Starting phenix.real_space_refine on Wed Jul 30 18:18:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9a_62899/07_2025/9l9a_62899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9a_62899/07_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_62899/07_2025/9l9a_62899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2025/9l9a_62899.map" model { file = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2025/9l9a_62899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9a_62899/07_2025/9l9a_62899.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.08, per 1000 atoms: 0.64 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.75 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: 3.62 Time building geometry restraints manager: 3.59 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: 0.570 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.170 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- 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 : 8.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP G 407 HIS 0.003 0.001 HIS A 331 PHE 0.010 0.001 PHE B 142 TYR 0.012 0.001 TYR A 308 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.28317 ( 269) hydrogen bonds : angle 10.05124 ( 648) SS BOND : bond 0.10307 ( 34) SS BOND : angle 1.93408 ( 68) covalent geometry : bond 0.00298 (13068) covalent geometry : angle 0.61092 (17799) *********************** 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 : 1.486 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: 0.2700 time to fit residues: 64.8424 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 : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 175 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118049 restraints weight = 19252.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115264 restraints weight = 21524.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116269 restraints weight = 23005.319| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13102 Z= 0.210 Angle : 0.644 7.410 17867 Z= 0.336 Chirality : 0.047 0.184 1974 Planarity : 0.004 0.057 2294 Dihedral : 4.886 20.725 1771 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.24 % Allowed : 24.38 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1632 helix: -0.90 (0.58), residues: 74 sheet: -1.28 (0.22), residues: 548 loop : -1.44 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 330 HIS 0.005 0.001 HIS G 118 PHE 0.012 0.001 PHE H 134 TYR 0.014 0.002 TYR A 308 ARG 0.005 0.001 ARG H 317 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 269) hydrogen bonds : angle 7.34800 ( 648) SS BOND : bond 0.00473 ( 34) SS BOND : angle 1.72334 ( 68) covalent geometry : bond 0.00509 (13068) covalent geometry : angle 0.63634 (17799) *********************** 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 239 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 165 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 324 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.8141 (ptm-80) REVERT: B 146 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: B 188 TYR cc_start: 0.8461 (m-10) cc_final: 0.8230 (m-10) REVERT: B 217 MET cc_start: 0.6765 (mmp) cc_final: 0.6185 (mmm) REVERT: M 110 MET cc_start: 0.2319 (ttt) cc_final: 0.1723 (ptm) outliers start: 74 outliers final: 50 residues processed: 222 average time/residue: 0.2075 time to fit residues: 69.3925 Evaluate side-chains 205 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 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 262 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 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 157 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 134 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3627 r_free = 0.3627 target = 0.148434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113812 restraints weight = 19772.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111610 restraints weight = 21665.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.112532 restraints weight = 23024.227| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13102 Z= 0.115 Angle : 0.570 7.161 17867 Z= 0.295 Chirality : 0.045 0.186 1974 Planarity : 0.004 0.050 2294 Dihedral : 4.584 19.690 1771 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.32 % Allowed : 23.88 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1632 helix: -0.00 (0.65), residues: 62 sheet: -1.17 (0.22), residues: 548 loop : -1.34 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 243 HIS 0.003 0.001 HIS B 174 PHE 0.009 0.001 PHE B 142 TYR 0.012 0.001 TYR A 308 ARG 0.005 0.000 ARG G 157 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 269) hydrogen bonds : angle 6.60075 ( 648) SS BOND : bond 0.00302 ( 34) SS BOND : angle 1.37983 ( 68) covalent geometry : bond 0.00273 (13068) covalent geometry : angle 0.56470 (17799) *********************** 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 246 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 171 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8543 (p0) cc_final: 0.8190 (p0) REVERT: A 311 ASP cc_start: 0.8279 (p0) cc_final: 0.8062 (p0) REVERT: A 324 ARG cc_start: 0.8430 (ptm-80) cc_final: 0.7900 (ptm-80) REVERT: B 6 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7217 (t80) REVERT: B 146 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: B 217 MET cc_start: 0.6837 (mmp) cc_final: 0.6470 (mmm) REVERT: M 110 MET cc_start: 0.3299 (ttt) cc_final: 0.2359 (ptm) outliers start: 75 outliers final: 53 residues processed: 225 average time/residue: 0.2307 time to fit residues: 76.7351 Evaluate side-chains 203 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 204 GLN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 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 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 158 optimal weight: 0.0030 chunk 160 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 174 HIS H 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111894 restraints weight = 19793.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.109007 restraints weight = 18428.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110472 restraints weight = 20263.323| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13102 Z= 0.118 Angle : 0.560 8.142 17867 Z= 0.289 Chirality : 0.045 0.185 1974 Planarity : 0.004 0.047 2294 Dihedral : 4.486 19.454 1771 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.66 % Allowed : 22.82 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1632 helix: 0.32 (0.67), residues: 62 sheet: -1.18 (0.22), residues: 552 loop : -1.28 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 407 HIS 0.003 0.001 HIS B 174 PHE 0.011 0.001 PHE B 51 TYR 0.027 0.001 TYR G 46 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 269) hydrogen bonds : angle 6.25092 ( 648) SS BOND : bond 0.00287 ( 34) SS BOND : angle 1.29342 ( 68) covalent geometry : bond 0.00284 (13068) covalent geometry : angle 0.55578 (17799) *********************** 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 252 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 158 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.8311 (p0) cc_final: 0.8010 (p0) REVERT: A 324 ARG cc_start: 0.8416 (ptm-80) cc_final: 0.7874 (ptm-80) REVERT: A 386 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7054 (p-80) REVERT: B 6 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 146 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: B 217 MET cc_start: 0.7097 (mmp) cc_final: 0.6759 (mmm) REVERT: B 327 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: H 254 LYS cc_start: 0.9110 (mppt) cc_final: 0.8591 (mttt) REVERT: M 110 MET cc_start: 0.3418 (ttt) cc_final: 0.2092 (ptm) outliers start: 94 outliers final: 72 residues processed: 232 average time/residue: 0.2335 time to fit residues: 80.6590 Evaluate side-chains 229 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 153 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 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 301 CYS 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 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 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 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 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 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 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 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 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 7 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 103 optimal weight: 0.0570 chunk 125 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.0370 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS G 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.160413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127234 restraints weight = 18891.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125790 restraints weight = 20388.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127078 restraints weight = 23019.365| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13102 Z= 0.092 Angle : 0.542 7.610 17867 Z= 0.277 Chirality : 0.044 0.182 1974 Planarity : 0.004 0.045 2294 Dihedral : 4.236 18.557 1771 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.31 % Allowed : 23.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1632 helix: 0.35 (0.66), residues: 66 sheet: -1.03 (0.22), residues: 548 loop : -1.21 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 407 HIS 0.004 0.000 HIS B 256 PHE 0.016 0.001 PHE B 51 TYR 0.027 0.001 TYR G 46 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 269) hydrogen bonds : angle 5.82874 ( 648) SS BOND : bond 0.00258 ( 34) SS BOND : angle 1.09617 ( 68) covalent geometry : bond 0.00217 (13068) covalent geometry : angle 0.53905 (17799) *********************** 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 268 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 179 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7863 (mtm-85) REVERT: A 188 ASP cc_start: 0.8588 (p0) cc_final: 0.8357 (p0) REVERT: A 212 ASP cc_start: 0.8302 (p0) cc_final: 0.7926 (p0) REVERT: A 311 ASP cc_start: 0.8271 (p0) cc_final: 0.7969 (p0) REVERT: A 386 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.6602 (p-80) REVERT: B 6 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 146 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: B 162 SER cc_start: 0.8277 (m) cc_final: 0.7674 (p) REVERT: B 217 MET cc_start: 0.6826 (mmp) cc_final: 0.6501 (mmm) REVERT: B 303 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8290 (mtm110) REVERT: H 109 ASP cc_start: 0.7659 (t70) cc_final: 0.7434 (t70) REVERT: H 254 LYS cc_start: 0.8953 (mppt) cc_final: 0.8515 (mttt) REVERT: H 324 GLU cc_start: 0.7222 (pm20) cc_final: 0.6989 (pm20) REVERT: M 110 MET cc_start: 0.3386 (ttt) cc_final: 0.2113 (ptm) outliers start: 89 outliers final: 60 residues processed: 248 average time/residue: 0.2207 time to fit residues: 81.8516 Evaluate side-chains 224 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 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 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 301 CYS Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 ARG 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 370 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 148 VAL 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 301 CYS Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 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 277 THR 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 156 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.0030 chunk 127 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.9396 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.110550 restraints weight = 19502.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.108234 restraints weight = 27677.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109643 restraints weight = 28551.065| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 13102 Z= 0.269 Angle : 0.672 9.759 17867 Z= 0.350 Chirality : 0.049 0.188 1974 Planarity : 0.005 0.052 2294 Dihedral : 4.992 21.725 1771 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 7.87 % Allowed : 22.18 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1632 helix: -0.36 (0.61), residues: 74 sheet: -1.26 (0.22), residues: 538 loop : -1.43 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.006 0.001 HIS H 153 PHE 0.019 0.002 PHE H 134 TYR 0.024 0.002 TYR G 46 ARG 0.004 0.001 ARG H 317 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 269) hydrogen bonds : angle 6.29523 ( 648) SS BOND : bond 0.00355 ( 34) SS BOND : angle 1.58846 ( 68) covalent geometry : bond 0.00651 (13068) covalent geometry : angle 0.66620 (17799) *********************** 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 273 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 162 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 146 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: B 217 MET cc_start: 0.6587 (mmp) cc_final: 0.6324 (mmm) REVERT: G 252 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: H 109 ASP cc_start: 0.7763 (t70) cc_final: 0.7550 (t70) REVERT: H 217 MET cc_start: 0.6514 (mmp) cc_final: 0.6085 (mmp) REVERT: M 110 MET cc_start: 0.2851 (ttt) cc_final: 0.1588 (ptm) outliers start: 111 outliers final: 87 residues processed: 247 average time/residue: 0.2229 time to fit residues: 82.4195 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 : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 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 214 VAL Chi-restraints excluded: chain A residue 237 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 332 SER 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 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 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 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 170 PHE Chi-restraints excluded: chain G residue 213 ILE 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 288 VAL Chi-restraints excluded: chain G residue 300 SER 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 347 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain H residue 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 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 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 147 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 158 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.114128 restraints weight = 19442.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.111110 restraints weight = 19549.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112727 restraints weight = 20497.393| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13102 Z= 0.117 Angle : 0.584 9.840 17867 Z= 0.299 Chirality : 0.046 0.256 1974 Planarity : 0.004 0.057 2294 Dihedral : 4.580 20.007 1771 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.09 % Allowed : 24.10 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1632 helix: 0.40 (0.67), residues: 62 sheet: -1.15 (0.22), residues: 546 loop : -1.24 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 351 HIS 0.004 0.000 HIS B 174 PHE 0.010 0.001 PHE B 51 TYR 0.027 0.001 TYR G 46 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 269) hydrogen bonds : angle 5.91120 ( 648) SS BOND : bond 0.00286 ( 34) SS BOND : angle 1.17012 ( 68) covalent geometry : bond 0.00281 (13068) covalent geometry : angle 0.58020 (17799) *********************** 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 244 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 158 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8056 (t0) cc_final: 0.7495 (p0) REVERT: A 212 ASP cc_start: 0.8306 (p0) cc_final: 0.7919 (p0) REVERT: A 386 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.7370 (p-80) REVERT: B 6 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7084 (t80) REVERT: B 146 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: B 217 MET cc_start: 0.6627 (mmp) cc_final: 0.6413 (mmm) REVERT: B 242 ASP cc_start: 0.8089 (m-30) cc_final: 0.7841 (t0) REVERT: G 354 LEU cc_start: 0.8397 (mt) cc_final: 0.8064 (mt) REVERT: H 109 ASP cc_start: 0.7770 (t70) cc_final: 0.7505 (t70) REVERT: H 217 MET cc_start: 0.6408 (mmp) cc_final: 0.6006 (mmp) REVERT: M 110 MET cc_start: 0.2727 (ttt) cc_final: 0.1551 (ptm) outliers start: 86 outliers final: 73 residues processed: 227 average time/residue: 0.2223 time to fit residues: 75.2515 Evaluate side-chains 224 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 148 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 291 SER 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 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 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 321 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 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 211 THR 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 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 106 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN G 396 GLN ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.110691 restraints weight = 19895.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.109078 restraints weight = 20680.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.110164 restraints weight = 22855.088| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13102 Z= 0.236 Angle : 0.675 13.668 17867 Z= 0.348 Chirality : 0.049 0.303 1974 Planarity : 0.005 0.063 2294 Dihedral : 4.937 21.152 1771 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 7.09 % Allowed : 23.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1632 helix: -0.29 (0.62), residues: 74 sheet: -1.25 (0.22), residues: 538 loop : -1.39 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 243 HIS 0.006 0.001 HIS B 174 PHE 0.016 0.002 PHE H 134 TYR 0.025 0.002 TYR G 46 ARG 0.004 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 269) hydrogen bonds : angle 6.11108 ( 648) SS BOND : bond 0.00346 ( 34) SS BOND : angle 2.10946 ( 68) covalent geometry : bond 0.00570 (13068) covalent geometry : angle 0.66365 (17799) *********************** 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 258 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 158 time to evaluate : 1.468 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 242 MET cc_start: 0.7921 (tmm) cc_final: 0.7714 (tmm) REVERT: A 386 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.7564 (p-80) REVERT: B 6 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7225 (t80) REVERT: B 146 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: B 217 MET cc_start: 0.6798 (mmp) cc_final: 0.6523 (mmm) REVERT: G 354 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (mt) REVERT: G 396 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: M 110 MET cc_start: 0.2098 (ttt) cc_final: 0.1165 (ptm) outliers start: 100 outliers final: 87 residues processed: 240 average time/residue: 0.2188 time to fit residues: 78.8316 Evaluate side-chains 246 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 154 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 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 203 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 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 145 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 312 THR 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 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 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 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 204 GLN 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 300 SER 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 354 LEU Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain M residue 120 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 144 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115344 restraints weight = 19239.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113467 restraints weight = 19088.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114252 restraints weight = 21678.070| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1902 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= 0.119 Angle : 0.618 11.802 17867 Z= 0.316 Chirality : 0.046 0.189 1974 Planarity : 0.004 0.062 2294 Dihedral : 4.690 25.780 1771 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 6.09 % Allowed : 24.10 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1632 helix: 0.44 (0.68), residues: 62 sheet: -1.08 (0.22), residues: 538 loop : -1.26 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 PHE 0.014 0.001 PHE A 95 TYR 0.028 0.001 TYR G 46 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 269) hydrogen bonds : angle 5.84985 ( 648) SS BOND : bond 0.00241 ( 34) SS BOND : angle 1.95648 ( 68) covalent geometry : bond 0.00283 (13068) covalent geometry : angle 0.60677 (17799) *********************** 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 250 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 164 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8036 (t0) cc_final: 0.7490 (p0) REVERT: A 386 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7335 (p-80) REVERT: B 6 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7179 (t80) REVERT: B 146 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: G 204 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8328 (mm-40) REVERT: G 252 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: G 354 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7983 (mt) REVERT: H 217 MET cc_start: 0.6187 (mmp) cc_final: 0.5583 (mmm) REVERT: M 110 MET cc_start: 0.2041 (ttt) cc_final: 0.1152 (ptm) outliers start: 86 outliers final: 75 residues processed: 231 average time/residue: 0.2188 time to fit residues: 75.3777 Evaluate side-chains 233 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 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 291 SER 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 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 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 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 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 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 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 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 114 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 156 optimal weight: 0.0040 chunk 19 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113612 restraints weight = 19340.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111841 restraints weight = 18155.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112905 restraints weight = 22562.439| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13102 Z= 0.108 Angle : 0.596 11.290 17867 Z= 0.305 Chirality : 0.045 0.180 1974 Planarity : 0.004 0.066 2294 Dihedral : 4.559 24.183 1771 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.67 % Allowed : 24.59 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1632 helix: 0.49 (0.68), residues: 62 sheet: -1.03 (0.22), residues: 552 loop : -1.20 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 407 HIS 0.004 0.000 HIS B 174 PHE 0.015 0.001 PHE A 95 TYR 0.028 0.001 TYR G 46 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 269) hydrogen bonds : angle 5.66939 ( 648) SS BOND : bond 0.00227 ( 34) SS BOND : angle 1.62653 ( 68) covalent geometry : bond 0.00259 (13068) covalent geometry : angle 0.58855 (17799) ********************** 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 245 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 165 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8058 (t0) cc_final: 0.7527 (p0) REVERT: A 386 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7005 (p-80) REVERT: B 6 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7353 (t80) REVERT: B 146 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: B 188 TYR cc_start: 0.8300 (m-10) cc_final: 0.7926 (m-80) REVERT: B 200 GLU cc_start: 0.6885 (pp20) cc_final: 0.6081 (pp20) REVERT: G 204 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8146 (mm-40) REVERT: G 252 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: G 354 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8037 (mt) REVERT: H 217 MET cc_start: 0.6172 (mmp) cc_final: 0.5564 (mmm) REVERT: M 110 MET cc_start: 0.2822 (ttt) cc_final: 0.1680 (ptm) outliers start: 80 outliers final: 71 residues processed: 228 average time/residue: 0.2319 time to fit residues: 79.0245 Evaluate side-chains 235 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 159 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 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 291 SER 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 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 146 GLN Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 321 VAL 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 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 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 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 316 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 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 46 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.113868 restraints weight = 19463.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.112095 restraints weight = 18525.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113348 restraints weight = 21384.675| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13102 Z= 0.175 Angle : 0.635 10.631 17867 Z= 0.326 Chirality : 0.047 0.179 1974 Planarity : 0.004 0.063 2294 Dihedral : 4.756 25.618 1771 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.88 % Allowed : 24.38 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.21), residues: 1632 helix: 0.52 (0.69), residues: 62 sheet: -1.08 (0.22), residues: 534 loop : -1.28 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 243 HIS 0.005 0.001 HIS B 174 PHE 0.016 0.001 PHE B 51 TYR 0.028 0.002 TYR G 46 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 269) hydrogen bonds : angle 5.81443 ( 648) SS BOND : bond 0.00282 ( 34) SS BOND : angle 2.12802 ( 68) covalent geometry : bond 0.00425 (13068) covalent geometry : angle 0.62229 (17799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4180.05 seconds wall clock time: 73 minutes 45.53 seconds (4425.53 seconds total)