Starting phenix.real_space_refine on Fri Jul 3 06:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9a_62899/07_2026/9l9a_62899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9a_62899/07_2026/9l9a_62899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2026/9l9a_62899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2026/9l9a_62899.map" model { file = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2026/9l9a_62899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2026/9l9a_62899.cif" } resolution = 3.9 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 83 5.16 5 C 8037 2.51 5 N 2190 2.21 5 O 2411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12723 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3122 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 27, 'TRANS': 383} Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 25, 'TRANS': 343} Chain: "G" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3122 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 27, 'TRANS': 383} Chain: "H" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 25, 'TRANS': 343} Chain: "M" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 619 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 3.09, per 1000 atoms: 0.24 Number of scatterers: 12723 At special positions: 0 Unit cell: (154.1, 144.72, 140.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 83 16.00 O 2411 8.00 N 2190 7.00 C 8037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.04 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.02 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.63 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 72 " - pdb=" SG CYS M 84 " distance=2.03 Simple disulfide: pdb=" SG CYS M 79 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 108 " distance=2.03 Simple disulfide: pdb=" SG CYS M 113 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 120 " - pdb=" SG CYS M 140 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 149 " 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: 0.96 Conformation dependent library (CDL) restraints added in 592.0 milliseconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3058 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 40 sheets defined 6.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.686A pdb=" N ASN A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.139A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.928A pdb=" N ILE B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.009A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.516A pdb=" N ALA G 286 " --> pdb=" O PRO G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 410 Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 354 through 362 removed outlier: 4.162A pdb=" N HIS H 358 " --> pdb=" O GLU H 354 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG H 362 " --> pdb=" O HIS H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 370 removed outlier: 3.796A pdb=" N ILE H 369 " --> pdb=" O VAL H 365 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL H 370 " --> pdb=" O TYR H 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 365 through 370' Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.734A pdb=" N ILE A 280 " --> pdb=" O HIS A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 19 removed outlier: 5.830A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 144 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 5.661A pdb=" N THR A 42 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS A 125 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS A 123 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 removed outlier: 4.013A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 303 removed outlier: 5.694A pdb=" N GLU A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS A 321 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 352 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 338 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 332 removed outlier: 4.089A pdb=" N PHE A 365 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS A 376 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB3, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.883A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 11.071A pdb=" N ILE B 45 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N GLN B 104 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N VAL B 47 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N LEU B 102 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N ALA B 49 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 100 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.729A pdb=" N PHE B 64 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 78 " --> pdb=" O PHE B 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.858A pdb=" N ILE B 130 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 110 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LYS B 128 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 112 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER B 114 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS B 124 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 148 through 155 Processing sheet with id=AB7, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AB8, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'B' and resid 201 through 202 removed outlier: 3.528A pdb=" N SER B 207 " --> pdb=" O CYS B 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 275 through 279 removed outlier: 4.007A pdb=" N THR B 275 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 279 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 307 through 311 removed outlier: 3.610A pdb=" N GLU B 309 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 295 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 8 removed outlier: 4.445A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.703A pdb=" N VAL G 19 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU G 30 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL G 136 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER G 36 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS G 130 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 46 through 48 removed outlier: 4.288A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL G 178 " --> pdb=" O TYR G 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.783A pdb=" N GLU G 109 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR G 101 " --> pdb=" O LYS G 61 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.783A pdb=" N GLU G 109 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AC9, first strand: chain 'G' and resid 296 through 302 removed outlier: 4.976A pdb=" N GLU G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS G 321 " --> pdb=" O GLU G 298 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN G 319 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR G 302 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 306 through 307 removed outlier: 7.187A pdb=" N CYS G 306 " --> pdb=" O LYS G 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.778A pdb=" N THR G 344 " --> pdb=" O CYS G 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS G 331 " --> pdb=" O SER G 368 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G 367 " --> pdb=" O THR G 374 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 374 " --> pdb=" O VAL G 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.706A pdb=" N VAL H 336 " --> pdb=" O TYR H 328 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 31 through 35 removed outlier: 7.161A pdb=" N GLN H 46 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL H 34 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG H 44 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ILE H 45 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N GLN H 104 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N VAL H 47 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N LEU H 102 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ALA H 49 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE H 100 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 63 through 67 removed outlier: 3.687A pdb=" N PHE H 64 " --> pdb=" O ASP H 78 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP H 78 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H 66 " --> pdb=" O LYS H 76 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 90 through 91 removed outlier: 4.518A pdb=" N ILE H 85 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 113 " --> pdb=" O CYS H 124 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 148 through 155 removed outlier: 3.607A pdb=" N LYS H 148 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 262 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 237 through 238 removed outlier: 3.596A pdb=" N LEU H 255 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 180 through 181 removed outlier: 3.752A pdb=" N ILE H 189 " --> pdb=" O THR H 215 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 207 through 211 removed outlier: 3.718A pdb=" N GLU H 200 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE H 227 " --> pdb=" O GLU H 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 275 through 279 removed outlier: 3.899A pdb=" N TRP H 279 " --> pdb=" O GLY H 282 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AE4, first strand: chain 'M' and resid 117 through 120 removed outlier: 3.689A pdb=" N GLN M 126 " --> pdb=" O CYS M 120 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 648 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: 1.89 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4139 1.35 - 1.47: 3317 1.47 - 1.59: 5513 1.59 - 1.72: 1 1.72 - 1.84: 98 Bond restraints: 13068 Sorted by residual: bond pdb=" CB PRO B 348 " pdb=" CG PRO B 348 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.04e+00 bond pdb=" CG PRO B 348 " pdb=" CD PRO B 348 " ideal model delta sigma weight residual 1.503 1.451 0.052 3.40e-02 8.65e+02 2.31e+00 bond pdb=" CB ASN A 139 " pdb=" CG ASN A 139 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.15e+00 bond pdb=" CA LYS H 202 " pdb=" CB LYS H 202 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.37e+00 bond pdb=" CA GLN A 362 " pdb=" CB GLN A 362 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.74e-02 3.30e+03 1.25e+00 ... (remaining 13063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 17439 1.86 - 3.72: 310 3.72 - 5.59: 33 5.59 - 7.45: 12 7.45 - 9.31: 5 Bond angle restraints: 17799 Sorted by residual: angle pdb=" CA PRO B 348 " pdb=" N PRO B 348 " pdb=" CD PRO B 348 " ideal model delta sigma weight residual 112.00 103.25 8.75 1.40e+00 5.10e-01 3.90e+01 angle pdb=" N PRO B 348 " pdb=" CD PRO B 348 " pdb=" CG PRO B 348 " ideal model delta sigma weight residual 103.20 96.77 6.43 1.50e+00 4.44e-01 1.83e+01 angle pdb=" CA LYS H 202 " pdb=" CB LYS H 202 " pdb=" CG LYS H 202 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.59e+01 angle pdb=" N CYS H 201 " pdb=" CA CYS H 201 " pdb=" C CYS H 201 " ideal model delta sigma weight residual 109.07 114.33 -5.26 1.52e+00 4.33e-01 1.20e+01 angle pdb=" CA GLN A 399 " pdb=" CB GLN A 399 " pdb=" CG GLN A 399 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 17794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6830 17.98 - 35.96: 815 35.96 - 53.94: 184 53.94 - 71.92: 26 71.92 - 89.91: 17 Dihedral angle restraints: 7872 sinusoidal: 3109 harmonic: 4763 Sorted by residual: dihedral pdb=" CB CYS H 203 " pdb=" SG CYS H 203 " pdb=" SG CYS H 220 " pdb=" CB CYS H 220 " ideal model delta sinusoidal sigma weight residual -86.00 -174.80 88.80 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual 93.00 179.05 -86.05 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS M 79 " pdb=" SG CYS M 79 " pdb=" SG CYS M 97 " pdb=" CB CYS M 97 " ideal model delta sinusoidal sigma weight residual -86.00 -167.75 81.75 1 1.00e+01 1.00e-02 8.22e+01 ... (remaining 7869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1348 0.038 - 0.076: 401 0.076 - 0.114: 190 0.114 - 0.152: 32 0.152 - 0.190: 3 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CA ASN A 139 " pdb=" N ASN A 139 " pdb=" C ASN A 139 " pdb=" CB ASN A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB ILE H 29 " pdb=" CA ILE H 29 " pdb=" CG1 ILE H 29 " pdb=" CG2 ILE H 29 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA CYS A 63 " pdb=" N CYS A 63 " pdb=" C CYS A 63 " pdb=" CB CYS A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 1971 not shown) Planarity restraints: 2294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 328 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO A 329 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 347 " -0.035 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 348 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 348 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 348 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 126 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C THR A 126 " 0.031 2.00e-02 2.50e+03 pdb=" O THR A 126 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 127 " -0.010 2.00e-02 2.50e+03 ... (remaining 2291 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 1 1.96 - 2.70: 411 2.70 - 3.43: 16889 3.43 - 4.17: 27140 4.17 - 4.90: 47874 Nonbonded interactions: 92315 Sorted by model distance: nonbonded pdb=" O GLY G 138 " pdb=" OD1 ASN G 139 " model vdw 1.228 3.040 nonbonded pdb=" N GLN H 214 " pdb=" OE1 GLN H 214 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR G 76 " pdb=" OE1 GLU G 105 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP G 113 " pdb=" OH TYR H 155 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASN B 54 " pdb=" N GLN B 55 " model vdw 2.191 3.120 ... (remaining 92310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } 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 group one per residue 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: 0.740 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 0.006 0.601 13102 Z= 0.292 Angle : 0.621 9.310 17867 Z= 0.330 Chirality : 0.045 0.190 1974 Planarity : 0.004 0.067 2294 Dihedral : 15.619 89.905 4712 Min Nonbonded Distance : 1.228 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.07 % Allowed : 26.72 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1632 helix: -0.24 (0.66), residues: 62 sheet: -1.19 (0.23), residues: 532 loop : -1.42 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.012 0.001 TYR A 308 PHE 0.010 0.001 PHE B 142 TRP 0.010 0.001 TRP G 407 HIS 0.003 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13068) covalent geometry : angle 0.61092 / 0.33 (17799) SS BOND : bond 0.10307 / 7.36 ( 34) SS BOND : angle 1.93408 / 1.50 ( 68) hydrogen bonds : bond 0.28317 / 19.69 ( 269) hydrogen bonds : angle 10.05124 / 7.10 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8958 (p0) cc_final: 0.8701 (p0) REVERT: A 195 MET cc_start: 0.8477 (mpp) cc_final: 0.8244 (mpp) REVERT: B 217 MET cc_start: 0.6879 (mmp) cc_final: 0.6486 (mmm) REVERT: H 217 MET cc_start: 0.6490 (mmp) cc_final: 0.5840 (mmm) REVERT: M 110 MET cc_start: 0.2849 (ttt) cc_final: 0.1993 (mtp) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1150 time to fit residues: 27.9110 Evaluate side-chains 150 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 143 HIS A 333 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 246 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN G 43 ASN G 125 HIS G 275 HIS G 345 HIS G 396 GLN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 HIS H 225 GLN H 246 HIS ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS M 83 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110882 restraints weight = 19670.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.108065 restraints weight = 21498.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109844 restraints weight = 24057.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.110097 restraints weight = 14356.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110614 restraints weight = 13270.712| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13102 Z= 0.210 Angle : 0.645 7.360 17867 Z= 0.337 Chirality : 0.047 0.184 1974 Planarity : 0.005 0.057 2294 Dihedral : 4.884 20.731 1771 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.46 % Allowed : 24.10 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.20), residues: 1632 helix: -0.88 (0.58), residues: 74 sheet: -1.28 (0.22), residues: 548 loop : -1.42 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 317 TYR 0.014 0.002 TYR A 308 PHE 0.012 0.001 PHE H 134 TRP 0.007 0.001 TRP G 407 HIS 0.005 0.001 HIS G 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (13068) covalent geometry : angle 0.63775 / 0.33 (17799) SS BOND : bond 0.00444 / 0.30 ( 34) SS BOND : angle 1.71379 / 1.28 ( 68) hydrogen bonds : bond 0.04847 / 3.37 ( 269) hydrogen bonds : angle 7.32658 / 5.12 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 166 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 324 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.8119 (ptm-80) REVERT: B 146 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: B 188 TYR cc_start: 0.8480 (m-10) cc_final: 0.8247 (m-10) REVERT: B 217 MET cc_start: 0.6814 (mmp) cc_final: 0.6226 (mmm) REVERT: H 36 ASP cc_start: 0.7861 (t0) cc_final: 0.7660 (t0) REVERT: M 110 MET cc_start: 0.2320 (ttt) cc_final: 0.1735 (ptm) outliers start: 77 outliers final: 48 residues processed: 225 average time/residue: 0.1000 time to fit residues: 33.8443 Evaluate side-chains 204 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 253 GLU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.0010 chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN H 174 HIS ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121589 restraints weight = 19267.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118578 restraints weight = 22569.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120653 restraints weight = 22293.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121022 restraints weight = 13239.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121337 restraints weight = 12402.481| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13102 Z= 0.107 Angle : 0.567 7.211 17867 Z= 0.294 Chirality : 0.045 0.187 1974 Planarity : 0.004 0.049 2294 Dihedral : 4.548 19.582 1771 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.10 % Allowed : 23.81 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.20), residues: 1632 helix: -0.02 (0.64), residues: 62 sheet: -1.14 (0.22), residues: 548 loop : -1.31 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 157 TYR 0.014 0.001 TYR H 165 PHE 0.010 0.001 PHE B 142 TRP 0.008 0.001 TRP G 243 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13068) covalent geometry : angle 0.56217 / 0.29 (17799) SS BOND : bond 0.00353 / 0.22 ( 34) SS BOND : angle 1.34636 / 1.05 ( 68) hydrogen bonds : bond 0.03811 / 2.69 ( 269) hydrogen bonds : angle 6.60274 / 4.61 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8483 (p0) cc_final: 0.8106 (p0) REVERT: A 324 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.7935 (ptm-80) REVERT: B 6 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7181 (t80) REVERT: B 18 TYR cc_start: 0.5673 (m-80) cc_final: 0.4889 (m-80) REVERT: B 146 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: B 217 MET cc_start: 0.6731 (mmp) cc_final: 0.6384 (mmm) REVERT: B 303 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8282 (mtm110) REVERT: B 327 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: H 36 ASP cc_start: 0.7685 (t0) cc_final: 0.7445 (t0) REVERT: M 110 MET cc_start: 0.3279 (ttt) cc_final: 0.2356 (ptm) outliers start: 72 outliers final: 50 residues processed: 221 average time/residue: 0.0955 time to fit residues: 31.1586 Evaluate side-chains 208 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 253 GLU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 125 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 0.0770 chunk 103 optimal weight: 0.0870 chunk 29 optimal weight: 0.0970 chunk 19 optimal weight: 0.0000 chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 HIS G 52 HIS H 174 HIS H 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118095 restraints weight = 19686.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116200 restraints weight = 20565.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117494 restraints weight = 23590.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117890 restraints weight = 14731.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.118363 restraints weight = 13459.968| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13102 Z= 0.092 Angle : 0.538 7.807 17867 Z= 0.277 Chirality : 0.044 0.198 1974 Planarity : 0.004 0.045 2294 Dihedral : 4.229 18.491 1771 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.95 % Allowed : 23.53 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.21), residues: 1632 helix: 0.31 (0.66), residues: 66 sheet: -1.09 (0.22), residues: 552 loop : -1.21 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 157 TYR 0.026 0.001 TYR G 46 PHE 0.012 0.001 PHE B 51 TRP 0.008 0.001 TRP G 407 HIS 0.003 0.000 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (13068) covalent geometry : angle 0.53455 / 0.28 (17799) SS BOND : bond 0.00247 / 0.17 ( 34) SS BOND : angle 1.13835 / 0.89 ( 68) hydrogen bonds : bond 0.03136 / 2.22 ( 269) hydrogen bonds : angle 5.98417 / 4.16 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 184 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8570 (p0) cc_final: 0.8320 (p0) REVERT: A 212 ASP cc_start: 0.8291 (p0) cc_final: 0.7915 (p0) REVERT: A 386 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.6437 (p-80) REVERT: B 6 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7167 (t80) REVERT: B 18 TYR cc_start: 0.6115 (m-80) cc_final: 0.5548 (m-80) REVERT: B 146 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: B 217 MET cc_start: 0.6870 (mmp) cc_final: 0.6590 (mmm) REVERT: H 36 ASP cc_start: 0.7803 (t0) cc_final: 0.7503 (t0) REVERT: H 109 ASP cc_start: 0.7657 (t70) cc_final: 0.7407 (t70) REVERT: H 254 LYS cc_start: 0.8890 (mppt) cc_final: 0.8464 (mttp) REVERT: M 110 MET cc_start: 0.3328 (ttt) cc_final: 0.2081 (ptm) outliers start: 84 outliers final: 52 residues processed: 249 average time/residue: 0.1046 time to fit residues: 38.6341 Evaluate side-chains 214 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 43 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN B 286 HIS G 175 HIS H 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.106485 restraints weight = 19858.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.104039 restraints weight = 27348.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.104916 restraints weight = 29655.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.106179 restraints weight = 19342.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.106236 restraints weight = 15902.558| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.086 13102 Z= 0.441 Angle : 0.829 9.207 17867 Z= 0.436 Chirality : 0.055 0.188 1974 Planarity : 0.006 0.051 2294 Dihedral : 5.646 24.466 1771 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 9.00 % Allowed : 21.19 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.20), residues: 1632 helix: -0.60 (0.60), residues: 74 sheet: -1.51 (0.22), residues: 538 loop : -1.66 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.028 0.003 TYR A 76 PHE 0.029 0.003 PHE H 134 TRP 0.022 0.002 TRP A 243 HIS 0.010 0.002 HIS H 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01066 / 0.44 (13068) covalent geometry : angle 0.82077 / 0.43 (17799) SS BOND : bond 0.00464 / 0.28 ( 34) SS BOND : angle 2.04769 / 1.41 ( 68) hydrogen bonds : bond 0.04840 / 3.37 ( 269) hydrogen bonds : angle 6.73455 / 4.69 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 155 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 324 ARG cc_start: 0.8324 (ptm-80) cc_final: 0.7943 (ptm-80) REVERT: B 6 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 146 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: B 217 MET cc_start: 0.6884 (mmp) cc_final: 0.6470 (mmm) REVERT: G 52 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8259 (t-90) REVERT: G 252 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: H 36 ASP cc_start: 0.8226 (t0) cc_final: 0.7857 (t0) REVERT: M 110 MET cc_start: 0.3000 (ttt) cc_final: 0.1860 (ptm) outliers start: 127 outliers final: 97 residues processed: 257 average time/residue: 0.0992 time to fit residues: 38.4950 Evaluate side-chains 247 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 145 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 253 GLU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain M residue 120 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** B 146 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 = 0.3552 r_free = 0.3552 target = 0.143273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.111898 restraints weight = 19266.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109474 restraints weight = 26345.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110942 restraints weight = 28062.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.111150 restraints weight = 17286.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111495 restraints weight = 15763.586| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13102 Z= 0.160 Angle : 0.628 8.288 17867 Z= 0.323 Chirality : 0.047 0.235 1974 Planarity : 0.004 0.047 2294 Dihedral : 4.995 20.893 1771 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.73 % Allowed : 23.46 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.20), residues: 1632 helix: -0.45 (0.61), residues: 74 sheet: -1.35 (0.22), residues: 538 loop : -1.53 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 88 TYR 0.019 0.001 TYR G 46 PHE 0.013 0.001 PHE B 51 TRP 0.011 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (13068) covalent geometry : angle 0.62314 / 0.32 (17799) SS BOND : bond 0.00321 / 0.21 ( 34) SS BOND : angle 1.43848 / 1.03 ( 68) hydrogen bonds : bond 0.03467 / 2.43 ( 269) hydrogen bonds : angle 6.29447 / 4.38 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 158 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8350 (p0) cc_final: 0.7965 (p0) REVERT: A 386 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.7551 (p-80) REVERT: B 6 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 146 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: B 165 TYR cc_start: 0.8065 (t80) cc_final: 0.7789 (t80) REVERT: G 354 LEU cc_start: 0.8310 (mt) cc_final: 0.7966 (mt) REVERT: H 36 ASP cc_start: 0.7996 (t0) cc_final: 0.7592 (t0) REVERT: M 110 MET cc_start: 0.2164 (ttt) cc_final: 0.1159 (ptm) outliers start: 95 outliers final: 72 residues processed: 234 average time/residue: 0.0913 time to fit residues: 32.2114 Evaluate side-chains 230 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 155 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 160 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.8778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** 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 = 0.3590 r_free = 0.3590 target = 0.146454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.115098 restraints weight = 19180.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112781 restraints weight = 26888.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114217 restraints weight = 28436.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.114621 restraints weight = 16553.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115064 restraints weight = 14831.257| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13102 Z= 0.121 Angle : 0.610 12.419 17867 Z= 0.313 Chirality : 0.046 0.256 1974 Planarity : 0.004 0.046 2294 Dihedral : 4.738 20.639 1771 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.31 % Allowed : 23.88 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.20), residues: 1632 helix: -0.40 (0.60), residues: 74 sheet: -1.18 (0.22), residues: 536 loop : -1.41 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 134 TYR 0.032 0.001 TYR G 46 PHE 0.012 0.001 PHE A 95 TRP 0.008 0.001 TRP G 243 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13068) covalent geometry : angle 0.60154 / 0.31 (17799) SS BOND : bond 0.00247 / 0.15 ( 34) SS BOND : angle 1.78377 / 1.44 ( 68) hydrogen bonds : bond 0.03121 / 2.21 ( 269) hydrogen bonds : angle 5.94379 / 4.12 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 163 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7291 (p-80) REVERT: B 6 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7152 (t80) REVERT: B 146 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 168 MET cc_start: 0.8908 (mmt) cc_final: 0.7904 (mmt) REVERT: H 36 ASP cc_start: 0.8009 (t0) cc_final: 0.7662 (t0) REVERT: M 110 MET cc_start: 0.2007 (ttt) cc_final: 0.1176 (ptm) outliers start: 89 outliers final: 74 residues processed: 233 average time/residue: 0.0942 time to fit residues: 33.2062 Evaluate side-chains 227 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN G 396 GLN ** H 249 HIS ** 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 = 0.3588 r_free = 0.3588 target = 0.147122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114430 restraints weight = 19094.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.112259 restraints weight = 19929.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.113611 restraints weight = 22170.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.114021 restraints weight = 13947.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.114236 restraints weight = 13062.009| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13102 Z= 0.173 Angle : 0.637 9.654 17867 Z= 0.326 Chirality : 0.047 0.222 1974 Planarity : 0.004 0.046 2294 Dihedral : 4.861 20.915 1771 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 6.66 % Allowed : 24.17 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.20), residues: 1632 helix: -0.33 (0.62), residues: 74 sheet: -1.20 (0.22), residues: 534 loop : -1.45 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 88 TYR 0.033 0.002 TYR G 46 PHE 0.015 0.001 PHE B 142 TRP 0.006 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (13068) covalent geometry : angle 0.62779 / 0.32 (17799) SS BOND : bond 0.00274 / 0.17 ( 34) SS BOND : angle 1.85884 / 1.47 ( 68) hydrogen bonds : bond 0.03301 / 2.32 ( 269) hydrogen bonds : angle 5.98204 / 4.13 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 160 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.7352 (p-80) REVERT: B 6 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 146 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: B 168 MET cc_start: 0.8948 (mmt) cc_final: 0.7908 (mmt) REVERT: G 145 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7667 (p0) REVERT: G 396 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: H 36 ASP cc_start: 0.8057 (t0) cc_final: 0.7622 (t0) REVERT: M 110 MET cc_start: 0.2138 (ttt) cc_final: 0.1205 (ptm) outliers start: 94 outliers final: 82 residues processed: 235 average time/residue: 0.0998 time to fit residues: 35.5099 Evaluate side-chains 239 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 152 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 253 GLU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain M residue 120 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 0.0770 chunk 131 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.113705 restraints weight = 19162.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.111566 restraints weight = 24758.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112490 restraints weight = 27303.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.113537 restraints weight = 18122.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.113715 restraints weight = 16321.494| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13102 Z= 0.122 Angle : 0.607 8.936 17867 Z= 0.312 Chirality : 0.046 0.192 1974 Planarity : 0.004 0.045 2294 Dihedral : 4.679 20.342 1771 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.09 % Allowed : 24.38 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.82 (0.20), residues: 1632 helix: 0.47 (0.68), residues: 62 sheet: -1.13 (0.22), residues: 536 loop : -1.38 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 88 TYR 0.029 0.001 TYR G 46 PHE 0.011 0.001 PHE G 398 TRP 0.009 0.001 TRP G 243 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (13068) covalent geometry : angle 0.59890 / 0.31 (17799) SS BOND : bond 0.00274 / 0.16 ( 34) SS BOND : angle 1.68764 / 1.36 ( 68) hydrogen bonds : bond 0.03038 / 2.16 ( 269) hydrogen bonds : angle 5.79845 / 4.00 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 161 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7180 (p-80) REVERT: B 6 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 146 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: B 168 MET cc_start: 0.8910 (mmt) cc_final: 0.8001 (mmt) REVERT: H 36 ASP cc_start: 0.8038 (t0) cc_final: 0.7703 (t0) REVERT: M 110 MET cc_start: 0.2256 (ttt) cc_final: 0.1342 (ptm) outliers start: 86 outliers final: 79 residues processed: 232 average time/residue: 0.1011 time to fit residues: 35.2386 Evaluate side-chains 235 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 153 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 120 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 134 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN B 225 GLN ** H 249 HIS ** 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 = 0.3591 r_free = 0.3591 target = 0.147373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.114850 restraints weight = 19250.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.111890 restraints weight = 21546.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113519 restraints weight = 22504.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.114074 restraints weight = 13734.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.114221 restraints weight = 12919.750| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13102 Z= 0.177 Angle : 0.637 9.012 17867 Z= 0.328 Chirality : 0.047 0.187 1974 Planarity : 0.004 0.045 2294 Dihedral : 4.799 20.728 1771 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 6.59 % Allowed : 24.24 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.20), residues: 1632 helix: 0.51 (0.69), residues: 62 sheet: -1.17 (0.22), residues: 536 loop : -1.44 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.030 0.002 TYR G 46 PHE 0.012 0.001 PHE H 134 TRP 0.005 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (13068) covalent geometry : angle 0.62843 / 0.32 (17799) SS BOND : bond 0.00280 / 0.17 ( 34) SS BOND : angle 1.78498 / 1.40 ( 68) hydrogen bonds : bond 0.03267 / 2.31 ( 269) hydrogen bonds : angle 5.85077 / 4.04 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 154 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7329 (p-80) REVERT: B 6 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7239 (t80) REVERT: B 146 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: G 145 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7653 (p0) REVERT: G 252 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: H 36 ASP cc_start: 0.8062 (t0) cc_final: 0.7629 (t0) REVERT: M 110 MET cc_start: 0.2453 (ttt) cc_final: 0.1391 (ptm) outliers start: 93 outliers final: 82 residues processed: 229 average time/residue: 0.0908 time to fit residues: 31.6482 Evaluate side-chains 241 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 154 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain M residue 120 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN G 396 GLN M 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109928 restraints weight = 19547.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107004 restraints weight = 20356.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108612 restraints weight = 23576.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108998 restraints weight = 13999.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109291 restraints weight = 12604.638| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13102 Z= 0.278 Angle : 0.719 10.067 17867 Z= 0.375 Chirality : 0.050 0.198 1974 Planarity : 0.005 0.046 2294 Dihedral : 5.323 21.800 1771 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 6.80 % Allowed : 23.88 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.20), residues: 1632 helix: -0.32 (0.62), residues: 74 sheet: -1.34 (0.22), residues: 534 loop : -1.62 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.024 0.002 TYR G 46 PHE 0.018 0.002 PHE H 134 TRP 0.011 0.001 TRP A 243 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.28 (13068) covalent geometry : angle 0.70793 / 0.37 (17799) SS BOND : bond 0.00354 / 0.21 ( 34) SS BOND : angle 2.12809 / 1.63 ( 68) hydrogen bonds : bond 0.03813 / 2.66 ( 269) hydrogen bonds : angle 6.17974 / 4.28 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.68 seconds wall clock time: 34 minutes 32.52 seconds (2072.52 seconds total)