Starting phenix.real_space_refine on Tue Jun 17 23:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwq_26838/06_2025/7uwq_26838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwq_26838/06_2025/7uwq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwq_26838/06_2025/7uwq_26838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwq_26838/06_2025/7uwq_26838.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwq_26838/06_2025/7uwq_26838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwq_26838/06_2025/7uwq_26838.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 8.06, per 1000 atoms: 0.39 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: 4.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.22 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: 5.94 Time building geometry restraints manager: 5.64 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 39.870 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), 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 TRP 0.007 0.001 TRP D 238 HIS 0.004 0.001 HIS A 264 PHE 0.014 0.002 PHE A 181 TYR 0.012 0.001 TYR B 206 ARG 0.003 0.000 ARG C 484 Details of bonding type rmsd hydrogen bonds : bond 0.14564 ( 816) hydrogen bonds : angle 5.68768 ( 2358) covalent geometry : bond 0.00458 (21048) covalent geometry : angle 0.57387 (28686) *********************** 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 : 2.348 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: 0.3527 time to fit residues: 120.6071 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 : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 122 optimal weight: 0.0670 chunk 150 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.157963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108510 restraints weight = 24138.825| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.67 r_work: 0.3110 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0835 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= 0.099 Angle : 0.486 6.172 28686 Z= 0.256 Chirality : 0.041 0.160 3204 Planarity : 0.004 0.040 3702 Dihedral : 3.921 26.403 2874 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.28 % Allowed : 6.47 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2538 helix: 0.53 (0.17), residues: 1038 sheet: 0.85 (0.25), residues: 468 loop : -1.17 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 383 HIS 0.004 0.001 HIS B 322 PHE 0.009 0.001 PHE E 146 TYR 0.010 0.001 TYR E 206 ARG 0.002 0.000 ARG E 369 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 816) hydrogen bonds : angle 4.50822 ( 2358) covalent geometry : bond 0.00222 (21048) covalent geometry : angle 0.48582 (28686) *********************** 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 206 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 200 time to evaluate : 2.167 Fit side-chains REVERT: B 257 LYS cc_start: 0.8387 (mmtp) cc_final: 0.8162 (mmtm) REVERT: D 257 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7992 (mmtp) outliers start: 6 outliers final: 4 residues processed: 205 average time/residue: 0.3399 time to fit residues: 106.2488 Evaluate side-chains 182 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain E residue 182 SER 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 195 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 224 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.0870 chunk 192 optimal weight: 0.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107480 restraints weight = 24200.294| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.64 r_work: 0.3096 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1078 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= 0.115 Angle : 0.480 6.153 28686 Z= 0.251 Chirality : 0.042 0.170 3204 Planarity : 0.004 0.040 3702 Dihedral : 3.771 26.033 2874 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.92 % Allowed : 8.72 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2538 helix: 0.52 (0.17), residues: 1074 sheet: 0.81 (0.25), residues: 468 loop : -1.09 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.001 HIS B 322 PHE 0.009 0.001 PHE E 181 TYR 0.010 0.001 TYR F 414 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 816) hydrogen bonds : angle 4.35800 ( 2358) covalent geometry : bond 0.00280 (21048) covalent geometry : angle 0.47955 (28686) *********************** 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 208 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 2.126 Fit side-chains REVERT: D 257 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8021 (mmtp) REVERT: F 404 MET cc_start: 0.8315 (mtp) cc_final: 0.8027 (mtp) outliers start: 20 outliers final: 19 residues processed: 207 average time/residue: 0.3420 time to fit residues: 108.7691 Evaluate side-chains 200 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 245 optimal weight: 0.4980 chunk 196 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN B 56 GLN E 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108203 restraints weight = 24259.084| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.66 r_work: 0.3130 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21048 Z= 0.093 Angle : 0.452 6.111 28686 Z= 0.236 Chirality : 0.041 0.171 3204 Planarity : 0.003 0.039 3702 Dihedral : 3.579 25.287 2874 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.78 % Allowed : 9.37 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2538 helix: 0.69 (0.17), residues: 1074 sheet: 0.87 (0.25), residues: 468 loop : -1.05 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.000 HIS B 322 PHE 0.007 0.001 PHE B 181 TYR 0.007 0.001 TYR D 123 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 816) hydrogen bonds : angle 4.23290 ( 2358) covalent geometry : bond 0.00217 (21048) covalent geometry : angle 0.45228 (28686) *********************** 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 212 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 4.006 Fit side-chains REVERT: C 51 LEU cc_start: 0.7714 (tp) cc_final: 0.7483 (tp) REVERT: C 356 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7901 (ttmm) REVERT: D 257 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8050 (mmtp) outliers start: 17 outliers final: 15 residues processed: 212 average time/residue: 0.4036 time to fit residues: 134.8396 Evaluate side-chains 203 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 3.314 ------------------------------------------------------------------------------- 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 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 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 170 optimal weight: 2.9990 chunk 199 optimal weight: 0.3980 chunk 233 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 150 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.156197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106392 restraints weight = 24420.839| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.63 r_work: 0.3015 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1287 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 : 0.487 6.173 28686 Z= 0.254 Chirality : 0.042 0.172 3204 Planarity : 0.004 0.049 3702 Dihedral : 3.704 25.788 2874 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.83 % Allowed : 10.70 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2538 helix: 0.83 (0.17), residues: 1038 sheet: 0.76 (0.25), residues: 468 loop : -1.15 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.003 0.001 HIS E 322 PHE 0.012 0.001 PHE E 181 TYR 0.010 0.001 TYR D 123 ARG 0.001 0.000 ARG F 178 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 816) hydrogen bonds : angle 4.30330 ( 2358) covalent geometry : bond 0.00329 (21048) covalent geometry : angle 0.48705 (28686) *********************** 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 205 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 2.139 Fit side-chains REVERT: A 356 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7974 (ttmm) REVERT: C 51 LEU cc_start: 0.7625 (tp) cc_final: 0.7393 (tp) REVERT: D 257 LYS cc_start: 0.8274 (mmmt) cc_final: 0.8040 (mmtp) REVERT: F 404 MET cc_start: 0.8341 (mtp) cc_final: 0.8099 (mtp) outliers start: 18 outliers final: 17 residues processed: 204 average time/residue: 0.3428 time to fit residues: 106.0984 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 : 2.140 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.158161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109850 restraints weight = 24090.718| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.73 r_work: 0.3031 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21048 Z= 0.091 Angle : 0.446 6.121 28686 Z= 0.234 Chirality : 0.041 0.174 3204 Planarity : 0.003 0.043 3702 Dihedral : 3.503 25.291 2874 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.87 % Allowed : 11.07 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2538 helix: 1.01 (0.17), residues: 1038 sheet: 0.88 (0.25), residues: 468 loop : -1.08 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.003 0.000 HIS B 322 PHE 0.007 0.001 PHE D 181 TYR 0.008 0.001 TYR D 123 ARG 0.001 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 816) hydrogen bonds : angle 4.16834 ( 2358) covalent geometry : bond 0.00215 (21048) covalent geometry : angle 0.44629 (28686) *********************** 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 212 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 2.278 Fit side-chains REVERT: A 356 LYS cc_start: 0.8230 (ttmm) cc_final: 0.8027 (ttmm) REVERT: B 290 ASP cc_start: 0.8706 (m-30) cc_final: 0.8318 (m-30) REVERT: C 51 LEU cc_start: 0.7672 (tp) cc_final: 0.7438 (tp) REVERT: D 257 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8085 (mmtp) REVERT: F 51 LEU cc_start: 0.7602 (tp) cc_final: 0.7402 (tp) outliers start: 19 outliers final: 14 residues processed: 210 average time/residue: 0.3541 time to fit residues: 113.4669 Evaluate side-chains 204 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 2.803 ------------------------------------------------------------------------------- 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 149 THR Chi-restraints excluded: chain B residue 182 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 6 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 168 optimal weight: 0.0370 chunk 238 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.158605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108695 restraints weight = 24072.499| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.65 r_work: 0.3067 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1571 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= 0.090 Angle : 0.446 6.120 28686 Z= 0.232 Chirality : 0.040 0.169 3204 Planarity : 0.003 0.052 3702 Dihedral : 3.404 24.362 2874 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.83 % Allowed : 11.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2538 helix: 1.10 (0.17), residues: 1044 sheet: 0.99 (0.25), residues: 468 loop : -1.15 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 238 HIS 0.004 0.000 HIS E 322 PHE 0.007 0.001 PHE D 181 TYR 0.009 0.001 TYR D 123 ARG 0.001 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 816) hydrogen bonds : angle 4.11092 ( 2358) covalent geometry : bond 0.00210 (21048) covalent geometry : angle 0.44608 (28686) *********************** 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 213 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 2.129 Fit side-chains REVERT: A 356 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7950 (ttmm) REVERT: C 51 LEU cc_start: 0.7604 (tp) cc_final: 0.7385 (tp) REVERT: D 257 LYS cc_start: 0.8258 (mmmt) cc_final: 0.8030 (mmtp) REVERT: F 51 LEU cc_start: 0.7585 (tp) cc_final: 0.7371 (tp) outliers start: 18 outliers final: 17 residues processed: 212 average time/residue: 0.3551 time to fit residues: 113.9392 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 : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 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 85 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 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 161 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 0.0170 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.159463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109404 restraints weight = 24308.649| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.67 r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1666 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 : 0.437 6.119 28686 Z= 0.228 Chirality : 0.040 0.176 3204 Planarity : 0.003 0.053 3702 Dihedral : 3.313 23.741 2874 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.78 % Allowed : 12.08 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2538 helix: 1.21 (0.17), residues: 1044 sheet: 0.94 (0.25), residues: 480 loop : -1.00 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.000 HIS B 322 PHE 0.006 0.001 PHE D 181 TYR 0.008 0.001 TYR C 123 ARG 0.004 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 816) hydrogen bonds : angle 4.05047 ( 2358) covalent geometry : bond 0.00195 (21048) covalent geometry : angle 0.43689 (28686) *********************** 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 214 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 2.748 Fit side-chains REVERT: C 51 LEU cc_start: 0.7612 (tp) cc_final: 0.7381 (tp) REVERT: D 257 LYS cc_start: 0.8274 (mmmt) cc_final: 0.8039 (mmtp) REVERT: E 290 ASP cc_start: 0.8645 (m-30) cc_final: 0.8373 (m-30) REVERT: F 51 LEU cc_start: 0.7585 (tp) cc_final: 0.7373 (tp) outliers start: 17 outliers final: 16 residues processed: 214 average time/residue: 0.3836 time to fit residues: 124.7724 Evaluate side-chains 206 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 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 85 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 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 139 optimal weight: 0.0670 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.158442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108231 restraints weight = 24314.260| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.68 r_work: 0.3087 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1686 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 : 0.455 6.148 28686 Z= 0.237 Chirality : 0.041 0.167 3204 Planarity : 0.003 0.057 3702 Dihedral : 3.355 23.792 2874 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.92 % Allowed : 12.44 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2538 helix: 1.07 (0.17), residues: 1074 sheet: 1.05 (0.25), residues: 468 loop : -0.81 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 238 HIS 0.004 0.000 HIS E 322 PHE 0.008 0.001 PHE D 181 TYR 0.009 0.001 TYR C 123 ARG 0.002 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 816) hydrogen bonds : angle 4.07185 ( 2358) covalent geometry : bond 0.00232 (21048) covalent geometry : angle 0.45490 (28686) *********************** 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 205 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 2.095 Fit side-chains REVERT: A 51 LEU cc_start: 0.7674 (tp) cc_final: 0.7420 (tp) REVERT: A 356 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7916 (ttmm) REVERT: C 51 LEU cc_start: 0.7587 (tp) cc_final: 0.7355 (tp) REVERT: C 315 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8312 (mp) REVERT: D 257 LYS cc_start: 0.8239 (mmmt) cc_final: 0.8011 (mmtp) REVERT: F 51 LEU cc_start: 0.7542 (tp) cc_final: 0.7325 (tp) outliers start: 20 outliers final: 18 residues processed: 203 average time/residue: 0.3678 time to fit residues: 111.8434 Evaluate side-chains 202 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 2.192 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 177 optimal weight: 10.0000 chunk 168 optimal weight: 0.0980 chunk 195 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 255 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 209 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110023 restraints weight = 24138.404| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.67 r_work: 0.3126 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1799 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= 0.082 Angle : 0.437 6.109 28686 Z= 0.228 Chirality : 0.040 0.168 3204 Planarity : 0.003 0.052 3702 Dihedral : 3.238 23.118 2874 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.69 % Allowed : 12.72 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2538 helix: 1.22 (0.17), residues: 1074 sheet: 1.12 (0.25), residues: 468 loop : -0.73 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 238 HIS 0.004 0.000 HIS D 322 PHE 0.007 0.001 PHE A 146 TYR 0.008 0.001 TYR C 123 ARG 0.004 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.02766 ( 816) hydrogen bonds : angle 3.99814 ( 2358) covalent geometry : bond 0.00186 (21048) covalent geometry : angle 0.43730 (28686) ********************** 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 211 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 3.844 Fit side-chains REVERT: A 51 LEU cc_start: 0.7577 (tp) cc_final: 0.7330 (tp) REVERT: A 356 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7865 (ttmm) REVERT: C 51 LEU cc_start: 0.7657 (tp) cc_final: 0.7416 (tp) REVERT: C 315 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8301 (mp) REVERT: D 51 LEU cc_start: 0.7642 (tp) cc_final: 0.7424 (tp) REVERT: D 257 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8008 (mmtp) REVERT: F 51 LEU cc_start: 0.7579 (tp) cc_final: 0.7358 (tp) outliers start: 15 outliers final: 14 residues processed: 211 average time/residue: 0.4099 time to fit residues: 129.6837 Evaluate side-chains 204 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 154 ILE 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 149 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 315 ILE 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 149 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 174 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 50 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.159233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110706 restraints weight = 24217.520| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.75 r_work: 0.3075 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1801 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= 0.093 Angle : 0.450 6.135 28686 Z= 0.234 Chirality : 0.041 0.166 3204 Planarity : 0.003 0.050 3702 Dihedral : 3.269 23.168 2874 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.73 % Allowed : 12.81 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2538 helix: 1.20 (0.17), residues: 1074 sheet: 1.12 (0.25), residues: 468 loop : -0.70 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 238 HIS 0.004 0.000 HIS B 322 PHE 0.008 0.001 PHE E 181 TYR 0.009 0.001 TYR C 123 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 816) hydrogen bonds : angle 4.01920 ( 2358) covalent geometry : bond 0.00219 (21048) covalent geometry : angle 0.45010 (28686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8878.57 seconds wall clock time: 155 minutes 40.29 seconds (9340.29 seconds total)