Starting phenix.real_space_refine on Thu Mar 5 07:51:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwq_26838/03_2026/7uwq_26838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwq_26838/03_2026/7uwq_26838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uwq_26838/03_2026/7uwq_26838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwq_26838/03_2026/7uwq_26838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwq_26838/03_2026/7uwq_26838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwq_26838/03_2026/7uwq_26838.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 13098 2.51 5 N 3528 2.21 5 O 3846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20538 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 407} Chain breaks: 4 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.99, per 1000 atoms: 0.15 Number of scatterers: 20538 At special positions: 0 Unit cell: (143.145, 133.365, 118.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3846 8.00 N 3528 7.00 C 13098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 788.7 milliseconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 41.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.551A pdb=" N LEU A 104 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.747A pdb=" N PHE A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.880A pdb=" N THR A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 344 through 360 removed outlier: 3.550A pdb=" N GLY A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.701A pdb=" N SER A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.552A pdb=" N LEU B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.747A pdb=" N PHE B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.881A pdb=" N THR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.550A pdb=" N GLY B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 385 Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.701A pdb=" N SER B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.736A pdb=" N GLY B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 466 removed outlier: 3.615A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.552A pdb=" N LEU C 104 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.749A pdb=" N PHE C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL C 210 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 222 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.645A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 3.881A pdb=" N THR C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 344 through 360 removed outlier: 3.548A pdb=" N GLY C 360 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 385 Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.701A pdb=" N SER C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY C 433 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA D 13 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.551A pdb=" N LEU D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 4.138A pdb=" N ILE D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 175 through 190 removed outlier: 3.748A pdb=" N PHE D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 222 removed outlier: 3.901A pdb=" N VAL D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 222 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 3.879A pdb=" N THR D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 288 " --> pdb=" O ASN D 284 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 344 through 360 removed outlier: 3.549A pdb=" N GLY D 360 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 385 Processing helix chain 'D' and resid 386 through 397 removed outlier: 3.702A pdb=" N SER D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG D 393 " --> pdb=" O ALA D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY D 433 " --> pdb=" O PRO D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 466 removed outlier: 3.615A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 39 removed outlier: 3.515A pdb=" N ALA E 13 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 104 removed outlier: 3.553A pdb=" N LEU E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.137A pdb=" N ILE E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 175 through 190 removed outlier: 3.748A pdb=" N PHE E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 184 " --> pdb=" O ASP E 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 185 " --> pdb=" O PHE E 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 222 removed outlier: 3.903A pdb=" N VAL E 210 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 222 " --> pdb=" O CYS E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.644A pdb=" N LYS E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 293 removed outlier: 3.881A pdb=" N THR E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 344 through 360 removed outlier: 3.548A pdb=" N GLY E 360 " --> pdb=" O LYS E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 385 Processing helix chain 'E' and resid 386 through 397 removed outlier: 3.702A pdb=" N SER E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG E 393 " --> pdb=" O ALA E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 416 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.738A pdb=" N GLY E 433 " --> pdb=" O PRO E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 39 removed outlier: 3.514A pdb=" N ALA F 13 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.553A pdb=" N LEU F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 4.136A pdb=" N ILE F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 Processing helix chain 'F' and resid 175 through 190 removed outlier: 3.748A pdb=" N PHE F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 185 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 222 removed outlier: 3.902A pdb=" N VAL F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 222 " --> pdb=" O CYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 258 removed outlier: 3.645A pdb=" N LYS F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 293 removed outlier: 3.880A pdb=" N THR F 287 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 288 " --> pdb=" O ASN F 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 344 through 360 removed outlier: 3.549A pdb=" N GLY F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 Processing helix chain 'F' and resid 386 through 397 removed outlier: 3.702A pdb=" N SER F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG F 393 " --> pdb=" O ALA F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 416 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.737A pdb=" N GLY F 433 " --> pdb=" O PRO F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 466 removed outlier: 3.614A pdb=" N GLU F 466 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 86 removed outlier: 5.131A pdb=" N TYR A 54 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.702A pdb=" N ILE A 237 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 230 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 273 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 200 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 276 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 202 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LEU A 423 " --> pdb=" O TRP A 300 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET A 302 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS A 425 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 304 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER A 427 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS A 306 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL A 375 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 324 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR A 377 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG A 326 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 400 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR A 374 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 402 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 376 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR B 54 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.700A pdb=" N ILE B 237 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 230 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 273 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR B 200 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE B 276 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 202 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU B 423 " --> pdb=" O TRP B 300 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET B 302 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS B 425 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 304 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER B 427 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS B 306 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL B 375 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR B 324 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 377 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG B 326 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 400 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR B 374 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B 402 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 376 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR C 54 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.701A pdb=" N ILE C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 230 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 273 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR C 200 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE C 276 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 202 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU C 423 " --> pdb=" O TRP C 300 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET C 302 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS C 425 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 304 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER C 427 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N CYS C 306 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 375 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR C 324 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 377 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG C 326 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL C 400 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR C 374 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 402 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 376 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR D 54 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.701A pdb=" N ILE D 237 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA D 230 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 273 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR D 200 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE D 276 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU D 202 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU D 423 " --> pdb=" O TRP D 300 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET D 302 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS D 425 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 304 " --> pdb=" O CYS D 425 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER D 427 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS D 306 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL D 375 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR D 324 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR D 377 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG D 326 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL D 400 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR D 374 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE D 402 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 376 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 82 through 86 removed outlier: 5.130A pdb=" N TYR E 54 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.702A pdb=" N ILE E 237 " --> pdb=" O CYS E 233 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 230 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 273 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR E 200 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE E 276 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 202 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LEU E 423 " --> pdb=" O TRP E 300 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET E 302 " --> pdb=" O LEU E 423 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS E 425 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY E 304 " --> pdb=" O CYS E 425 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER E 427 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS E 306 " --> pdb=" O SER E 427 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL E 375 " --> pdb=" O HIS E 322 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR E 324 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR E 377 " --> pdb=" O TYR E 324 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG E 326 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL E 400 " --> pdb=" O THR E 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR E 374 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE E 402 " --> pdb=" O THR E 374 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 376 " --> pdb=" O ILE E 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 82 through 86 removed outlier: 5.131A pdb=" N TYR F 54 " --> pdb=" O SER F 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 237 through 239 removed outlier: 3.702A pdb=" N ILE F 237 " --> pdb=" O CYS F 233 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 230 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 273 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR F 200 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE F 276 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 202 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU F 423 " --> pdb=" O TRP F 300 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET F 302 " --> pdb=" O LEU F 423 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS F 425 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY F 304 " --> pdb=" O CYS F 425 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER F 427 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS F 306 " --> pdb=" O SER F 427 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL F 375 " --> pdb=" O HIS F 322 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR F 324 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR F 377 " --> pdb=" O TYR F 324 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG F 326 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL F 400 " --> pdb=" O THR F 372 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR F 374 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE F 402 " --> pdb=" O THR F 374 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 376 " --> pdb=" O ILE F 402 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2358 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: 2.85 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6763 1.34 - 1.46: 3896 1.46 - 1.57: 10293 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 21048 Sorted by residual: bond pdb=" CB THR A 190 " pdb=" CG2 THR A 190 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.05e-01 bond pdb=" CB THR B 190 " pdb=" CG2 THR B 190 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR C 190 " pdb=" CG2 THR C 190 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.72e-01 bond pdb=" CB THR E 190 " pdb=" CG2 THR E 190 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 bond pdb=" CB THR D 190 " pdb=" CG2 THR D 190 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.53e-01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 27737 1.36 - 2.73: 754 2.73 - 4.09: 165 4.09 - 5.46: 12 5.46 - 6.82: 18 Bond angle restraints: 28686 Sorted by residual: angle pdb=" N TYR D 123 " pdb=" CA TYR D 123 " pdb=" C TYR D 123 " ideal model delta sigma weight residual 109.81 114.62 -4.81 2.21e+00 2.05e-01 4.74e+00 angle pdb=" N TYR C 123 " pdb=" CA TYR C 123 " pdb=" C TYR C 123 " ideal model delta sigma weight residual 109.81 114.56 -4.75 2.21e+00 2.05e-01 4.62e+00 angle pdb=" N TYR F 123 " pdb=" CA TYR F 123 " pdb=" C TYR F 123 " ideal model delta sigma weight residual 109.81 114.51 -4.70 2.21e+00 2.05e-01 4.51e+00 angle pdb=" N TYR E 123 " pdb=" CA TYR E 123 " pdb=" C TYR E 123 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.51e+00 angle pdb=" N TYR A 123 " pdb=" CA TYR A 123 " pdb=" C TYR A 123 " ideal model delta sigma weight residual 109.81 114.48 -4.67 2.21e+00 2.05e-01 4.47e+00 ... (remaining 28681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 11192 17.26 - 34.52: 1021 34.52 - 51.78: 201 51.78 - 69.05: 30 69.05 - 86.31: 18 Dihedral angle restraints: 12462 sinusoidal: 4896 harmonic: 7566 Sorted by residual: dihedral pdb=" CA LYS A 256 " pdb=" C LYS A 256 " pdb=" N LYS A 257 " pdb=" CA LYS A 257 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LYS C 256 " pdb=" C LYS C 256 " pdb=" N LYS C 257 " pdb=" CA LYS C 257 " ideal model delta harmonic sigma weight residual -180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LYS E 256 " pdb=" C LYS E 256 " pdb=" N LYS E 257 " pdb=" CA LYS E 257 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 12459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2002 0.036 - 0.072: 890 0.072 - 0.108: 216 0.108 - 0.144: 87 0.144 - 0.181: 9 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB ILE E 250 " pdb=" CA ILE E 250 " pdb=" CG1 ILE E 250 " pdb=" CG2 ILE E 250 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CB ILE F 250 " pdb=" CA ILE F 250 " pdb=" CG1 ILE F 250 " pdb=" CG2 ILE F 250 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 3201 not shown) Planarity restraints: 3702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 245 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 246 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 245 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO F 246 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 246 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 246 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 245 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 246 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 246 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 246 " -0.030 5.00e-02 4.00e+02 ... (remaining 3699 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6524 2.83 - 3.35: 16777 3.35 - 3.87: 30583 3.87 - 4.38: 34200 4.38 - 4.90: 64111 Nonbonded interactions: 152195 Sorted by model distance: nonbonded pdb=" OE1 GLU A 150 " pdb=" NE2 GLN A 153 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLU D 150 " pdb=" NE2 GLN D 153 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLU B 150 " pdb=" NE2 GLN B 153 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLU E 150 " pdb=" NE2 GLN E 153 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLU C 150 " pdb=" NE2 GLN C 153 " model vdw 2.313 3.120 ... (remaining 152190 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.540 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.005 0.038 21048 Z= 0.191 Angle : 0.574 6.821 28686 Z= 0.323 Chirality : 0.044 0.181 3204 Planarity : 0.005 0.055 3702 Dihedral : 13.810 86.306 7602 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2538 helix: 0.21 (0.17), residues: 1032 sheet: 0.50 (0.24), residues: 468 loop : -1.47 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 484 TYR 0.012 0.001 TYR B 206 PHE 0.014 0.002 PHE A 181 TRP 0.007 0.001 TRP D 238 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00458 (21048) covalent geometry : angle 0.57387 (28686) hydrogen bonds : bond 0.14564 ( 816) hydrogen bonds : angle 5.68768 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.682 Fit side-chains REVERT: A 405 GLU cc_start: 0.8012 (mp0) cc_final: 0.7804 (mp0) REVERT: E 290 ASP cc_start: 0.8241 (m-30) cc_final: 0.7960 (m-30) REVERT: E 332 ASP cc_start: 0.8145 (m-30) cc_final: 0.7929 (m-30) REVERT: F 94 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7235 (ttt-90) REVERT: F 290 ASP cc_start: 0.8147 (m-30) cc_final: 0.7852 (m-30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1593 time to fit residues: 54.5693 Evaluate side-chains 186 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108061 restraints weight = 24237.525| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.68 r_work: 0.3102 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21048 Z= 0.105 Angle : 0.490 6.137 28686 Z= 0.258 Chirality : 0.042 0.162 3204 Planarity : 0.004 0.040 3702 Dihedral : 3.948 26.635 2874 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.41 % Allowed : 6.47 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2538 helix: 0.51 (0.17), residues: 1038 sheet: 0.83 (0.25), residues: 468 loop : -1.20 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 94 TYR 0.010 0.001 TYR E 206 PHE 0.009 0.001 PHE E 146 TRP 0.007 0.001 TRP F 383 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00242 (21048) covalent geometry : angle 0.49002 (28686) hydrogen bonds : bond 0.04167 ( 816) hydrogen bonds : angle 4.51516 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.680 Fit side-chains REVERT: B 257 LYS cc_start: 0.8398 (mmtp) cc_final: 0.8169 (mmtm) REVERT: D 257 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7980 (mmtp) outliers start: 9 outliers final: 6 residues processed: 208 average time/residue: 0.1547 time to fit residues: 49.0553 Evaluate side-chains 185 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105157 restraints weight = 24377.079| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.66 r_work: 0.3092 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21048 Z= 0.173 Angle : 0.530 6.212 28686 Z= 0.277 Chirality : 0.043 0.164 3204 Planarity : 0.004 0.042 3702 Dihedral : 4.041 27.500 2874 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.96 % Allowed : 8.72 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2538 helix: 0.49 (0.17), residues: 1044 sheet: 0.70 (0.25), residues: 468 loop : -1.26 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.013 0.001 TYR F 414 PHE 0.014 0.002 PHE B 181 TRP 0.006 0.001 TRP B 238 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00439 (21048) covalent geometry : angle 0.53026 (28686) hydrogen bonds : bond 0.05171 ( 816) hydrogen bonds : angle 4.53036 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.720 Fit side-chains REVERT: A 356 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7973 (ttmm) REVERT: D 257 LYS cc_start: 0.8257 (mmmt) cc_final: 0.8021 (mmtp) REVERT: F 404 MET cc_start: 0.8466 (mtp) cc_final: 0.8221 (mtp) outliers start: 21 outliers final: 19 residues processed: 202 average time/residue: 0.1489 time to fit residues: 45.7782 Evaluate side-chains 198 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 242 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN F 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106477 restraints weight = 24251.695| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.62 r_work: 0.2990 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21048 Z= 0.119 Angle : 0.479 6.125 28686 Z= 0.252 Chirality : 0.042 0.168 3204 Planarity : 0.004 0.041 3702 Dihedral : 3.828 27.579 2874 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.83 % Allowed : 10.28 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2538 helix: 0.50 (0.17), residues: 1074 sheet: 0.69 (0.25), residues: 468 loop : -1.17 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.009 0.001 TYR F 414 PHE 0.010 0.001 PHE B 181 TRP 0.006 0.001 TRP B 238 HIS 0.003 0.001 HIS E 322 Details of bonding type rmsd covalent geometry : bond 0.00290 (21048) covalent geometry : angle 0.47899 (28686) hydrogen bonds : bond 0.04118 ( 816) hydrogen bonds : angle 4.36630 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.747 Fit side-chains REVERT: A 356 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7981 (ttmm) REVERT: D 257 LYS cc_start: 0.8248 (mmmt) cc_final: 0.8024 (mmtp) REVERT: F 404 MET cc_start: 0.8387 (mtp) cc_final: 0.8138 (mtp) outliers start: 18 outliers final: 17 residues processed: 206 average time/residue: 0.1569 time to fit residues: 49.4172 Evaluate side-chains 197 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 13 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 244 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 230 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN E 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108065 restraints weight = 24202.622| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.61 r_work: 0.3011 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21048 Z= 0.097 Angle : 0.457 6.110 28686 Z= 0.239 Chirality : 0.041 0.177 3204 Planarity : 0.003 0.040 3702 Dihedral : 3.616 26.769 2874 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.87 % Allowed : 10.84 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2538 helix: 0.70 (0.17), residues: 1074 sheet: 0.77 (0.25), residues: 468 loop : -1.08 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.008 0.001 TYR D 123 PHE 0.008 0.001 PHE E 181 TRP 0.006 0.001 TRP C 238 HIS 0.004 0.000 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00230 (21048) covalent geometry : angle 0.45674 (28686) hydrogen bonds : bond 0.03475 ( 816) hydrogen bonds : angle 4.22732 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.820 Fit side-chains REVERT: A 290 ASP cc_start: 0.8662 (m-30) cc_final: 0.8247 (m-30) REVERT: A 356 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7989 (ttmm) REVERT: D 257 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8090 (mmtp) outliers start: 19 outliers final: 18 residues processed: 208 average time/residue: 0.1587 time to fit residues: 50.2684 Evaluate side-chains 202 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 0.0570 chunk 168 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106146 restraints weight = 24140.583| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.61 r_work: 0.3101 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21048 Z= 0.132 Angle : 0.488 6.161 28686 Z= 0.255 Chirality : 0.042 0.170 3204 Planarity : 0.004 0.040 3702 Dihedral : 3.716 26.684 2874 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.29 % Allowed : 11.39 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2538 helix: 0.67 (0.17), residues: 1074 sheet: 0.73 (0.24), residues: 468 loop : -1.11 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 178 TYR 0.010 0.001 TYR D 123 PHE 0.012 0.001 PHE E 181 TRP 0.005 0.001 TRP C 238 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00329 (21048) covalent geometry : angle 0.48846 (28686) hydrogen bonds : bond 0.04221 ( 816) hydrogen bonds : angle 4.29583 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.731 Fit side-chains REVERT: A 315 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8496 (mp) REVERT: C 315 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8410 (mp) REVERT: D 257 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8073 (mmtp) REVERT: D 315 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8415 (mp) REVERT: F 51 LEU cc_start: 0.7806 (tp) cc_final: 0.7570 (tp) REVERT: F 315 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8494 (mp) outliers start: 28 outliers final: 21 residues processed: 216 average time/residue: 0.1545 time to fit residues: 50.7868 Evaluate side-chains 216 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106880 restraints weight = 24205.363| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.61 r_work: 0.3023 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21048 Z= 0.114 Angle : 0.469 6.133 28686 Z= 0.246 Chirality : 0.041 0.170 3204 Planarity : 0.003 0.040 3702 Dihedral : 3.651 26.345 2874 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.19 % Allowed : 11.94 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2538 helix: 0.73 (0.17), residues: 1074 sheet: 0.75 (0.24), residues: 468 loop : -1.05 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 178 TYR 0.009 0.001 TYR D 123 PHE 0.010 0.001 PHE B 181 TRP 0.006 0.001 TRP C 238 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00280 (21048) covalent geometry : angle 0.46893 (28686) hydrogen bonds : bond 0.03863 ( 816) hydrogen bonds : angle 4.24483 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.764 Fit side-chains REVERT: A 315 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 315 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 257 LYS cc_start: 0.8283 (mmmt) cc_final: 0.8067 (mmtp) REVERT: D 315 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8403 (mp) REVERT: F 51 LEU cc_start: 0.7694 (tp) cc_final: 0.7441 (tp) REVERT: F 315 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8460 (mp) outliers start: 26 outliers final: 19 residues processed: 219 average time/residue: 0.1568 time to fit residues: 51.7912 Evaluate side-chains 217 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 248 optimal weight: 0.1980 chunk 62 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107735 restraints weight = 24156.881| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.65 r_work: 0.3049 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21048 Z= 0.095 Angle : 0.453 6.103 28686 Z= 0.237 Chirality : 0.041 0.167 3204 Planarity : 0.003 0.040 3702 Dihedral : 3.511 25.799 2874 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.06 % Allowed : 12.53 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2538 helix: 0.84 (0.17), residues: 1080 sheet: 0.87 (0.25), residues: 468 loop : -1.10 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 369 TYR 0.008 0.001 TYR D 123 PHE 0.007 0.001 PHE D 181 TRP 0.006 0.001 TRP C 238 HIS 0.004 0.000 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00225 (21048) covalent geometry : angle 0.45311 (28686) hydrogen bonds : bond 0.03345 ( 816) hydrogen bonds : angle 4.15505 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.575 Fit side-chains REVERT: C 315 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8351 (mp) REVERT: D 257 LYS cc_start: 0.8256 (mmmt) cc_final: 0.8037 (mmtp) REVERT: D 315 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8329 (mp) REVERT: F 51 LEU cc_start: 0.7594 (tp) cc_final: 0.7375 (tp) outliers start: 23 outliers final: 19 residues processed: 219 average time/residue: 0.1550 time to fit residues: 51.4897 Evaluate side-chains 217 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 168 optimal weight: 0.0980 chunk 223 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110723 restraints weight = 24165.508| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.75 r_work: 0.3066 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21048 Z= 0.084 Angle : 0.444 6.075 28686 Z= 0.232 Chirality : 0.040 0.173 3204 Planarity : 0.003 0.058 3702 Dihedral : 3.371 24.196 2874 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.73 % Allowed : 13.36 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2538 helix: 1.01 (0.17), residues: 1080 sheet: 1.01 (0.25), residues: 468 loop : -0.99 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 177 TYR 0.008 0.001 TYR C 123 PHE 0.007 0.001 PHE E 146 TRP 0.007 0.001 TRP E 238 HIS 0.004 0.000 HIS E 322 Details of bonding type rmsd covalent geometry : bond 0.00191 (21048) covalent geometry : angle 0.44428 (28686) hydrogen bonds : bond 0.02896 ( 816) hydrogen bonds : angle 4.07118 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.817 Fit side-chains REVERT: A 51 LEU cc_start: 0.7658 (tp) cc_final: 0.7419 (tp) REVERT: C 315 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8342 (mp) REVERT: D 51 LEU cc_start: 0.7655 (tp) cc_final: 0.7419 (tp) REVERT: D 257 LYS cc_start: 0.8308 (mmmt) cc_final: 0.8079 (mmtp) REVERT: F 51 LEU cc_start: 0.7640 (tp) cc_final: 0.7392 (tp) REVERT: F 315 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8452 (mp) outliers start: 16 outliers final: 14 residues processed: 210 average time/residue: 0.1530 time to fit residues: 48.7873 Evaluate side-chains 209 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 64 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 89 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 240 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108685 restraints weight = 24167.704| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.67 r_work: 0.3127 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21048 Z= 0.090 Angle : 0.450 6.088 28686 Z= 0.234 Chirality : 0.041 0.167 3204 Planarity : 0.003 0.060 3702 Dihedral : 3.341 24.181 2874 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 13.45 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2538 helix: 1.06 (0.17), residues: 1080 sheet: 1.05 (0.25), residues: 468 loop : -0.90 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 94 TYR 0.009 0.001 TYR D 123 PHE 0.007 0.001 PHE E 181 TRP 0.006 0.001 TRP E 238 HIS 0.004 0.000 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00209 (21048) covalent geometry : angle 0.44979 (28686) hydrogen bonds : bond 0.03053 ( 816) hydrogen bonds : angle 4.05983 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.774 Fit side-chains REVERT: A 51 LEU cc_start: 0.7602 (tp) cc_final: 0.7371 (tp) REVERT: C 315 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8307 (mp) REVERT: D 51 LEU cc_start: 0.7588 (tp) cc_final: 0.7360 (tp) REVERT: D 257 LYS cc_start: 0.8234 (mmmt) cc_final: 0.8016 (mmtp) REVERT: F 51 LEU cc_start: 0.7518 (tp) cc_final: 0.7291 (tp) REVERT: F 315 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8410 (mp) outliers start: 17 outliers final: 15 residues processed: 205 average time/residue: 0.1694 time to fit residues: 51.9849 Evaluate side-chains 207 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 92 optimal weight: 0.3980 chunk 215 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 184 optimal weight: 0.0050 chunk 109 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110656 restraints weight = 24224.409| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.75 r_work: 0.3061 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21048 Z= 0.089 Angle : 0.446 6.091 28686 Z= 0.232 Chirality : 0.041 0.167 3204 Planarity : 0.003 0.059 3702 Dihedral : 3.303 23.830 2874 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.78 % Allowed : 13.54 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2538 helix: 1.13 (0.17), residues: 1080 sheet: 1.07 (0.25), residues: 468 loop : -0.85 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.008 0.001 TYR D 123 PHE 0.007 0.001 PHE E 181 TRP 0.006 0.001 TRP E 238 HIS 0.004 0.000 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00206 (21048) covalent geometry : angle 0.44576 (28686) hydrogen bonds : bond 0.02975 ( 816) hydrogen bonds : angle 4.04482 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4101.23 seconds wall clock time: 71 minutes 3.36 seconds (4263.36 seconds total)