAL cc_start: 0.4470 (t) cc_final: 0.4233 (t) REVERT: E 474 GLU cc_start: 0.5265 (mm-30) cc_final: 0.4451 (mm-30) REVERT: F 139 PRO cc_start: 0.7403 (Cg_exo) cc_final: 0.7194 (Cg_endo) REVERT: F 158 ASN cc_start: 0.7457 (m-40) cc_final: 0.6983 (m110) REVERT: F 393 ASP cc_start: 0.7911 (t70) cc_final: 0.7505 (t0) outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 0.9372 time to fit residues: 843.5467 Evaluate side-chains 372 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 4.9990 chunk 275 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.0070 chunk 147 optimal weight: 0.0570 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 212 optimal weight: 0.4980 chunk 330 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN D 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5258 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27594 Z= 0.180 Angle : 0.537 4.609 37233 Z= 0.298 Chirality : 0.042 0.164 4557 Planarity : 0.004 0.044 4802 Dihedral : 3.988 20.405 3829 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.81 % Allowed : 5.19 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3654 helix: 1.38 (0.12), residues: 1932 sheet: -0.50 (0.22), residues: 567 loop : -1.45 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 HIS 0.002 0.001 HIS D 314 PHE 0.013 0.002 PHE C 193 TYR 0.011 0.001 TYR E 359 ARG 0.007 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 390 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 ILE cc_start: 0.7389 (mt) cc_final: 0.6973 (mt) REVERT: G 70 LYS cc_start: 0.7309 (tptt) cc_final: 0.7080 (tptt) REVERT: G 77 ASN cc_start: 0.7664 (m-40) cc_final: 0.7348 (m110) REVERT: G 142 ILE cc_start: 0.8559 (mt) cc_final: 0.8307 (mt) REVERT: G 284 LYS cc_start: 0.7759 (tmtt) cc_final: 0.7031 (mmtp) REVERT: G 451 MET cc_start: 0.6846 (mmm) cc_final: 0.6504 (tpp) REVERT: G 485 VAL cc_start: 0.7946 (t) cc_final: 0.7663 (t) REVERT: A 28 THR cc_start: 0.3844 (p) cc_final: 0.3604 (p) REVERT: A 290 MET cc_start: 0.5898 (ttm) cc_final: 0.5687 (ttm) REVERT: A 514 THR cc_start: 0.6828 (m) cc_final: 0.6602 (m) REVERT: B 28 THR cc_start: 0.3780 (p) cc_final: 0.3493 (p) REVERT: B 126 ILE cc_start: 0.6294 (mm) cc_final: 0.5436 (mt) REVERT: B 487 MET cc_start: 0.5892 (mmm) cc_final: 0.5301 (mmt) REVERT: B 512 LEU cc_start: 0.6343 (tp) cc_final: 0.4777 (mp) REVERT: C 359 TYR cc_start: 0.7494 (t80) cc_final: 0.6760 (t80) REVERT: D 164 MET cc_start: 0.6520 (mmm) cc_final: 0.6310 (mtt) REVERT: D 189 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6765 (mt-10) REVERT: D 236 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: D 452 THR cc_start: 0.4839 (p) cc_final: 0.4344 (p) REVERT: E 136 VAL cc_start: 0.4513 (t) cc_final: 0.4080 (t) REVERT: E 160 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5924 (mt) REVERT: E 236 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: F 393 ASP cc_start: 0.7883 (t70) cc_final: 0.7505 (t0) REVERT: F 517 GLU cc_start: 0.8412 (tp30) cc_final: 0.8093 (tp30) outliers start: 24 outliers final: 11 residues processed: 405 average time/residue: 0.8583 time to fit residues: 559.2578 Evaluate side-chains 339 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 325 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 347 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 357 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 ASN E 400 ASN F 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 27594 Z= 0.324 Angle : 0.692 10.001 37233 Z= 0.380 Chirality : 0.048 0.288 4557 Planarity : 0.005 0.090 4802 Dihedral : 4.481 28.930 3829 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.38 % Allowed : 7.14 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 3654 helix: 1.00 (0.11), residues: 1967 sheet: -0.53 (0.26), residues: 420 loop : -1.46 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 42 HIS 0.003 0.001 HIS F 314 PHE 0.035 0.003 PHE C 484 TYR 0.021 0.002 TYR C 64 ARG 0.018 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 419 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7723 (mt) REVERT: G 211 CYS cc_start: 0.7175 (t) cc_final: 0.6891 (t) REVERT: G 284 LYS cc_start: 0.7967 (tmtt) cc_final: 0.7212 (mmtt) REVERT: G 403 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7647 (mtm180) REVERT: G 505 ASP cc_start: 0.7478 (m-30) cc_final: 0.7270 (m-30) REVERT: A 18 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8060 (t) REVERT: A 359 TYR cc_start: 0.6705 (t80) cc_final: 0.6386 (t80) REVERT: A 514 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7850 (m) REVERT: B 222 GLU cc_start: 0.5717 (tm-30) cc_final: 0.5124 (tm-30) REVERT: B 330 MET cc_start: 0.6597 (ptm) cc_final: 0.6323 (ptm) REVERT: C 29 MET cc_start: 0.7355 (mmm) cc_final: 0.7140 (mtp) REVERT: C 96 SER cc_start: 0.7248 (t) cc_final: 0.6927 (t) REVERT: C 359 TYR cc_start: 0.7489 (t80) cc_final: 0.6827 (t80) REVERT: D 78 ASN cc_start: 0.5636 (m-40) cc_final: 0.5394 (m-40) REVERT: D 164 MET cc_start: 0.7158 (mmm) cc_final: 0.6899 (mtt) REVERT: D 236 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: D 474 GLU cc_start: 0.5680 (mm-30) cc_final: 0.5191 (mm-30) REVERT: D 503 LEU cc_start: 0.7378 (tp) cc_final: 0.7119 (tp) REVERT: E 78 ASN cc_start: 0.6709 (m-40) cc_final: 0.6077 (m-40) REVERT: E 236 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: E 327 ASP cc_start: 0.7515 (t70) cc_final: 0.7276 (t70) REVERT: F 284 LYS cc_start: 0.7883 (tmtt) cc_final: 0.7666 (mtpt) REVERT: F 393 ASP cc_start: 0.7854 (t70) cc_final: 0.7525 (t0) outliers start: 41 outliers final: 16 residues processed: 444 average time/residue: 0.9367 time to fit residues: 655.1625 Evaluate side-chains 347 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 326 time to evaluate : 4.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 496 THR Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 515 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 351 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN D 144 GLN D 282 ASN ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27594 Z= 0.259 Angle : 0.564 6.935 37233 Z= 0.308 Chirality : 0.044 0.195 4557 Planarity : 0.004 0.056 4802 Dihedral : 4.194 24.397 3829 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.65 % Allowed : 9.67 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.14), residues: 3654 helix: 1.28 (0.11), residues: 1981 sheet: -0.62 (0.22), residues: 567 loop : -1.40 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 42 HIS 0.003 0.001 HIS A 314 PHE 0.031 0.002 PHE E 484 TYR 0.012 0.001 TYR F 64 ARG 0.012 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 4.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 211 CYS cc_start: 0.7219 (t) cc_final: 0.6955 (t) REVERT: G 487 MET cc_start: 0.7622 (mmm) cc_final: 0.7143 (mmm) REVERT: G 505 ASP cc_start: 0.7693 (m-30) cc_final: 0.7423 (m-30) REVERT: A 119 MET cc_start: 0.7077 (mmp) cc_final: 0.6619 (mmp) REVERT: A 330 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.7002 (mtp) REVERT: B 222 GLU cc_start: 0.5670 (tm-30) cc_final: 0.5244 (tm-30) REVERT: B 359 TYR cc_start: 0.7175 (t80) cc_final: 0.6973 (t80) REVERT: C 29 MET cc_start: 0.8180 (mmm) cc_final: 0.7880 (mtp) REVERT: C 326 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7445 (ttpt) REVERT: C 359 TYR cc_start: 0.7438 (t80) cc_final: 0.6793 (t80) REVERT: C 480 MET cc_start: 0.6300 (mmm) cc_final: 0.6091 (mmt) REVERT: D 236 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 474 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5988 (mm-30) REVERT: D 504 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7841 (mp) REVERT: E 78 ASN cc_start: 0.6911 (m-40) cc_final: 0.6417 (m-40) REVERT: E 236 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: E 290 MET cc_start: 0.6466 (mtp) cc_final: 0.6225 (mtp) REVERT: E 327 ASP cc_start: 0.7764 (t70) cc_final: 0.7256 (t70) REVERT: E 469 MET cc_start: 0.7478 (mmm) cc_final: 0.7143 (mmm) REVERT: F 284 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7597 (mtpt) REVERT: F 390 GLU cc_start: 0.7592 (tp30) cc_final: 0.7323 (tm-30) REVERT: F 393 ASP cc_start: 0.7820 (t70) cc_final: 0.7503 (t0) REVERT: F 517 GLU cc_start: 0.8486 (tp30) cc_final: 0.8269 (tp30) outliers start: 49 outliers final: 26 residues processed: 370 average time/residue: 0.8791 time to fit residues: 515.5356 Evaluate side-chains 315 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 511 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 0.0570 chunk 199 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 315 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27594 Z= 0.221 Angle : 0.502 6.097 37233 Z= 0.273 Chirality : 0.041 0.155 4557 Planarity : 0.003 0.050 4802 Dihedral : 4.032 23.598 3829 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.18 % Allowed : 11.29 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.14), residues: 3654 helix: 1.64 (0.11), residues: 1981 sheet: -0.55 (0.22), residues: 567 loop : -1.26 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 HIS 0.002 0.001 HIS D 314 PHE 0.015 0.001 PHE B 193 TYR 0.011 0.001 TYR B 64 ARG 0.004 0.000 ARG G 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 284 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7157 (mtpt) REVERT: G 487 MET cc_start: 0.7430 (mmm) cc_final: 0.7149 (mmm) REVERT: G 505 ASP cc_start: 0.7726 (m-30) cc_final: 0.7456 (m-30) REVERT: A 241 HIS cc_start: 0.4098 (OUTLIER) cc_final: 0.3334 (t-90) REVERT: A 478 ASP cc_start: 0.7196 (t0) cc_final: 0.6838 (t0) REVERT: B 222 GLU cc_start: 0.5796 (tm-30) cc_final: 0.5343 (tm-30) REVERT: C 144 GLN cc_start: 0.7533 (tp40) cc_final: 0.7099 (tt0) REVERT: C 326 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7636 (ttpt) REVERT: C 359 TYR cc_start: 0.7398 (t80) cc_final: 0.6807 (t80) REVERT: D 236 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: D 504 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7852 (mp) REVERT: E 78 ASN cc_start: 0.6914 (m-40) cc_final: 0.6466 (m-40) REVERT: E 236 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: E 290 MET cc_start: 0.6391 (mtp) cc_final: 0.6139 (mtp) REVERT: E 327 ASP cc_start: 0.7743 (t70) cc_final: 0.7237 (t70) REVERT: E 469 MET cc_start: 0.7503 (mmm) cc_final: 0.7081 (mmm) REVERT: F 284 LYS cc_start: 0.8123 (tmtt) cc_final: 0.7598 (mtpt) REVERT: F 390 GLU cc_start: 0.7566 (tp30) cc_final: 0.7261 (tm-30) REVERT: F 393 ASP cc_start: 0.7774 (t70) cc_final: 0.7499 (t0) outliers start: 35 outliers final: 18 residues processed: 328 average time/residue: 0.9011 time to fit residues: 471.0233 Evaluate side-chains 314 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 496 THR Chi-restraints excluded: chain F residue 511 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.8372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27594 Z= 0.299 Angle : 0.555 8.398 37233 Z= 0.306 Chirality : 0.043 0.152 4557 Planarity : 0.004 0.076 4802 Dihedral : 4.282 20.517 3829 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.55 % Allowed : 11.69 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.14), residues: 3654 helix: 1.46 (0.11), residues: 1988 sheet: -0.58 (0.22), residues: 567 loop : -1.51 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 42 HIS 0.003 0.001 HIS F 314 PHE 0.014 0.002 PHE G 193 TYR 0.013 0.002 TYR E 64 ARG 0.009 0.001 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 3.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 284 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7302 (mtpt) REVERT: G 451 MET cc_start: 0.7589 (mmm) cc_final: 0.7100 (tpp) REVERT: A 444 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7835 (ttp-110) REVERT: A 451 MET cc_start: 0.7182 (tpp) cc_final: 0.6894 (tpp) REVERT: B 222 GLU cc_start: 0.5868 (tm-30) cc_final: 0.5410 (tm-30) REVERT: C 326 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7865 (ttpt) REVERT: C 359 TYR cc_start: 0.7333 (t80) cc_final: 0.6912 (t80) REVERT: C 390 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6265 (tm-30) REVERT: C 403 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7524 (mtm180) REVERT: C 478 ASP cc_start: 0.7547 (t0) cc_final: 0.7188 (t0) REVERT: D 236 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: D 504 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7852 (mp) REVERT: E 78 ASN cc_start: 0.6960 (m-40) cc_final: 0.6624 (m-40) REVERT: E 236 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: E 327 ASP cc_start: 0.8031 (t70) cc_final: 0.7494 (t70) REVERT: E 469 MET cc_start: 0.7883 (mmm) cc_final: 0.7495 (mmm) REVERT: F 284 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7669 (mtpt) REVERT: F 390 GLU cc_start: 0.7658 (tp30) cc_final: 0.7407 (tm-30) REVERT: F 393 ASP cc_start: 0.7731 (t70) cc_final: 0.7512 (t0) outliers start: 46 outliers final: 35 residues processed: 371 average time/residue: 0.9548 time to fit residues: 559.9880 Evaluate side-chains 337 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 496 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 496 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 523 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 200 optimal weight: 0.0570 chunk 257 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 296 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.8563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 27594 Z= 0.147 Angle : 0.463 6.143 37233 Z= 0.250 Chirality : 0.041 0.180 4557 Planarity : 0.003 0.044 4802 Dihedral : 3.980 20.589 3829 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.88 % Allowed : 12.37 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.14), residues: 3654 helix: 1.90 (0.12), residues: 1981 sheet: -0.44 (0.23), residues: 567 loop : -1.28 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 42 HIS 0.002 0.001 HIS C 314 PHE 0.010 0.001 PHE A 193 TYR 0.010 0.001 TYR D 359 ARG 0.006 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 284 LYS cc_start: 0.8086 (tmtt) cc_final: 0.7270 (mtpt) REVERT: G 451 MET cc_start: 0.7516 (mmm) cc_final: 0.7042 (tpp) REVERT: A 72 ILE cc_start: 0.8553 (tt) cc_final: 0.8260 (tt) REVERT: A 241 HIS cc_start: 0.4579 (OUTLIER) cc_final: 0.3793 (t-90) REVERT: A 444 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7789 (ttp-110) REVERT: A 451 MET cc_start: 0.7019 (tpp) cc_final: 0.6724 (tpp) REVERT: B 222 GLU cc_start: 0.5861 (tm-30) cc_final: 0.5412 (tm-30) REVERT: C 326 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7763 (ttpt) REVERT: C 359 TYR cc_start: 0.7281 (t80) cc_final: 0.6911 (t80) REVERT: C 390 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6305 (tm-30) REVERT: D 236 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: D 301 GLU cc_start: 0.6312 (mm-30) cc_final: 0.4825 (tp30) REVERT: E 78 ASN cc_start: 0.6986 (m-40) cc_final: 0.6719 (m-40) REVERT: E 236 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: E 327 ASP cc_start: 0.8003 (t70) cc_final: 0.7480 (t70) REVERT: E 469 MET cc_start: 0.7854 (mmm) cc_final: 0.7483 (mmm) REVERT: E 470 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6753 (mt0) REVERT: F 284 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7642 (mtpt) outliers start: 26 outliers final: 14 residues processed: 326 average time/residue: 0.8818 time to fit residues: 459.6301 Evaluate side-chains 309 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 511 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.8837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27594 Z= 0.182 Angle : 0.463 4.396 37233 Z= 0.251 Chirality : 0.041 0.144 4557 Planarity : 0.003 0.032 4802 Dihedral : 3.922 22.081 3829 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.94 % Allowed : 12.40 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.14), residues: 3654 helix: 2.02 (0.12), residues: 1946 sheet: -0.35 (0.23), residues: 567 loop : -1.31 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 42 HIS 0.003 0.001 HIS C 314 PHE 0.010 0.001 PHE E 193 TYR 0.011 0.001 TYR D 359 ARG 0.003 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 303 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 284 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7286 (mtpt) REVERT: G 451 MET cc_start: 0.7454 (mmm) cc_final: 0.6994 (tpp) REVERT: A 241 HIS cc_start: 0.4744 (OUTLIER) cc_final: 0.4007 (t-90) REVERT: A 444 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7775 (ttp-110) REVERT: A 451 MET cc_start: 0.6940 (tpp) cc_final: 0.6650 (tpp) REVERT: B 222 GLU cc_start: 0.5901 (tm-30) cc_final: 0.5451 (tm-30) REVERT: C 326 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7762 (ttpt) REVERT: C 359 TYR cc_start: 0.7309 (t80) cc_final: 0.6951 (t80) REVERT: C 390 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6422 (tm-30) REVERT: D 236 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: E 78 ASN cc_start: 0.7014 (m-40) cc_final: 0.6769 (m-40) REVERT: E 236 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: E 327 ASP cc_start: 0.7968 (t70) cc_final: 0.7470 (t70) REVERT: E 469 MET cc_start: 0.7986 (mmm) cc_final: 0.7606 (mmm) REVERT: E 470 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6743 (mt0) REVERT: F 284 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7664 (mtpt) outliers start: 28 outliers final: 19 residues processed: 318 average time/residue: 0.9201 time to fit residues: 464.3845 Evaluate side-chains 310 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 241 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 511 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 295 optimal weight: 0.6980 chunk 309 optimal weight: 0.4980 chunk 325 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.9097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27594 Z= 0.165 Angle : 0.456 4.978 37233 Z= 0.245 Chirality : 0.040 0.141 4557 Planarity : 0.003 0.041 4802 Dihedral : 3.868 22.738 3829 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.84 % Allowed : 12.70 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.14), residues: 3654 helix: 2.13 (0.12), residues: 1946 sheet: -0.28 (0.23), residues: 567 loop : -1.31 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 42 HIS 0.002 0.001 HIS C 314 PHE 0.011 0.001 PHE D 484 TYR 0.010 0.001 TYR D 359 ARG 0.003 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 4.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 284 LYS cc_start: 0.8065 (tmtt) cc_final: 0.7269 (mtpt) REVERT: G 451 MET cc_start: 0.7418 (mmm) cc_final: 0.7002 (tpp) REVERT: A 72 ILE cc_start: 0.8579 (tt) cc_final: 0.8320 (tt) REVERT: A 241 HIS cc_start: 0.4843 (OUTLIER) cc_final: 0.4133 (t-90) REVERT: A 444 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7792 (ttp-110) REVERT: A 451 MET cc_start: 0.6903 (tpp) cc_final: 0.6633 (tpp) REVERT: C 326 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7859 (ttpt) REVERT: C 359 TYR cc_start: 0.7304 (t80) cc_final: 0.6958 (t80) REVERT: C 390 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6433 (tm-30) REVERT: D 162 ASP cc_start: 0.6590 (m-30) cc_final: 0.6385 (m-30) REVERT: D 236 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: E 78 ASN cc_start: 0.6951 (m-40) cc_final: 0.6729 (m-40) REVERT: E 191 MET cc_start: 0.7483 (ppp) cc_final: 0.7119 (ptp) REVERT: E 236 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: E 327 ASP cc_start: 0.8007 (t70) cc_final: 0.7711 (t70) REVERT: E 469 MET cc_start: 0.7994 (mmm) cc_final: 0.7647 (mmm) REVERT: E 470 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6855 (mt0) REVERT: F 140 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6503 (tm-30) REVERT: F 284 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7632 (mtpt) outliers start: 25 outliers final: 20 residues processed: 315 average time/residue: 0.9072 time to fit residues: 457.1111 Evaluate side-chains 307 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 4.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 241 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 511 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.7980 chunk 345 optimal weight: 0.4980 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 362 optimal weight: 0.9990 chunk 333 optimal weight: 0.5980 chunk 288 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.9292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27594 Z= 0.166 Angle : 0.458 4.560 37233 Z= 0.247 Chirality : 0.040 0.140 4557 Planarity : 0.003 0.032 4802 Dihedral : 3.847 21.514 3829 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.77 % Allowed : 13.01 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.14), residues: 3654 helix: 2.20 (0.12), residues: 1946 sheet: -0.26 (0.22), residues: 567 loop : -1.30 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 42 HIS 0.003 0.001 HIS C 314 PHE 0.009 0.001 PHE E 193 TYR 0.010 0.001 TYR D 359 ARG 0.002 0.000 ARG B 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 284 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7273 (mtpt) REVERT: G 451 MET cc_start: 0.7422 (mmm) cc_final: 0.7013 (tpp) REVERT: A 241 HIS cc_start: 0.4947 (OUTLIER) cc_final: 0.4170 (t-90) REVERT: A 444 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7804 (ttp-110) REVERT: A 451 MET cc_start: 0.6886 (tpp) cc_final: 0.6631 (tpp) REVERT: C 119 MET cc_start: 0.7361 (mmp) cc_final: 0.7064 (mmp) REVERT: C 326 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7887 (ttpt) REVERT: C 359 TYR cc_start: 0.7296 (t80) cc_final: 0.6978 (t80) REVERT: D 236 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: E 78 ASN cc_start: 0.6943 (m-40) cc_final: 0.6717 (m-40) REVERT: E 191 MET cc_start: 0.7441 (ppp) cc_final: 0.7218 (ptp) REVERT: E 236 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: E 327 ASP cc_start: 0.7996 (t70) cc_final: 0.7637 (t70) REVERT: E 469 MET cc_start: 0.8006 (mmm) cc_final: 0.7692 (mmm) REVERT: E 470 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6875 (mt0) REVERT: F 140 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6502 (tm-30) REVERT: F 191 MET cc_start: 0.7209 (ptt) cc_final: 0.6813 (ptp) outliers start: 23 outliers final: 17 residues processed: 299 average time/residue: 0.8678 time to fit residues: 418.1794 Evaluate side-chains 300 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 511 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 GLN C 470 GLN E 80 ASN E 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.205004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132022 restraints weight = 78710.932| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.17 r_work: 0.3267 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.9668 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: