Starting phenix.real_space_refine on Thu Feb 5 20:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uih_64194/02_2026/9uih_64194.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uih_64194/02_2026/9uih_64194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uih_64194/02_2026/9uih_64194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uih_64194/02_2026/9uih_64194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uih_64194/02_2026/9uih_64194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uih_64194/02_2026/9uih_64194.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.108 sd= 0.806 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 126 5.16 5 C 12561 2.51 5 N 3408 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19782 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3326 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "B" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3268 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3326 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "D" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3268 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Chain: "E" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3326 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "F" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3268 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Time building chain proxies: 4.55, per 1000 atoms: 0.23 Number of scatterers: 19782 At special positions: 0 Unit cell: (147.7, 160.36, 161.415, 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 126 16.00 O 3687 8.00 N 3408 7.00 C 12561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 25 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 226 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.02 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.04 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 25 " distance=2.03 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 266 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 226 " distance=2.03 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 901.5 milliseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4794 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 66 sheets defined 15.1% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.183A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 439 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.537A pdb=" N LEU B 8 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 363 through 398 removed outlier: 4.124A pdb=" N GLY B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.219A pdb=" N THR C 115 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.886A pdb=" N VAL C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 439 Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.585A pdb=" N LEU D 8 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 363 through 383 removed outlier: 4.372A pdb=" N GLY D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.279A pdb=" N THR E 115 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 256 through 259 Processing helix chain 'E' and resid 403 through 439 removed outlier: 3.724A pdb=" N MET E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.639A pdb=" N LEU F 8 " --> pdb=" O ASP F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 180 Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 363 through 383 removed outlier: 4.202A pdb=" N GLY F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 398 Processing helix chain 'F' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 148 removed outlier: 4.670A pdb=" N LEU A 129 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.890A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 61 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.783A pdb=" N VAL A 108 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP A 75 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 303 removed outlier: 6.716A pdb=" N LYS A 321 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 299 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN A 319 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N CYS A 301 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 352 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 306 through 307 removed outlier: 6.682A pdb=" N CYS A 306 " --> pdb=" O LYS A 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB4, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB5, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB6, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.620A pdb=" N LEU B 285 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE B 319 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 287 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG B 317 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA B 289 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR B 315 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG B 291 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY B 313 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.662A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 16.655A pdb=" N GLN B 46 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 13.477A pdb=" N TYR B 66 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N SER B 48 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N PHE B 64 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N GLN B 50 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N THR B 62 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B 52 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.662A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N ILE B 45 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N GLN B 104 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N VAL B 47 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N LEU B 102 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ALA B 49 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE B 100 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR B 53 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N HIS B 96 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AC2, first strand: chain 'B' and resid 148 through 155 removed outlier: 3.528A pdb=" N LEU B 150 " --> pdb=" O CYS B 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 237 through 238 removed outlier: 6.188A pdb=" N ILE B 257 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR B 165 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 255 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR B 167 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 253 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AC5, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AC6, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AC7, first strand: chain 'C' and resid 14 through 19 removed outlier: 3.660A pdb=" N SER C 35 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 129 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 14 through 19 Processing sheet with id=AC9, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.957A pdb=" N ALA C 121 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA C 119 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.529A pdb=" N GLN C 59 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD3, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AD5, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD7, first strand: chain 'C' and resid 345 through 354 removed outlier: 6.340A pdb=" N VAL C 346 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG C 324 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA C 348 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 352 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 318 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER C 315 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 321 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 298 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP C 323 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ILE C 296 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LYS C 381 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS C 306 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AD9, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AE1, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AE2, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AE3, first strand: chain 'D' and resid 31 through 35 removed outlier: 8.634A pdb=" N ILE D 31 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER D 48 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN D 33 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 16.600A pdb=" N GLN D 46 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 13.378A pdb=" N TYR D 66 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N SER D 48 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N PHE D 64 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N GLN D 50 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N THR D 62 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY D 52 " --> pdb=" O ASP D 60 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 31 through 35 removed outlier: 8.634A pdb=" N ILE D 31 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER D 48 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN D 33 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 11.294A pdb=" N ILE D 45 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N GLN D 104 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N VAL D 47 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N LEU D 102 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ALA D 49 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE D 100 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TYR D 53 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 11.906A pdb=" N HIS D 96 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.642A pdb=" N SER D 110 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS D 128 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR D 112 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL D 126 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER D 114 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS D 124 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AE7, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AE8, first strand: chain 'D' and resid 206 through 211 removed outlier: 3.572A pdb=" N GLY D 209 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 275 through 279 Processing sheet with id=AF1, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AF2, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AF3, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'E' and resid 140 through 148 removed outlier: 4.767A pdb=" N LEU E 129 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR E 46 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS E 123 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS E 44 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS E 125 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR E 42 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA E 127 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 129 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU E 38 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 131 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 36 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU E 133 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 34 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.526A pdb=" N GLN E 59 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.731A pdb=" N VAL E 108 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP E 75 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF8, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AF9, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AG1, first strand: chain 'E' and resid 296 through 302 removed outlier: 4.187A pdb=" N GLU E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 318 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE E 352 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 326 through 327 removed outlier: 3.974A pdb=" N GLY E 326 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 330 through 332 Processing sheet with id=AG4, first strand: chain 'E' and resid 387 through 388 removed outlier: 3.520A pdb=" N VAL F 336 " --> pdb=" O TYR F 328 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 387 through 388 removed outlier: 3.520A pdb=" N VAL F 336 " --> pdb=" O TYR F 328 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 285 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE F 319 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU F 287 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG F 317 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA F 289 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 315 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG F 291 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY F 313 " --> pdb=" O ARG F 291 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.260A pdb=" N HIS F 256 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL F 251 " --> pdb=" O HIS F 169 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS F 169 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY F 253 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR F 167 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU F 255 " --> pdb=" O TYR F 165 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR F 165 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE F 257 " --> pdb=" O ALA F 163 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AG8, first strand: chain 'F' and resid 31 through 35 removed outlier: 8.603A pdb=" N ILE F 31 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER F 48 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 33 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 16.781A pdb=" N GLN F 46 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N TYR F 66 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N SER F 48 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N PHE F 64 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 11.350A pdb=" N GLN F 50 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N THR F 62 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY F 52 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 31 through 35 removed outlier: 8.603A pdb=" N ILE F 31 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER F 48 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 33 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR F 99 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ALA F 49 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LYS F 97 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE F 51 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N GLY F 95 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 15.445A pdb=" N TYR F 53 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 17.788A pdb=" N ARG F 93 " --> pdb=" O TYR F 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 83 through 86 removed outlier: 5.586A pdb=" N LYS F 128 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR F 112 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL F 126 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER F 114 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N CYS F 124 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 148 through 155 Processing sheet with id=AH3, first strand: chain 'F' and resid 206 through 211 716 hydrogen bonds defined for protein. 1878 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: 4.08 Time building geometry restraints manager: 2.09 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: 6382 1.34 - 1.46: 4902 1.46 - 1.59: 8873 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 20307 Sorted by residual: bond pdb=" N SER F 193 " pdb=" CA SER F 193 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.03e+00 bond pdb=" C THR D 87 " pdb=" N SER D 88 " ideal model delta sigma weight residual 1.332 1.314 0.018 1.40e-02 5.10e+03 1.72e+00 bond pdb=" CB GLU C 298 " pdb=" CG GLU C 298 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CA THR C 347 " pdb=" CB THR C 347 " ideal model delta sigma weight residual 1.524 1.543 -0.018 1.46e-02 4.69e+03 1.56e+00 bond pdb=" CB ASN C 139 " pdb=" CG ASN C 139 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.44e+00 ... (remaining 20302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 27050 1.89 - 3.78: 543 3.78 - 5.66: 58 5.66 - 7.55: 17 7.55 - 9.44: 10 Bond angle restraints: 27678 Sorted by residual: angle pdb=" CA GLU F 182 " pdb=" CB GLU F 182 " pdb=" CG GLU F 182 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB GLU C 298 " pdb=" CG GLU C 298 " pdb=" CD GLU C 298 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CA CYS E 370 " pdb=" CB CYS E 370 " pdb=" SG CYS E 370 " ideal model delta sigma weight residual 114.40 122.22 -7.82 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA GLU D 354 " pdb=" CB GLU D 354 " pdb=" CG GLU D 354 " ideal model delta sigma weight residual 114.10 120.55 -6.45 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA GLU E 298 " pdb=" CB GLU E 298 " pdb=" CG GLU E 298 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.83e+00 ... (remaining 27673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10420 17.93 - 35.85: 1327 35.85 - 53.78: 378 53.78 - 71.70: 51 71.70 - 89.63: 13 Dihedral angle restraints: 12189 sinusoidal: 4722 harmonic: 7467 Sorted by residual: dihedral pdb=" CA CYS E 62 " pdb=" C CYS E 62 " pdb=" N CYS E 63 " pdb=" CA CYS E 63 " ideal model delta harmonic sigma weight residual 180.00 146.67 33.33 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -136.29 50.29 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CA CYS A 62 " pdb=" C CYS A 62 " pdb=" N CYS A 63 " pdb=" CA CYS A 63 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 12186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2198 0.040 - 0.080: 645 0.080 - 0.120: 262 0.120 - 0.160: 35 0.160 - 0.200: 4 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB ILE D 378 " pdb=" CA ILE D 378 " pdb=" CG1 ILE D 378 " pdb=" CG2 ILE D 378 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL C 427 " pdb=" CA VAL C 427 " pdb=" CG1 VAL C 427 " pdb=" CG2 VAL C 427 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA GLU D 354 " pdb=" N GLU D 354 " pdb=" C GLU D 354 " pdb=" CB GLU D 354 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 3141 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 381 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C GLY D 381 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY D 381 " -0.019 2.00e-02 2.50e+03 pdb=" N THR D 382 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 381 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C GLY B 381 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY B 381 " 0.018 2.00e-02 2.50e+03 pdb=" N THR B 382 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 276 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 277 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " -0.027 5.00e-02 4.00e+02 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 9027 2.96 - 3.45: 18161 3.45 - 3.93: 32118 3.93 - 4.42: 36715 4.42 - 4.90: 62235 Nonbonded interactions: 158256 Sorted by model distance: nonbonded pdb=" O TRP D 351 " pdb=" OE1 GLU D 354 " model vdw 2.476 3.040 nonbonded pdb=" N GLU E 99 " pdb=" OE1 GLU E 99 " model vdw 2.486 3.120 nonbonded pdb=" O ASP C 284 " pdb=" OD1 ASP C 284 " model vdw 2.513 3.040 nonbonded pdb=" O ASN C 28 " pdb=" OD1 ASN C 28 " model vdw 2.529 3.040 nonbonded pdb=" N GLU C 298 " pdb=" OE1 GLU C 298 " model vdw 2.550 3.120 ... (remaining 158251 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' 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: 1.240 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.240 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 : 0.003 0.038 20346 Z= 0.161 Angle : 0.670 9.442 27756 Z= 0.351 Chirality : 0.045 0.200 3144 Planarity : 0.005 0.049 3528 Dihedral : 16.855 89.627 7278 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.93 % Allowed : 26.32 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2559 helix: 0.72 (0.29), residues: 297 sheet: -0.20 (0.17), residues: 897 loop : -0.94 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 303 TYR 0.016 0.001 TYR B 165 PHE 0.023 0.002 PHE C 312 TRP 0.011 0.001 TRP B 35 HIS 0.011 0.001 HIS F 353 Details of bonding type rmsd covalent geometry : bond 0.00348 (20307) covalent geometry : angle 0.66647 (27678) SS BOND : bond 0.00319 ( 39) SS BOND : angle 1.48318 ( 78) hydrogen bonds : bond 0.17813 ( 670) hydrogen bonds : angle 7.49136 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.8878 (ptpp) REVERT: A 399 GLN cc_start: 0.8730 (pm20) cc_final: 0.8435 (pm20) REVERT: B 222 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8689 (mptt) REVERT: C 242 MET cc_start: 0.8945 (mmm) cc_final: 0.8147 (mmm) REVERT: C 319 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8416 (tp-100) REVERT: C 433 MET cc_start: 0.8075 (tmm) cc_final: 0.7818 (tmm) REVERT: D 67 MET cc_start: 0.9435 (mmt) cc_final: 0.8765 (tpt) REVERT: D 72 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7740 (t0) REVERT: D 80 MET cc_start: 0.9495 (tpt) cc_final: 0.9278 (mmm) REVERT: D 391 LYS cc_start: 0.8619 (tppp) cc_final: 0.8235 (tptp) REVERT: E 420 LEU cc_start: 0.9095 (mt) cc_final: 0.8796 (mt) outliers start: 64 outliers final: 42 residues processed: 268 average time/residue: 0.1739 time to fit residues: 68.2052 Evaluate side-chains 235 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 417 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 143 HIS A 345 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN B 174 HIS B 196 ASN B 249 HIS B 252 GLN B 318 ASN B 332 ASN C 28 ASN C 43 ASN C 59 GLN C 228 ASN C 396 GLN C 436 ASN D 174 HIS D 196 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS D 249 HIS D 318 ASN D 332 ASN D 353 HIS D 361 HIS E 43 ASN E 59 GLN E 118 HIS E 143 HIS E 436 ASN F 169 HIS F 174 HIS F 196 ASN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS F 318 ASN F 353 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.050742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.040465 restraints weight = 61997.672| |-----------------------------------------------------------------------------| r_work (start): 0.2466 rms_B_bonded: 2.02 r_work: 0.2386 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2295 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 20346 Z= 0.394 Angle : 0.789 10.387 27756 Z= 0.407 Chirality : 0.051 0.193 3144 Planarity : 0.006 0.053 3528 Dihedral : 7.530 64.360 2850 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.88 % Allowed : 23.25 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2559 helix: 0.18 (0.28), residues: 315 sheet: -0.06 (0.18), residues: 858 loop : -1.20 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.032 0.003 TYR A 308 PHE 0.026 0.003 PHE B 142 TRP 0.012 0.002 TRP C 89 HIS 0.010 0.002 HIS F 353 Details of bonding type rmsd covalent geometry : bond 0.00945 (20307) covalent geometry : angle 0.78434 (27678) SS BOND : bond 0.00709 ( 39) SS BOND : angle 1.87235 ( 78) hydrogen bonds : bond 0.04920 ( 670) hydrogen bonds : angle 5.76908 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 196 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8870 (p0) cc_final: 0.8666 (p0) REVERT: A 297 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 325 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 372 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8708 (tppp) REVERT: A 399 GLN cc_start: 0.8976 (pm20) cc_final: 0.8600 (pm20) REVERT: B 394 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8263 (ttp80) REVERT: C 101 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8949 (t) REVERT: C 288 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8918 (m) REVERT: C 289 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8396 (mmm160) REVERT: C 319 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8377 (tp-100) REVERT: C 396 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9164 (tt0) REVERT: C 404 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8752 (mtmm) REVERT: C 433 MET cc_start: 0.7995 (tmm) cc_final: 0.7755 (tmm) REVERT: D 67 MET cc_start: 0.9374 (mmt) cc_final: 0.8785 (tpt) REVERT: D 72 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8418 (t0) REVERT: D 80 MET cc_start: 0.9541 (tpt) cc_final: 0.9297 (mmm) REVERT: D 385 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8217 (m) REVERT: E 166 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8920 (tp) REVERT: E 374 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8895 (p) REVERT: F 78 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.9205 (t0) REVERT: F 216 LYS cc_start: 0.9361 (tttm) cc_final: 0.9145 (tttm) REVERT: F 360 TYR cc_start: 0.9160 (t80) cc_final: 0.8680 (t80) outliers start: 150 outliers final: 91 residues processed: 322 average time/residue: 0.1543 time to fit residues: 73.9444 Evaluate side-chains 290 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 188 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 396 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS F 214 GLN F 225 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.053847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.043376 restraints weight = 61784.830| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 2.05 r_work: 0.2479 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20346 Z= 0.118 Angle : 0.584 8.499 27756 Z= 0.299 Chirality : 0.044 0.149 3144 Planarity : 0.004 0.044 3528 Dihedral : 6.604 60.619 2831 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.68 % Allowed : 25.54 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2559 helix: 0.56 (0.28), residues: 315 sheet: 0.09 (0.18), residues: 879 loop : -1.04 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 303 TYR 0.018 0.001 TYR D 328 PHE 0.016 0.001 PHE B 142 TRP 0.010 0.001 TRP A 89 HIS 0.006 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00271 (20307) covalent geometry : angle 0.58242 (27678) SS BOND : bond 0.00306 ( 39) SS BOND : angle 1.07913 ( 78) hydrogen bonds : bond 0.03659 ( 670) hydrogen bonds : angle 5.28737 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 199 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8822 (p0) cc_final: 0.8614 (p0) REVERT: A 381 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.8893 (ptpp) REVERT: A 399 GLN cc_start: 0.8954 (pm20) cc_final: 0.8567 (pm20) REVERT: B 394 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8317 (ttp80) REVERT: C 288 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9021 (m) REVERT: C 289 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8379 (mmm160) REVERT: C 362 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8288 (mm-40) REVERT: C 404 LYS cc_start: 0.8879 (mtmm) cc_final: 0.8628 (mtmm) REVERT: D 67 MET cc_start: 0.9346 (mmt) cc_final: 0.8782 (tpt) REVERT: D 72 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8247 (t0) REVERT: D 217 MET cc_start: 0.8545 (mmm) cc_final: 0.8118 (mmm) REVERT: D 278 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8434 (mtmm) REVERT: F 354 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8166 (mm-30) outliers start: 102 outliers final: 63 residues processed: 285 average time/residue: 0.1600 time to fit residues: 67.4582 Evaluate side-chains 257 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 GLN Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 204 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 203 optimal weight: 0.0770 chunk 98 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 396 GLN D 96 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS F 214 GLN F 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.052863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.042519 restraints weight = 62204.241| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 2.04 r_work: 0.2453 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20346 Z= 0.183 Angle : 0.622 14.473 27756 Z= 0.317 Chirality : 0.045 0.304 3144 Planarity : 0.004 0.040 3528 Dihedral : 6.486 59.483 2825 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.27 % Allowed : 24.90 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2559 helix: 0.69 (0.28), residues: 315 sheet: 0.14 (0.18), residues: 879 loop : -1.02 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 303 TYR 0.022 0.002 TYR A 308 PHE 0.015 0.002 PHE E 170 TRP 0.009 0.001 TRP E 89 HIS 0.006 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00436 (20307) covalent geometry : angle 0.61862 (27678) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.42655 ( 78) hydrogen bonds : bond 0.03715 ( 670) hydrogen bonds : angle 5.16397 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8836 (p0) cc_final: 0.8633 (p0) REVERT: A 339 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8947 (mp) REVERT: A 381 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8903 (ptpp) REVERT: B 394 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8336 (ttp80) REVERT: C 101 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8889 (t) REVERT: C 288 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9066 (m) REVERT: D 67 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8826 (tpt) REVERT: D 72 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8331 (t0) REVERT: D 216 LYS cc_start: 0.8957 (tptt) cc_final: 0.8629 (tppt) REVERT: D 278 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8445 (mtmm) REVERT: E 325 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7466 (mm-30) REVERT: E 393 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8560 (mttm) REVERT: F 214 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: F 347 ASP cc_start: 0.9026 (t0) cc_final: 0.8773 (t0) outliers start: 115 outliers final: 81 residues processed: 289 average time/residue: 0.1541 time to fit residues: 66.0567 Evaluate side-chains 273 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 183 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 GLN Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 133 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 239 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 28 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 214 GLN F 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.051367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.041191 restraints weight = 61965.997| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 2.01 r_work: 0.2414 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2324 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 20346 Z= 0.272 Angle : 0.685 9.454 27756 Z= 0.351 Chirality : 0.047 0.274 3144 Planarity : 0.005 0.045 3528 Dihedral : 6.706 60.554 2824 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.24 % Allowed : 24.12 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2559 helix: 0.63 (0.28), residues: 315 sheet: 0.16 (0.18), residues: 849 loop : -1.14 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 303 TYR 0.027 0.002 TYR A 308 PHE 0.019 0.002 PHE E 170 TRP 0.009 0.002 TRP C 89 HIS 0.016 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00654 (20307) covalent geometry : angle 0.68131 (27678) SS BOND : bond 0.00605 ( 39) SS BOND : angle 1.57325 ( 78) hydrogen bonds : bond 0.04019 ( 670) hydrogen bonds : angle 5.27874 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 194 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8837 (p0) cc_final: 0.8628 (p0) REVERT: A 339 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 362 GLN cc_start: 0.8547 (mt0) cc_final: 0.7605 (mm-40) REVERT: B 218 ASN cc_start: 0.8194 (m-40) cc_final: 0.7970 (m110) REVERT: B 394 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8320 (ttp80) REVERT: C 101 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.8883 (t) REVERT: D 67 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.8828 (tpt) REVERT: D 278 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8478 (mtmm) REVERT: E 166 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8865 (tp) REVERT: E 393 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: F 287 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9144 (mt) outliers start: 136 outliers final: 101 residues processed: 304 average time/residue: 0.1584 time to fit residues: 71.1447 Evaluate side-chains 289 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 181 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 GLN F 218 ASN F 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.051686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.041551 restraints weight = 61772.711| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 1.99 r_work: 0.2426 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2336 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20346 Z= 0.215 Angle : 0.649 8.752 27756 Z= 0.331 Chirality : 0.045 0.215 3144 Planarity : 0.005 0.044 3528 Dihedral : 6.349 60.034 2817 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.01 % Allowed : 24.90 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2559 helix: 0.71 (0.28), residues: 315 sheet: 0.17 (0.18), residues: 873 loop : -1.12 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 303 TYR 0.023 0.002 TYR A 308 PHE 0.020 0.002 PHE B 142 TRP 0.012 0.002 TRP F 35 HIS 0.014 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00515 (20307) covalent geometry : angle 0.64594 (27678) SS BOND : bond 0.00506 ( 39) SS BOND : angle 1.36164 ( 78) hydrogen bonds : bond 0.03770 ( 670) hydrogen bonds : angle 5.19340 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 190 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8854 (p0) cc_final: 0.8652 (p0) REVERT: A 297 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 339 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8957 (mp) REVERT: A 362 GLN cc_start: 0.8400 (mt0) cc_final: 0.7748 (mm-40) REVERT: B 69 TYR cc_start: 0.9165 (m-80) cc_final: 0.8819 (m-80) REVERT: C 101 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8897 (t) REVERT: C 289 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8099 (mmm160) REVERT: C 292 GLU cc_start: 0.8996 (tp30) cc_final: 0.8747 (tp30) REVERT: C 324 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7764 (tmm160) REVERT: D 67 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8817 (tpt) REVERT: D 216 LYS cc_start: 0.9032 (tptt) cc_final: 0.8813 (tptt) REVERT: D 278 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8499 (mtmm) REVERT: E 166 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8846 (tp) REVERT: E 393 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8567 (mttm) REVERT: F 287 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9132 (mt) outliers start: 131 outliers final: 98 residues processed: 296 average time/residue: 0.1690 time to fit residues: 73.5931 Evaluate side-chains 294 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 188 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 218 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 143 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 GLN F 33 ASN F 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.051173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.041127 restraints weight = 62097.274| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 1.99 r_work: 0.2415 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2325 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20346 Z= 0.241 Angle : 0.674 9.618 27756 Z= 0.343 Chirality : 0.046 0.207 3144 Planarity : 0.005 0.055 3528 Dihedral : 6.392 59.728 2817 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.64 % Allowed : 25.49 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2559 helix: 0.67 (0.28), residues: 315 sheet: 0.12 (0.18), residues: 879 loop : -1.14 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 303 TYR 0.023 0.002 TYR A 308 PHE 0.021 0.002 PHE C 1 TRP 0.010 0.002 TRP C 89 HIS 0.011 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00577 (20307) covalent geometry : angle 0.67111 (27678) SS BOND : bond 0.00530 ( 39) SS BOND : angle 1.42336 ( 78) hydrogen bonds : bond 0.03844 ( 670) hydrogen bonds : angle 5.19975 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 192 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 339 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8960 (mp) REVERT: A 404 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7804 (mtmm) REVERT: B 69 TYR cc_start: 0.9129 (m-80) cc_final: 0.8858 (m-80) REVERT: C 101 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8903 (t) REVERT: C 289 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7944 (mmm160) REVERT: C 292 GLU cc_start: 0.9001 (tp30) cc_final: 0.8703 (tp30) REVERT: C 324 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7697 (tmm160) REVERT: D 67 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.8840 (tpt) REVERT: D 278 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8492 (mtmm) REVERT: E 393 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8617 (mttm) REVERT: F 216 LYS cc_start: 0.9237 (tttm) cc_final: 0.8964 (tmtt) REVERT: F 287 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9141 (mt) outliers start: 123 outliers final: 102 residues processed: 295 average time/residue: 0.1682 time to fit residues: 72.8641 Evaluate side-chains 289 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 180 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 59 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 247 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN C 28 ASN ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.042928 restraints weight = 61470.530| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 1.96 r_work: 0.2470 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20346 Z= 0.128 Angle : 0.605 10.630 27756 Z= 0.307 Chirality : 0.044 0.163 3144 Planarity : 0.004 0.040 3528 Dihedral : 6.013 57.275 2816 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.95 % Allowed : 26.32 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2559 helix: 0.98 (0.29), residues: 306 sheet: 0.24 (0.18), residues: 873 loop : -1.00 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 303 TYR 0.017 0.001 TYR A 308 PHE 0.022 0.001 PHE C 1 TRP 0.011 0.001 TRP E 89 HIS 0.009 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00303 (20307) covalent geometry : angle 0.60258 (27678) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.11968 ( 78) hydrogen bonds : bond 0.03384 ( 670) hydrogen bonds : angle 4.99178 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 186 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 339 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 362 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: A 372 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8504 (tppp) REVERT: A 404 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8235 (mptt) REVERT: B 69 TYR cc_start: 0.9038 (m-80) cc_final: 0.8751 (m-80) REVERT: C 101 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8868 (t) REVERT: C 292 GLU cc_start: 0.8953 (tp30) cc_final: 0.8691 (tm-30) REVERT: C 319 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8575 (tp40) REVERT: C 324 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7724 (tmm160) REVERT: D 67 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8797 (tpt) REVERT: D 278 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8438 (mtmm) REVERT: D 391 LYS cc_start: 0.8561 (tppp) cc_final: 0.8355 (tppt) REVERT: E 122 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8978 (mt) REVERT: E 393 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8528 (mttm) REVERT: F 216 LYS cc_start: 0.9196 (tttm) cc_final: 0.8939 (tmtt) REVERT: F 287 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9071 (mt) outliers start: 108 outliers final: 79 residues processed: 272 average time/residue: 0.1688 time to fit residues: 67.7249 Evaluate side-chains 273 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 184 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.052521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.042462 restraints weight = 61566.082| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 1.99 r_work: 0.2457 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2367 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20346 Z= 0.156 Angle : 0.617 11.501 27756 Z= 0.312 Chirality : 0.044 0.166 3144 Planarity : 0.004 0.040 3528 Dihedral : 6.006 56.303 2816 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.49 % Allowed : 26.78 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2559 helix: 0.96 (0.29), residues: 309 sheet: 0.25 (0.18), residues: 873 loop : -0.96 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 303 TYR 0.017 0.001 TYR A 308 PHE 0.032 0.002 PHE C 1 TRP 0.009 0.001 TRP E 89 HIS 0.008 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00375 (20307) covalent geometry : angle 0.61488 (27678) SS BOND : bond 0.00381 ( 39) SS BOND : angle 1.17506 ( 78) hydrogen bonds : bond 0.03504 ( 670) hydrogen bonds : angle 4.95848 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 187 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 339 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8927 (mp) REVERT: A 372 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8554 (tppp) REVERT: B 69 TYR cc_start: 0.9040 (m-80) cc_final: 0.8778 (m-80) REVERT: C 101 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8884 (t) REVERT: C 292 GLU cc_start: 0.8994 (tp30) cc_final: 0.8701 (tm-30) REVERT: C 298 GLU cc_start: 0.8442 (pm20) cc_final: 0.8066 (pm20) REVERT: C 319 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8596 (tp40) REVERT: C 324 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7752 (tmm160) REVERT: C 325 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: D 67 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8834 (tpt) REVERT: D 278 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8427 (mtmm) REVERT: E 122 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8979 (mt) REVERT: E 393 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8558 (mttm) REVERT: F 216 LYS cc_start: 0.9203 (tttm) cc_final: 0.8933 (tmtt) REVERT: F 287 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9106 (mt) REVERT: F 303 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8952 (mtm-85) outliers start: 98 outliers final: 82 residues processed: 267 average time/residue: 0.1695 time to fit residues: 66.8372 Evaluate side-chains 273 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 181 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 236 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 251 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.051846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.041842 restraints weight = 62031.136| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 1.99 r_work: 0.2438 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20346 Z= 0.200 Angle : 0.654 12.777 27756 Z= 0.330 Chirality : 0.045 0.179 3144 Planarity : 0.005 0.058 3528 Dihedral : 6.117 56.432 2816 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.45 % Allowed : 26.91 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2559 helix: 0.96 (0.29), residues: 309 sheet: 0.20 (0.18), residues: 879 loop : -1.01 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 393 TYR 0.020 0.002 TYR A 308 PHE 0.036 0.002 PHE C 1 TRP 0.009 0.001 TRP E 89 HIS 0.008 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00482 (20307) covalent geometry : angle 0.65090 (27678) SS BOND : bond 0.00448 ( 39) SS BOND : angle 1.27752 ( 78) hydrogen bonds : bond 0.03659 ( 670) hydrogen bonds : angle 5.00275 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 186 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 339 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 69 TYR cc_start: 0.9057 (m-80) cc_final: 0.8817 (m-80) REVERT: B 80 MET cc_start: 0.9154 (mmm) cc_final: 0.8855 (mmm) REVERT: C 101 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8894 (t) REVERT: C 292 GLU cc_start: 0.9014 (tp30) cc_final: 0.8695 (tm-30) REVERT: C 319 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8597 (tp40) REVERT: C 324 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7729 (tmm160) REVERT: C 325 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: D 67 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8799 (tpt) REVERT: D 278 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: E 122 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8943 (mt) REVERT: E 393 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: F 287 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9134 (mt) outliers start: 97 outliers final: 82 residues processed: 265 average time/residue: 0.1758 time to fit residues: 68.3869 Evaluate side-chains 269 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 405 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 116 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN F 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.043749 restraints weight = 61663.292| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 2.01 r_work: 0.2497 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20346 Z= 0.115 Angle : 0.603 12.658 27756 Z= 0.303 Chirality : 0.044 0.151 3144 Planarity : 0.004 0.051 3528 Dihedral : 5.800 56.295 2816 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.90 % Allowed : 27.46 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2559 helix: 1.11 (0.29), residues: 306 sheet: 0.27 (0.18), residues: 876 loop : -0.91 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 394 TYR 0.016 0.001 TYR A 308 PHE 0.027 0.001 PHE C 1 TRP 0.012 0.001 TRP E 89 HIS 0.007 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00272 (20307) covalent geometry : angle 0.60088 (27678) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.09842 ( 78) hydrogen bonds : bond 0.03235 ( 670) hydrogen bonds : angle 4.82996 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5397.19 seconds wall clock time: 93 minutes 12.40 seconds (5592.40 seconds total)