Starting phenix.real_space_refine on Sat Aug 23 14:21:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9a_62899/08_2025/9l9a_62899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9a_62899/08_2025/9l9a_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_62899/08_2025/9l9a_62899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9a_62899/08_2025/9l9a_62899.map" model { file = "/net/cci-nas-00/data/ceres_data/9l9a_62899/08_2025/9l9a_62899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9a_62899/08_2025/9l9a_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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.34, per 1000 atoms: 0.26 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: 0.80 Conformation dependent library (CDL) restraints added in 623.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.41 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: 1.68 Time building geometry restraints manager: 1.08 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 aren 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 covalent geometry : bond 0.00298 (13068) covalent geometry : angle 0.61092 (17799) SS BOND : bond 0.10307 ( 34) SS BOND : angle 1.93408 ( 68) hydrogen bonds : bond 0.28317 ( 269) hydrogen bonds : angle 10.05124 ( 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 : 0.390 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: 0.0937 time to fit residues: 22.6071 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 : 0.400 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3666 r_free = 0.3666 target = 0.151492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117850 restraints weight = 19189.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115135 restraints weight = 21537.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116229 restraints weight = 22741.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.118132 restraints weight = 15132.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118095 restraints weight = 11517.736| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1051 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= 0.208 Angle : 0.644 7.262 17867 Z= 0.336 Chirality : 0.047 0.187 1974 Planarity : 0.004 0.057 2294 Dihedral : 4.905 20.863 1771 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.60 % Allowed : 23.81 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.20), residues: 1632 helix: -0.90 (0.58), residues: 74 sheet: -1.29 (0.22), residues: 548 loop : -1.44 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 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 B 35 HIS 0.005 0.001 HIS H 361 Details of bonding type rmsd covalent geometry : bond 0.00504 (13068) covalent geometry : angle 0.63690 (17799) SS BOND : bond 0.00458 ( 34) SS BOND : angle 1.69302 ( 68) hydrogen bonds : bond 0.04864 ( 269) hydrogen bonds : angle 7.28082 ( 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 244 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 165 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 324 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.8164 (ptm-80) REVERT: B 146 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: B 188 TYR cc_start: 0.8437 (m-10) cc_final: 0.8205 (m-10) REVERT: B 217 MET cc_start: 0.6736 (mmp) cc_final: 0.6162 (mmm) REVERT: H 36 ASP cc_start: 0.7867 (t0) cc_final: 0.7666 (t0) REVERT: M 110 MET cc_start: 0.2302 (ttt) cc_final: 0.1718 (ptm) outliers start: 79 outliers final: 51 residues processed: 225 average time/residue: 0.0842 time to fit residues: 29.0060 Evaluate side-chains 205 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 141 THR 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 183 LEU 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 Chi-restraints excluded: chain H residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3656 r_free = 0.3656 target = 0.150539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116705 restraints weight = 19480.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114071 restraints weight = 21342.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115519 restraints weight = 22795.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.116045 restraints weight = 14032.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.116352 restraints weight = 12760.031| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13102 Z= 0.145 Angle : 0.589 7.129 17867 Z= 0.306 Chirality : 0.046 0.186 1974 Planarity : 0.004 0.051 2294 Dihedral : 4.739 20.065 1771 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.95 % Allowed : 23.39 % Favored : 70.66 % 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 aren not related in a simple way. whole: -1.95 (0.20), residues: 1632 helix: -0.68 (0.58), residues: 74 sheet: -1.22 (0.22), residues: 538 loop : -1.38 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 157 TYR 0.016 0.001 TYR H 165 PHE 0.009 0.001 PHE H 134 TRP 0.008 0.001 TRP G 243 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00348 (13068) covalent geometry : angle 0.58340 (17799) SS BOND : bond 0.00378 ( 34) SS BOND : angle 1.46137 ( 68) hydrogen bonds : bond 0.03983 ( 269) hydrogen bonds : angle 6.63547 ( 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 250 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 166 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.8315 (p0) cc_final: 0.7968 (p0) REVERT: A 324 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.7953 (ptm-80) REVERT: B 6 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7179 (t80) REVERT: B 146 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: B 165 TYR cc_start: 0.8083 (t80) cc_final: 0.7775 (t80) REVERT: B 217 MET cc_start: 0.6908 (mmp) cc_final: 0.6500 (mmm) REVERT: B 327 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8395 (pt0) REVERT: H 36 ASP cc_start: 0.7760 (t0) cc_final: 0.7467 (t0) REVERT: H 78 ASP cc_start: 0.8179 (t0) cc_final: 0.7966 (t0) REVERT: M 110 MET cc_start: 0.3316 (ttt) cc_final: 0.2336 (ptm) outliers start: 84 outliers final: 65 residues processed: 230 average time/residue: 0.0903 time to fit residues: 30.7440 Evaluate side-chains 212 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 204 GLN 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 335 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 201 CYS 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 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 VAL 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 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 108 VAL 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 344 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 8 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 75 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN H 174 HIS ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118079 restraints weight = 19418.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.115498 restraints weight = 21380.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117067 restraints weight = 22014.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117609 restraints weight = 13450.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117933 restraints weight = 12063.571| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1403 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= 0.150 Angle : 0.584 8.697 17867 Z= 0.302 Chirality : 0.046 0.193 1974 Planarity : 0.004 0.049 2294 Dihedral : 4.706 20.044 1771 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 7.51 % Allowed : 22.82 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.20), residues: 1632 helix: -0.47 (0.60), residues: 74 sheet: -1.27 (0.22), residues: 542 loop : -1.35 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 134 TYR 0.014 0.001 TYR A 308 PHE 0.011 0.001 PHE B 51 TRP 0.007 0.001 TRP G 243 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00363 (13068) covalent geometry : angle 0.57917 (17799) SS BOND : bond 0.00293 ( 34) SS BOND : angle 1.39167 ( 68) hydrogen bonds : bond 0.03589 ( 269) hydrogen bonds : angle 6.36581 ( 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 266 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 160 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.8349 (p0) cc_final: 0.7926 (p0) REVERT: A 324 ARG cc_start: 0.8438 (ptm-80) cc_final: 0.7952 (ptm-80) REVERT: B 6 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 146 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: B 217 MET cc_start: 0.6920 (mmp) cc_final: 0.6514 (mmm) REVERT: B 327 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: H 36 ASP cc_start: 0.7774 (t0) cc_final: 0.7363 (t0) REVERT: H 217 MET cc_start: 0.6601 (mmp) cc_final: 0.6084 (mmp) REVERT: H 254 LYS cc_start: 0.9118 (mppt) cc_final: 0.8628 (mttt) REVERT: M 110 MET cc_start: 0.3443 (ttt) cc_final: 0.2064 (ptm) outliers start: 106 outliers final: 81 residues processed: 246 average time/residue: 0.0819 time to fit residues: 30.5189 Evaluate side-chains 232 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 148 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL 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 178 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 204 GLN 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 306 CYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL 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 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 312 THR 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 370 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 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 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 211 THR 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 282 ILE 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 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 8 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 75 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS 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 321 VAL Chi-restraints excluded: chain H residue 327 GLU 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: 0.9980 chunk 135 optimal weight: 0.1980 chunk 140 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN H 174 HIS ** 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 = 0.3584 r_free = 0.3584 target = 0.145686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114409 restraints weight = 19399.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.112072 restraints weight = 25286.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.113010 restraints weight = 27690.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114219 restraints weight = 18440.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114289 restraints weight = 15669.095| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1552 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= 0.103 Angle : 0.555 8.025 17867 Z= 0.285 Chirality : 0.045 0.177 1974 Planarity : 0.004 0.047 2294 Dihedral : 4.448 19.352 1771 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 6.80 % Allowed : 23.53 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.20), residues: 1632 helix: 0.40 (0.68), residues: 62 sheet: -1.15 (0.22), residues: 548 loop : -1.27 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.027 0.001 TYR G 46 PHE 0.015 0.001 PHE B 51 TRP 0.008 0.001 TRP G 407 HIS 0.004 0.000 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00245 (13068) covalent geometry : angle 0.55079 (17799) SS BOND : bond 0.00253 ( 34) SS BOND : angle 1.20307 ( 68) hydrogen bonds : bond 0.03137 ( 269) hydrogen bonds : angle 6.01869 ( 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 265 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 169 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.8284 (p0) cc_final: 0.7883 (p0) REVERT: A 386 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.6981 (p-80) REVERT: B 6 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7044 (t80) REVERT: B 146 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: B 217 MET cc_start: 0.6908 (mmp) cc_final: 0.6492 (mmm) REVERT: B 303 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8228 (mtm110) REVERT: G 252 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: G 341 GLU cc_start: 0.7625 (mp0) cc_final: 0.7405 (mp0) REVERT: H 36 ASP cc_start: 0.7678 (t0) cc_final: 0.7340 (t0) REVERT: M 110 MET cc_start: 0.3330 (ttt) cc_final: 0.2058 (ptm) outliers start: 96 outliers final: 71 residues processed: 248 average time/residue: 0.0892 time to fit residues: 33.1545 Evaluate side-chains 230 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 154 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 LEU 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 108 VAL 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 177 VAL Chi-restraints excluded: chain A residue 203 ILE 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 296 ILE Chi-restraints excluded: chain A residue 301 CYS 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 109 ASP Chi-restraints excluded: chain B residue 113 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 262 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 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 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 252 GLN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 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 8 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 75 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 251 VAL Chi-restraints excluded: chain H residue 277 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 286 HIS G 396 GLN H 174 HIS H 233 GLN ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.107225 restraints weight = 19595.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.105163 restraints weight = 28439.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.105849 restraints weight = 28790.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107189 restraints weight = 19985.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107129 restraints weight = 16752.067| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13102 Z= 0.346 Angle : 0.740 9.472 17867 Z= 0.388 Chirality : 0.052 0.192 1974 Planarity : 0.005 0.067 2294 Dihedral : 5.403 23.279 1771 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 9.21 % Allowed : 21.40 % Favored : 69.38 % 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 aren not related in a simple way. whole: -2.30 (0.20), residues: 1632 helix: -0.49 (0.61), residues: 74 sheet: -1.52 (0.21), residues: 558 loop : -1.62 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.024 0.002 TYR G 46 PHE 0.023 0.002 PHE H 134 TRP 0.016 0.002 TRP A 243 HIS 0.008 0.002 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00836 (13068) covalent geometry : angle 0.73302 (17799) SS BOND : bond 0.00406 ( 34) SS BOND : angle 1.81420 ( 68) hydrogen bonds : bond 0.04287 ( 269) hydrogen bonds : angle 6.54075 ( 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 294 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 164 time to evaluate : 0.378 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 386 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.7912 (p-80) REVERT: B 2 ILE cc_start: 0.6243 (tp) cc_final: 0.6000 (tp) REVERT: B 6 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7370 (t80) REVERT: B 146 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: B 217 MET cc_start: 0.7049 (mmp) cc_final: 0.6511 (mmm) REVERT: G 252 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: G 354 LEU cc_start: 0.8792 (mt) cc_final: 0.8555 (mt) REVERT: G 396 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: H 36 ASP cc_start: 0.8124 (t0) cc_final: 0.7735 (t0) REVERT: M 110 MET cc_start: 0.2271 (ttt) cc_final: 0.1170 (ptm) outliers start: 130 outliers final: 98 residues processed: 267 average time/residue: 0.0878 time to fit residues: 34.8603 Evaluate side-chains 256 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 153 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 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 166 ILE Chi-restraints excluded: chain A residue 177 VAL 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 237 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 THR 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 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 145 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 165 TYR 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 312 THR 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 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 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 170 PHE Chi-restraints excluded: chain G residue 183 LEU 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 280 ILE Chi-restraints excluded: chain G residue 282 ILE 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 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 8 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3569 r_free = 0.3569 target = 0.145378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.114588 restraints weight = 19257.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112943 restraints weight = 25325.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113832 restraints weight = 27007.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.114333 restraints weight = 18216.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.114695 restraints weight = 16482.310| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13102 Z= 0.116 Angle : 0.594 7.937 17867 Z= 0.308 Chirality : 0.046 0.179 1974 Planarity : 0.004 0.059 2294 Dihedral : 4.759 19.784 1771 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.59 % Allowed : 24.03 % Favored : 69.38 % 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 aren not related in a simple way. whole: -1.98 (0.20), residues: 1632 helix: -0.34 (0.61), residues: 74 sheet: -1.29 (0.22), residues: 542 loop : -1.41 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.030 0.001 TYR G 46 PHE 0.010 0.001 PHE B 51 TRP 0.013 0.001 TRP G 243 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00275 (13068) covalent geometry : angle 0.58961 (17799) SS BOND : bond 0.00277 ( 34) SS BOND : angle 1.25516 ( 68) hydrogen bonds : bond 0.03157 ( 269) hydrogen bonds : angle 6.09470 ( 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 255 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 162 time to evaluate : 0.405 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: 0.8356 (p0) cc_final: 0.7988 (p0) REVERT: A 386 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.7470 (p-80) REVERT: B 6 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7136 (t80) REVERT: B 146 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: G 252 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: H 36 ASP cc_start: 0.8021 (t0) cc_final: 0.7676 (t0) REVERT: H 109 ASP cc_start: 0.7758 (t70) cc_final: 0.7466 (t70) REVERT: H 217 MET cc_start: 0.6118 (mmp) cc_final: 0.5575 (mmm) REVERT: M 81 ASN cc_start: 0.4405 (OUTLIER) cc_final: 0.3674 (m-40) REVERT: M 110 MET cc_start: 0.1982 (ttt) cc_final: 0.1191 (ptm) outliers start: 93 outliers final: 73 residues processed: 235 average time/residue: 0.0874 time to fit residues: 30.7571 Evaluate side-chains 226 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 38 LEU 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 148 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 214 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 386 HIS Chi-restraints excluded: chain B residue 6 PHE 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 166 ILE 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 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 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 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 146 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 280 ILE 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 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 8 LEU 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 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 156 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** 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 = 0.3586 r_free = 0.3586 target = 0.146235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.115270 restraints weight = 19080.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.113164 restraints weight = 23591.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114003 restraints weight = 27960.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.115272 restraints weight = 18390.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.115338 restraints weight = 15297.063| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13102 Z= 0.148 Angle : 0.622 13.350 17867 Z= 0.321 Chirality : 0.047 0.341 1974 Planarity : 0.004 0.057 2294 Dihedral : 4.769 20.076 1771 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 6.73 % Allowed : 24.17 % Favored : 69.10 % 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 aren not related in a simple way. whole: -1.91 (0.20), residues: 1632 helix: -0.36 (0.61), residues: 74 sheet: -1.19 (0.22), residues: 534 loop : -1.39 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.026 0.001 TYR G 46 PHE 0.012 0.001 PHE B 142 TRP 0.007 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00359 (13068) covalent geometry : angle 0.61112 (17799) SS BOND : bond 0.00251 ( 34) SS BOND : angle 1.97671 ( 68) hydrogen bonds : bond 0.03218 ( 269) hydrogen bonds : angle 6.03922 ( 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 248 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 153 time to evaluate : 0.327 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: 0.8425 (OUTLIER) cc_final: 0.7295 (p-80) REVERT: B 6 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 146 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: G 252 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: H 36 ASP cc_start: 0.8007 (t0) cc_final: 0.7608 (t0) REVERT: H 109 ASP cc_start: 0.7791 (t70) cc_final: 0.7500 (t70) REVERT: H 217 MET cc_start: 0.6191 (mmp) cc_final: 0.5617 (mmm) REVERT: M 81 ASN cc_start: 0.3966 (OUTLIER) cc_final: 0.3510 (m110) REVERT: M 110 MET cc_start: 0.1994 (ttt) cc_final: 0.1181 (ptm) outliers start: 95 outliers final: 81 residues processed: 227 average time/residue: 0.0917 time to fit residues: 30.9796 Evaluate side-chains 236 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 150 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 38 LEU 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 177 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 296 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 165 TYR Chi-restraints excluded: chain B residue 166 ILE 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 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 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 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 253 GLU Chi-restraints excluded: chain G residue 263 VAL 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 8 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 145 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** 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 = 0.3538 r_free = 0.3538 target = 0.142006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.110538 restraints weight = 19275.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107826 restraints weight = 27046.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109238 restraints weight = 27929.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109615 restraints weight = 17084.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.109919 restraints weight = 15050.523| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1916 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= 0.174 Angle : 0.632 10.982 17867 Z= 0.327 Chirality : 0.047 0.241 1974 Planarity : 0.004 0.055 2294 Dihedral : 4.843 20.282 1771 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 6.87 % Allowed : 23.81 % 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 aren not related in a simple way. whole: -1.95 (0.20), residues: 1632 helix: -0.32 (0.61), residues: 74 sheet: -1.22 (0.22), residues: 534 loop : -1.42 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.031 0.002 TYR G 46 PHE 0.011 0.001 PHE H 134 TRP 0.007 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00423 (13068) covalent geometry : angle 0.62153 (17799) SS BOND : bond 0.00285 ( 34) SS BOND : angle 1.94560 ( 68) hydrogen bonds : bond 0.03322 ( 269) hydrogen bonds : angle 6.02976 ( 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 253 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 156 time to evaluate : 0.499 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: 0.8474 (OUTLIER) cc_final: 0.7378 (p-80) REVERT: B 6 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7145 (t80) REVERT: B 146 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: B 217 MET cc_start: 0.6748 (mmp) cc_final: 0.6224 (mmm) REVERT: B 224 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8074 (tmm-80) REVERT: G 73 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7739 (tttt) REVERT: G 145 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7698 (p0) REVERT: G 252 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: H 36 ASP cc_start: 0.8033 (t0) cc_final: 0.7623 (t0) REVERT: H 109 ASP cc_start: 0.7829 (t70) cc_final: 0.7574 (t70) REVERT: H 217 MET cc_start: 0.6278 (mmp) cc_final: 0.5663 (mmm) REVERT: M 110 MET cc_start: 0.2068 (ttt) cc_final: 0.1185 (ptm) outliers start: 97 outliers final: 84 residues processed: 232 average time/residue: 0.0911 time to fit residues: 31.3870 Evaluate side-chains 240 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 150 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 38 LEU 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 177 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 296 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 165 TYR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 224 ARG 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 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 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 252 GLN 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 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 8 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 75 ILE Chi-restraints excluded: chain H residue 94 LEU 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 134 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 158 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN H 153 HIS ** 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 = 0.3613 r_free = 0.3613 target = 0.148560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116812 restraints weight = 19389.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.114028 restraints weight = 18969.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115443 restraints weight = 20220.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.116000 restraints weight = 12913.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.116312 restraints weight = 11251.151| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1974 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= 0.106 Angle : 0.593 8.736 17867 Z= 0.305 Chirality : 0.045 0.196 1974 Planarity : 0.004 0.048 2294 Dihedral : 4.527 19.269 1771 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 6.31 % Allowed : 24.59 % Favored : 69.10 % 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 aren not related in a simple way. whole: -1.74 (0.20), residues: 1632 helix: 0.52 (0.69), residues: 62 sheet: -1.09 (0.22), residues: 544 loop : -1.31 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.028 0.001 TYR G 46 PHE 0.012 0.001 PHE B 142 TRP 0.009 0.001 TRP G 407 HIS 0.003 0.000 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00253 (13068) covalent geometry : angle 0.58521 (17799) SS BOND : bond 0.00292 ( 34) SS BOND : angle 1.62641 ( 68) hydrogen bonds : bond 0.02886 ( 269) hydrogen bonds : angle 5.73191 ( 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 251 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 162 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7090 (p-80) REVERT: B 6 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 146 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: B 200 GLU cc_start: 0.6234 (pp20) cc_final: 0.5810 (pp20) REVERT: B 217 MET cc_start: 0.6536 (mmp) cc_final: 0.6061 (mmm) REVERT: G 73 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7612 (tttt) REVERT: G 204 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8409 (mm-40) REVERT: H 36 ASP cc_start: 0.7975 (t0) cc_final: 0.7640 (t0) REVERT: H 109 ASP cc_start: 0.7777 (t70) cc_final: 0.7451 (t70) REVERT: H 217 MET cc_start: 0.6198 (mmp) cc_final: 0.5317 (mmm) REVERT: M 110 MET cc_start: 0.2755 (ttt) cc_final: 0.1662 (ptm) outliers start: 89 outliers final: 77 residues processed: 232 average time/residue: 0.0920 time to fit residues: 31.4410 Evaluate side-chains 235 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 155 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 LEU 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 177 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 296 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 165 TYR Chi-restraints excluded: chain B residue 166 ILE 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 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 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 263 VAL Chi-restraints excluded: chain G residue 280 ILE 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 8 LEU 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 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 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: 3.9990 chunk 7 optimal weight: 0.0570 chunk 109 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 1.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** 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 = 0.3577 r_free = 0.3577 target = 0.145511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.113864 restraints weight = 19498.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111954 restraints weight = 18297.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.112848 restraints weight = 23070.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.113377 restraints weight = 14454.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.113686 restraints weight = 12515.785| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13102 Z= 0.181 Angle : 0.631 9.322 17867 Z= 0.326 Chirality : 0.047 0.190 1974 Planarity : 0.004 0.063 2294 Dihedral : 4.774 20.228 1771 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.38 % Allowed : 24.38 % Favored : 69.24 % 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 aren not related in a simple way. whole: -1.80 (0.20), residues: 1632 helix: 0.51 (0.69), residues: 62 sheet: -1.14 (0.22), residues: 534 loop : -1.35 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.030 0.002 TYR G 46 PHE 0.015 0.001 PHE B 142 TRP 0.008 0.001 TRP H 310 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00437 (13068) covalent geometry : angle 0.62187 (17799) SS BOND : bond 0.00270 ( 34) SS BOND : angle 1.82615 ( 68) hydrogen bonds : bond 0.03303 ( 269) hydrogen bonds : angle 5.91809 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1699.63 seconds wall clock time: 30 minutes 12.29 seconds (1812.29 seconds total)