Starting phenix.real_space_refine on Sat Sep 28 21:52:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/09_2024/7uwq_26838.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/09_2024/7uwq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/09_2024/7uwq_26838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/09_2024/7uwq_26838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/09_2024/7uwq_26838.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwq_26838/09_2024/7uwq_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.25, per 1000 atoms: 0.40 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: 4.83 Conformation dependent library (CDL) restraints added in 2.3 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: 2.65 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: 6.42 Time building geometry restraints manager: 5.69 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.870 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.550 ------------------------------------------------------------------------------- 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= 0.303 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.259 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: 0.3443 time to fit residues: 117.3548 Evaluate side-chains 186 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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= 0.147 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 2.254 Fit side-chains REVERT: B 257 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7978 (mmtm) REVERT: D 257 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7876 (mmtp) outliers start: 6 outliers final: 4 residues processed: 205 average time/residue: 0.3405 time to fit residues: 105.9252 Evaluate side-chains 182 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 0.0370 chunk 253 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 188 optimal weight: 0.4980 overall best weight: 0.8862 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21048 Z= 0.155 Angle : 0.462 6.146 28686 Z= 0.241 Chirality : 0.041 0.171 3204 Planarity : 0.003 0.039 3702 Dihedral : 3.658 25.400 2874 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.69 % Allowed : 8.54 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.17), residues: 2538 helix: 0.59 (0.17), residues: 1074 sheet: 0.86 (0.25), residues: 468 loop : -1.04 (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 0.008 0.001 PHE E 181 TYR 0.008 0.001 TYR F 414 ARG 0.001 0.000 ARG A 94 *********************** 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 206 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.089 Fit side-chains REVERT: B 290 ASP cc_start: 0.8379 (m-30) cc_final: 0.7955 (m-30) REVERT: C 356 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7869 (ttmm) REVERT: D 257 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7873 (mmtp) outliers start: 15 outliers final: 15 residues processed: 206 average time/residue: 0.3322 time to fit residues: 103.9187 Evaluate side-chains 196 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 21048 Z= 0.436 Angle : 0.595 6.677 28686 Z= 0.311 Chirality : 0.046 0.170 3204 Planarity : 0.004 0.048 3702 Dihedral : 4.220 28.210 2874 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.96 % Allowed : 10.01 % Favored : 89.03 % 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: -0.26 (0.17), residues: 2538 helix: 0.75 (0.17), residues: 990 sheet: 0.59 (0.24), residues: 468 loop : -1.40 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 61 HIS 0.004 0.001 HIS C 173 PHE 0.018 0.002 PHE E 181 TYR 0.015 0.002 TYR D 414 ARG 0.001 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 2.228 Fit side-chains REVERT: D 257 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7942 (mmtp) REVERT: F 404 MET cc_start: 0.8334 (mtp) cc_final: 0.8115 (mtp) outliers start: 21 outliers final: 19 residues processed: 206 average time/residue: 0.3455 time to fit residues: 107.4367 Evaluate side-chains 196 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 185 optimal weight: 0.4980 chunk 102 optimal weight: 0.4980 chunk 212 optimal weight: 0.0060 chunk 172 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21048 Z= 0.134 Angle : 0.452 6.124 28686 Z= 0.238 Chirality : 0.041 0.170 3204 Planarity : 0.003 0.041 3702 Dihedral : 3.690 27.605 2874 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.51 % Allowed : 11.25 % Favored : 88.25 % 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: -0.04 (0.17), residues: 2538 helix: 0.64 (0.17), residues: 1074 sheet: 0.74 (0.24), residues: 468 loop : -1.09 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 238 HIS 0.004 0.000 HIS E 322 PHE 0.008 0.001 PHE B 146 TYR 0.008 0.001 TYR E 206 ARG 0.001 0.000 ARG C 187 *********************** 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 207 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 2.272 Fit side-chains REVERT: A 428 ASP cc_start: 0.8600 (p0) cc_final: 0.8396 (p0) REVERT: B 290 ASP cc_start: 0.8384 (m-30) cc_final: 0.7934 (m-30) REVERT: D 257 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7876 (mmtp) REVERT: D 290 ASP cc_start: 0.8337 (m-30) cc_final: 0.8020 (m-30) REVERT: E 290 ASP cc_start: 0.8400 (m-30) cc_final: 0.7993 (m-30) REVERT: E 356 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7946 (ttmm) outliers start: 11 outliers final: 10 residues processed: 207 average time/residue: 0.3621 time to fit residues: 113.6362 Evaluate side-chains 200 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 182 SER 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 182 SER 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 83 optimal weight: 0.0010 chunk 224 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1442 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= 0.156 Angle : 0.457 6.109 28686 Z= 0.239 Chirality : 0.041 0.171 3204 Planarity : 0.003 0.039 3702 Dihedral : 3.584 26.718 2874 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.87 % Allowed : 11.48 % Favored : 87.65 % 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: 0.09 (0.17), residues: 2538 helix: 0.76 (0.17), residues: 1074 sheet: 0.83 (0.25), residues: 468 loop : -1.04 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 238 HIS 0.004 0.001 HIS E 322 PHE 0.008 0.001 PHE D 181 TYR 0.010 0.001 TYR F 145 ARG 0.001 0.000 ARG C 310 *********************** 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 215 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 1.991 Fit side-chains REVERT: A 315 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 428 ASP cc_start: 0.8585 (p0) cc_final: 0.8360 (p0) REVERT: B 51 LEU cc_start: 0.7493 (tp) cc_final: 0.7288 (tp) REVERT: B 290 ASP cc_start: 0.8385 (m-30) cc_final: 0.7956 (m-30) REVERT: C 315 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 356 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7896 (ttmm) REVERT: D 257 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7871 (mmtp) REVERT: D 315 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8298 (mp) REVERT: F 51 LEU cc_start: 0.7754 (tp) cc_final: 0.7543 (tp) REVERT: F 315 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8407 (mp) outliers start: 19 outliers final: 10 residues processed: 214 average time/residue: 0.3380 time to fit residues: 109.0439 Evaluate side-chains 206 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 182 SER 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 D residue 315 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 182 optimal weight: 0.0020 chunk 141 optimal weight: 7.9990 chunk 210 optimal weight: 0.5980 chunk 139 optimal weight: 0.0370 chunk 248 optimal weight: 0.0010 chunk 155 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.2472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1731 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= 0.113 Angle : 0.428 6.092 28686 Z= 0.222 Chirality : 0.040 0.170 3204 Planarity : 0.003 0.052 3702 Dihedral : 3.288 24.461 2874 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.55 % Allowed : 12.03 % Favored : 87.42 % 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: 0.34 (0.17), residues: 2538 helix: 1.01 (0.17), residues: 1080 sheet: 1.03 (0.25), residues: 468 loop : -1.03 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP C 238 HIS 0.004 0.000 HIS B 322 PHE 0.007 0.001 PHE A 146 TYR 0.009 0.001 TYR F 145 ARG 0.001 0.000 ARG B 177 *********************** 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 224 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 2.372 Fit side-chains REVERT: A 51 LEU cc_start: 0.7717 (tp) cc_final: 0.7490 (tp) REVERT: B 51 LEU cc_start: 0.7463 (tp) cc_final: 0.7229 (tp) REVERT: C 356 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7823 (ttmm) REVERT: D 257 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7863 (mmtp) REVERT: F 51 LEU cc_start: 0.7608 (tp) cc_final: 0.7402 (tp) outliers start: 12 outliers final: 8 residues processed: 224 average time/residue: 0.3560 time to fit residues: 120.4499 Evaluate side-chains 214 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 182 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21048 Z= 0.157 Angle : 0.455 6.146 28686 Z= 0.236 Chirality : 0.041 0.170 3204 Planarity : 0.003 0.057 3702 Dihedral : 3.355 23.807 2874 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.73 % Allowed : 12.76 % Favored : 86.50 % 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: 0.35 (0.17), residues: 2538 helix: 1.00 (0.17), residues: 1080 sheet: 0.93 (0.25), residues: 480 loop : -0.97 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 D 123 ARG 0.004 0.000 ARG A 94 *********************** 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 211 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.973 Fit side-chains REVERT: A 51 LEU cc_start: 0.7755 (tp) cc_final: 0.7526 (tp) REVERT: B 51 LEU cc_start: 0.7479 (tp) cc_final: 0.7234 (tp) REVERT: B 290 ASP cc_start: 0.8403 (m-30) cc_final: 0.8175 (m-30) REVERT: C 315 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8250 (mp) REVERT: C 356 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7875 (ttmm) REVERT: D 257 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7848 (mmtp) REVERT: F 51 LEU cc_start: 0.7591 (tp) cc_final: 0.7390 (tp) REVERT: F 315 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8376 (mp) outliers start: 16 outliers final: 11 residues processed: 210 average time/residue: 0.3443 time to fit residues: 108.4058 Evaluate side-chains 204 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 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 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 Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 230 optimal weight: 0.0980 chunk 152 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1759 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= 0.134 Angle : 0.443 6.124 28686 Z= 0.230 Chirality : 0.040 0.167 3204 Planarity : 0.003 0.058 3702 Dihedral : 3.293 23.557 2874 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.69 % Allowed : 12.95 % Favored : 86.36 % 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: 0.48 (0.17), residues: 2538 helix: 1.08 (0.17), residues: 1080 sheet: 1.11 (0.25), residues: 468 loop : -0.90 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.000 HIS D 322 PHE 0.007 0.001 PHE B 181 TYR 0.008 0.001 TYR C 123 ARG 0.001 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 2.236 Fit side-chains REVERT: A 51 LEU cc_start: 0.7725 (tp) cc_final: 0.7509 (tp) REVERT: A 315 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8382 (mp) REVERT: B 51 LEU cc_start: 0.7471 (tp) cc_final: 0.7223 (tp) REVERT: B 290 ASP cc_start: 0.8389 (m-30) cc_final: 0.8141 (m-30) REVERT: C 315 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 356 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7860 (ttmm) REVERT: D 51 LEU cc_start: 0.7661 (tp) cc_final: 0.7443 (tp) REVERT: D 257 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7866 (mmtp) REVERT: D 315 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8223 (mp) REVERT: F 51 LEU cc_start: 0.7576 (tp) cc_final: 0.7368 (tp) REVERT: F 315 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8371 (mp) outliers start: 15 outliers final: 11 residues processed: 211 average time/residue: 0.3527 time to fit residues: 112.1406 Evaluate side-chains 209 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 182 SER 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 D residue 315 ILE 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 Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 257 optimal weight: 0.6980 chunk 236 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 0.0060 chunk 162 optimal weight: 5.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21048 Z= 0.139 Angle : 0.445 6.127 28686 Z= 0.232 Chirality : 0.040 0.167 3204 Planarity : 0.003 0.056 3702 Dihedral : 3.273 23.442 2874 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.69 % Allowed : 13.09 % Favored : 86.23 % 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: 0.54 (0.17), residues: 2538 helix: 1.13 (0.17), residues: 1080 sheet: 1.11 (0.25), residues: 468 loop : -0.84 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 238 HIS 0.004 0.000 HIS B 322 PHE 0.007 0.001 PHE D 181 TYR 0.009 0.001 TYR C 123 ARG 0.004 0.000 ARG A 94 ********************** 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 214 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 2.060 Fit side-chains REVERT: A 51 LEU cc_start: 0.7681 (tp) cc_final: 0.7473 (tp) REVERT: A 315 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 51 LEU cc_start: 0.7458 (tp) cc_final: 0.7204 (tp) REVERT: C 315 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8241 (mp) REVERT: C 356 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7865 (ttmm) REVERT: D 51 LEU cc_start: 0.7642 (tp) cc_final: 0.7428 (tp) REVERT: D 257 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7859 (mmtp) REVERT: D 315 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8222 (mp) REVERT: F 51 LEU cc_start: 0.7588 (tp) cc_final: 0.7382 (tp) REVERT: F 315 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8383 (mp) outliers start: 15 outliers final: 11 residues processed: 213 average time/residue: 0.3378 time to fit residues: 108.4620 Evaluate side-chains 209 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 182 SER 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 D residue 315 ILE 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 Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 85 optimal weight: 0.0670 chunk 210 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.159920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110110 restraints weight = 24095.116| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.65 r_work: 0.3114 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1882 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= 0.130 Angle : 0.443 6.116 28686 Z= 0.230 Chirality : 0.040 0.167 3204 Planarity : 0.003 0.052 3702 Dihedral : 3.227 23.111 2874 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.73 % Allowed : 13.31 % Favored : 85.95 % 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: 0.72 (0.17), residues: 2538 helix: 1.25 (0.17), residues: 1074 sheet: 1.16 (0.25), residues: 468 loop : -0.66 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP C 238 HIS 0.004 0.000 HIS B 322 PHE 0.006 0.001 PHE D 181 TYR 0.009 0.001 TYR F 145 ARG 0.001 0.000 ARG A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3761.76 seconds wall clock time: 68 minutes 13.42 seconds (4093.42 seconds total)