Starting phenix.real_space_refine on Wed Jul 30 03:01:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq3_61721/07_2025/9jq3_61721_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq3_61721/07_2025/9jq3_61721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jq3_61721/07_2025/9jq3_61721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq3_61721/07_2025/9jq3_61721.map" model { file = "/net/cci-nas-00/data/ceres_data/9jq3_61721/07_2025/9jq3_61721_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq3_61721/07_2025/9jq3_61721_trim.cif" } resolution = 2.45 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= 0.002 sd= 0.127 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 P 8 5.49 5 S 88 5.16 5 C 7580 2.51 5 N 2108 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 12052 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2960 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "B" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2960 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "C" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2960 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "D" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2960 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.25, per 1000 atoms: 0.68 Number of scatterers: 12052 At special positions: 0 Unit cell: (103.824, 103, 103, 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) S 88 16.00 P 8 15.00 O 2268 8.00 N 2108 7.00 C 7580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 323 " distance=2.25 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: 3.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 12 sheets defined 59.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.831A pdb=" N GLU A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.758A pdb=" N HIS A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.782A pdb=" N VAL A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.766A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 290 through 319 Processing helix chain 'A' and resid 324 through 351 removed outlier: 3.849A pdb=" N ILE A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.727A pdb=" N ILE A 356 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'B' and resid 16 through 32 removed outlier: 3.670A pdb=" N GLU B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 47 through 58 removed outlier: 3.515A pdb=" N LEU B 58 " --> pdb=" O GLN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.750A pdb=" N HIS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.531A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.941A pdb=" N VAL B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 259 through 278 removed outlier: 3.680A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Proline residue: B 275 - end of helix removed outlier: 3.699A pdb=" N HIS B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 Processing helix chain 'B' and resid 324 through 351 removed outlier: 3.714A pdb=" N CYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 332 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.544A pdb=" N LEU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'C' and resid 14 through 32 Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.547A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.535A pdb=" N HIS C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.588A pdb=" N ARG C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 111 " --> pdb=" O GLN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.710A pdb=" N TYR C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 188 through 191 Processing helix chain 'C' and resid 244 through 250 removed outlier: 4.386A pdb=" N GLY C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.637A pdb=" N LEU C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Proline residue: C 275 - end of helix Processing helix chain 'C' and resid 290 through 319 Processing helix chain 'C' and resid 324 through 347 removed outlier: 3.541A pdb=" N CYS C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 332 " --> pdb=" O CYS C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.749A pdb=" N ILE C 356 " --> pdb=" O ASN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 374 removed outlier: 3.562A pdb=" N LEU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 371 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.619A pdb=" N PHE C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 32 removed outlier: 3.835A pdb=" N GLU D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.541A pdb=" N HIS D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 115 through 120 removed outlier: 3.506A pdb=" N TYR D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.978A pdb=" N VAL D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.848A pdb=" N VAL D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 277 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 290 through 319 Processing helix chain 'D' and resid 324 through 351 removed outlier: 4.124A pdb=" N ILE D 332 " --> pdb=" O CYS D 328 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 355 Processing helix chain 'D' and resid 360 through 369 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 377 through 388 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 4.416A pdb=" N ALA A 195 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.275A pdb=" N TYR A 158 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 230 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU A 160 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP A 166 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS A 222 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134 removed outlier: 4.515A pdb=" N ALA B 195 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.818A pdb=" N HIS B 157 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 158 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS B 230 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU B 160 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP B 166 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS B 222 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AA7, first strand: chain 'C' and resid 131 through 134 removed outlier: 4.052A pdb=" N ALA C 195 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 154 removed outlier: 6.132A pdb=" N TYR C 158 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 230 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 160 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP C 166 " --> pdb=" O CYS C 222 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS C 222 " --> pdb=" O TRP C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'D' and resid 131 through 134 removed outlier: 4.186A pdb=" N ALA D 195 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 149 through 153 removed outlier: 7.539A pdb=" N GLY D 162 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU D 227 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS D 164 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE D 225 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP D 166 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLU D 223 " --> pdb=" O TRP D 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR D 168 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR D 221 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 281 through 282 670 hydrogen bonds defined for protein. 1923 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: 5.59 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2039 1.31 - 1.44: 3123 1.44 - 1.56: 6958 1.56 - 1.69: 16 1.69 - 1.82: 140 Bond restraints: 12276 Sorted by residual: bond pdb=" CA GLU B 15 " pdb=" C GLU B 15 " ideal model delta sigma weight residual 1.525 1.457 0.068 1.25e-02 6.40e+03 2.96e+01 bond pdb=" CA SER B 14 " pdb=" C SER B 14 " ideal model delta sigma weight residual 1.527 1.462 0.065 1.41e-02 5.03e+03 2.13e+01 bond pdb=" C SER B 14 " pdb=" O SER B 14 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.32e-02 5.74e+03 1.61e+01 bond pdb=" C10 FAD C 401 " pdb=" N10 FAD C 401 " ideal model delta sigma weight residual 1.358 1.435 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5X FAD A 401 " pdb=" C9A FAD A 401 " ideal model delta sigma weight residual 1.412 1.489 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 12271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 16433 3.23 - 6.47: 110 6.47 - 9.70: 29 9.70 - 12.94: 6 12.94 - 16.17: 2 Bond angle restraints: 16580 Sorted by residual: angle pdb=" N GLU B 16 " pdb=" CA GLU B 16 " pdb=" C GLU B 16 " ideal model delta sigma weight residual 110.80 94.63 16.17 2.13e+00 2.20e-01 5.77e+01 angle pdb=" N GLU B 16 " pdb=" CA GLU B 16 " pdb=" CB GLU B 16 " ideal model delta sigma weight residual 110.49 120.13 -9.64 1.69e+00 3.50e-01 3.25e+01 angle pdb=" CG1 VAL D 269 " pdb=" CB VAL D 269 " pdb=" CG2 VAL D 269 " ideal model delta sigma weight residual 110.80 122.00 -11.20 2.20e+00 2.07e-01 2.59e+01 angle pdb=" N VAL C 279 " pdb=" CA VAL C 279 " pdb=" C VAL C 279 " ideal model delta sigma weight residual 113.71 108.99 4.72 9.50e-01 1.11e+00 2.47e+01 angle pdb=" C3B FAD D 401 " pdb=" C2B FAD D 401 " pdb=" O2B FAD D 401 " ideal model delta sigma weight residual 111.62 126.23 -14.61 3.00e+00 1.11e-01 2.37e+01 ... (remaining 16575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.86: 6968 28.86 - 57.72: 397 57.72 - 86.58: 54 86.58 - 115.44: 8 115.44 - 144.30: 1 Dihedral angle restraints: 7428 sinusoidal: 3064 harmonic: 4364 Sorted by residual: dihedral pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA VAL D 187 " pdb=" C VAL D 187 " pdb=" N PRO D 188 " pdb=" CA PRO D 188 " ideal model delta harmonic sigma weight residual 180.00 155.77 24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL A 187 " pdb=" C VAL A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 7425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 1800 0.346 - 0.693: 0 0.693 - 1.039: 0 1.039 - 1.385: 0 1.385 - 1.732: 4 Chirality restraints: 1804 Sorted by residual: chirality pdb=" CG LEU B 247 " pdb=" CB LEU B 247 " pdb=" CD1 LEU B 247 " pdb=" CD2 LEU B 247 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.50e+01 chirality pdb=" CG LEU D 370 " pdb=" CB LEU D 370 " pdb=" CD1 LEU D 370 " pdb=" CD2 LEU D 370 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.31e+01 chirality pdb=" C2B FAD D 401 " pdb=" C1B FAD D 401 " pdb=" C3B FAD D 401 " pdb=" O2B FAD D 401 " both_signs ideal model delta sigma weight residual False -2.53 -0.87 -1.67 2.00e-01 2.50e+01 6.95e+01 ... (remaining 1801 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 187 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO D 188 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 188 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 188 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 187 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 188 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 401 " 0.009 2.00e-02 2.50e+03 8.93e-03 3.79e+00 pdb=" C10 FAD C 401 " 0.007 2.00e-02 2.50e+03 pdb=" C2 FAD C 401 " -0.004 2.00e-02 2.50e+03 pdb=" C4 FAD C 401 " -0.000 2.00e-02 2.50e+03 pdb=" C4X FAD C 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5X FAD C 401 " 0.006 2.00e-02 2.50e+03 pdb=" C6 FAD C 401 " -0.002 2.00e-02 2.50e+03 pdb=" C7 FAD C 401 " -0.004 2.00e-02 2.50e+03 pdb=" C7M FAD C 401 " 0.011 2.00e-02 2.50e+03 pdb=" C8 FAD C 401 " -0.011 2.00e-02 2.50e+03 pdb=" C8M FAD C 401 " -0.016 2.00e-02 2.50e+03 pdb=" C9 FAD C 401 " -0.005 2.00e-02 2.50e+03 pdb=" C9A FAD C 401 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FAD C 401 " -0.005 2.00e-02 2.50e+03 pdb=" N10 FAD C 401 " 0.020 2.00e-02 2.50e+03 pdb=" N3 FAD C 401 " -0.013 2.00e-02 2.50e+03 pdb=" N5 FAD C 401 " -0.003 2.00e-02 2.50e+03 pdb=" O2 FAD C 401 " -0.008 2.00e-02 2.50e+03 pdb=" O4 FAD C 401 " 0.006 2.00e-02 2.50e+03 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 96 2.60 - 3.17: 10115 3.17 - 3.75: 19243 3.75 - 4.32: 29001 4.32 - 4.90: 47072 Nonbonded interactions: 105527 Sorted by model distance: nonbonded pdb=" OE1 GLU C 84 " pdb=" OH TYR C 312 " model vdw 2.021 3.040 nonbonded pdb=" O GLN C 348 " pdb=" O3B FAD D 401 " model vdw 2.055 3.040 nonbonded pdb=" O ARG C 366 " pdb=" OH TYR D 355 " model vdw 2.084 3.040 nonbonded pdb=" OE1 GLU B 84 " pdb=" OH TYR B 312 " model vdw 2.155 3.040 nonbonded pdb=" O SER D 190 " pdb=" CG2 VAL D 244 " model vdw 2.155 3.460 ... (remaining 105522 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 82.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.150 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:21.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 12280 Z= 0.275 Angle : 0.872 51.512 16588 Z= 0.450 Chirality : 0.087 1.732 1804 Planarity : 0.003 0.059 2132 Dihedral : 17.529 144.305 4656 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 0.97 % Favored : 98.96 % Rotamer: Outliers : 0.65 % Allowed : 17.05 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.05 (0.19), residues: 1540 helix: -0.74 (0.17), residues: 816 sheet: -1.33 (0.39), residues: 132 loop : -2.14 (0.20), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 52 HIS 0.003 0.001 HIS A 100 PHE 0.006 0.000 PHE D 165 TYR 0.004 0.000 TYR C 97 ARG 0.001 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.16631 ( 670) hydrogen bonds : angle 6.54159 ( 1923) SS BOND : bond 0.11018 ( 4) SS BOND : angle 18.45923 ( 8) covalent geometry : bond 0.00471 (12276) covalent geometry : angle 0.77200 (16580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 263 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6139 (pp-130) outliers start: 8 outliers final: 3 residues processed: 267 average time/residue: 1.4093 time to fit residues: 404.1239 Evaluate side-chains 192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 278 HIS A 294 GLN A 348 GLN B 11 ASN B 19 GLN B 37 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN B 102 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 241 ASN B 278 HIS B 309 GLN B 357 ASN C 22 GLN C 37 GLN C 107 GLN C 169 ASN C 241 ASN C 278 HIS C 294 GLN C 357 ASN D 11 ASN D 47 ASN D 57 ASN D 68 GLN D 102 ASN D 107 GLN D 139 ASN D 169 ASN D 241 ASN D 348 GLN D 357 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120604 restraints weight = 13236.780| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.58 r_work: 0.3276 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12280 Z= 0.173 Angle : 0.611 8.320 16588 Z= 0.314 Chirality : 0.045 0.340 1804 Planarity : 0.004 0.049 2132 Dihedral : 9.801 140.956 1868 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 3.98 % Allowed : 17.78 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1540 helix: 0.43 (0.18), residues: 836 sheet: -0.73 (0.34), residues: 188 loop : -1.70 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 166 HIS 0.006 0.001 HIS C 157 PHE 0.011 0.001 PHE C 165 TYR 0.017 0.002 TYR D 69 ARG 0.006 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 670) hydrogen bonds : angle 4.81216 ( 1923) SS BOND : bond 0.00556 ( 4) SS BOND : angle 1.49073 ( 8) covalent geometry : bond 0.00400 (12276) covalent geometry : angle 0.61050 (16580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8067 (tp) cc_final: 0.7788 (tm) REVERT: A 135 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5544 (pp-130) REVERT: A 227 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 249 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 382 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8392 (mtt180) REVERT: C 18 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7675 (mtt90) REVERT: C 165 PHE cc_start: 0.7476 (m-80) cc_final: 0.7264 (m-80) REVERT: C 208 SER cc_start: 0.8594 (m) cc_final: 0.8126 (p) REVERT: C 230 LYS cc_start: 0.8223 (tttt) cc_final: 0.7833 (tttm) REVERT: D 53 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6599 (mttt) REVERT: D 367 ASP cc_start: 0.8358 (m-30) cc_final: 0.8035 (m-30) outliers start: 49 outliers final: 21 residues processed: 230 average time/residue: 1.3740 time to fit residues: 342.5296 Evaluate side-chains 199 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 7.9990 chunk 89 optimal weight: 0.0270 chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS A 241 ASN A 278 HIS B 19 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN B 156 ASN C 19 GLN C 37 GLN C 163 ASN C 294 GLN D 57 ASN D 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122495 restraints weight = 13460.445| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.57 r_work: 0.3308 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12280 Z= 0.119 Angle : 0.528 7.605 16588 Z= 0.271 Chirality : 0.041 0.274 1804 Planarity : 0.004 0.041 2132 Dihedral : 9.378 144.068 1868 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 3.08 % Allowed : 18.99 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1540 helix: 1.00 (0.18), residues: 836 sheet: -0.66 (0.38), residues: 140 loop : -1.38 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 166 HIS 0.003 0.001 HIS A 322 PHE 0.010 0.001 PHE D 226 TYR 0.007 0.001 TYR D 129 ARG 0.005 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 670) hydrogen bonds : angle 4.50877 ( 1923) SS BOND : bond 0.00571 ( 4) SS BOND : angle 2.13922 ( 8) covalent geometry : bond 0.00267 (12276) covalent geometry : angle 0.52584 (16580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.5492 (pp-130) REVERT: A 154 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6954 (mmtm) REVERT: A 157 HIS cc_start: 0.6816 (m90) cc_final: 0.6190 (m-70) REVERT: A 249 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 300 MET cc_start: 0.8652 (mtp) cc_final: 0.8354 (mtm) REVERT: A 382 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8341 (mtt90) REVERT: B 19 GLN cc_start: 0.7504 (mt0) cc_final: 0.6611 (mp-120) REVERT: B 157 HIS cc_start: 0.7007 (p90) cc_final: 0.6455 (p-80) REVERT: C 165 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: C 208 SER cc_start: 0.8599 (m) cc_final: 0.8175 (p) REVERT: C 230 LYS cc_start: 0.8285 (tttt) cc_final: 0.7884 (tttp) REVERT: C 269 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8568 (t) REVERT: C 348 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8650 (tp40) REVERT: D 7 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: D 22 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: D 53 LYS cc_start: 0.7186 (mtmm) cc_final: 0.6768 (mttt) REVERT: D 367 ASP cc_start: 0.8424 (m-30) cc_final: 0.7756 (m-30) outliers start: 38 outliers final: 12 residues processed: 206 average time/residue: 1.4314 time to fit residues: 317.5109 Evaluate side-chains 193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 278 HIS A 390 ASN B 43 ASN C 19 GLN C 37 GLN C 57 ASN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119499 restraints weight = 13318.964| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.56 r_work: 0.3274 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12280 Z= 0.143 Angle : 0.543 7.809 16588 Z= 0.280 Chirality : 0.042 0.286 1804 Planarity : 0.004 0.044 2132 Dihedral : 9.103 145.308 1866 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 3.98 % Allowed : 18.67 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1540 helix: 1.18 (0.18), residues: 840 sheet: -0.54 (0.36), residues: 140 loop : -1.22 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 166 HIS 0.007 0.001 HIS A 239 PHE 0.008 0.001 PHE D 226 TYR 0.009 0.001 TYR C 76 ARG 0.005 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 670) hydrogen bonds : angle 4.44293 ( 1923) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.96804 ( 8) covalent geometry : bond 0.00332 (12276) covalent geometry : angle 0.54132 (16580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5493 (pp-130) REVERT: A 154 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7089 (mmtm) REVERT: A 157 HIS cc_start: 0.6864 (m90) cc_final: 0.6416 (m-70) REVERT: A 227 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 249 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 300 MET cc_start: 0.8816 (mtp) cc_final: 0.8512 (mtm) REVERT: A 382 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8368 (mtt90) REVERT: B 19 GLN cc_start: 0.7462 (mt0) cc_final: 0.6575 (mp-120) REVERT: B 157 HIS cc_start: 0.7070 (p90) cc_final: 0.6567 (p-80) REVERT: C 165 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: C 208 SER cc_start: 0.8573 (m) cc_final: 0.8162 (p) REVERT: C 230 LYS cc_start: 0.8280 (tttt) cc_final: 0.7840 (tttp) REVERT: D 7 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: D 10 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7470 (mt) REVERT: D 21 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6170 (ttp-170) REVERT: D 53 LYS cc_start: 0.7245 (mtmm) cc_final: 0.6814 (mttt) REVERT: D 68 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.5872 (pm20) REVERT: D 337 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7598 (mp0) outliers start: 49 outliers final: 22 residues processed: 218 average time/residue: 1.3657 time to fit residues: 320.7001 Evaluate side-chains 207 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 278 HIS B 157 HIS C 19 GLN C 37 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 390 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122146 restraints weight = 13294.190| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.57 r_work: 0.3307 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12280 Z= 0.104 Angle : 0.500 7.576 16588 Z= 0.256 Chirality : 0.040 0.288 1804 Planarity : 0.004 0.042 2132 Dihedral : 8.908 143.657 1865 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 3.08 % Allowed : 19.97 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1540 helix: 1.49 (0.18), residues: 840 sheet: -0.39 (0.37), residues: 140 loop : -1.04 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.004 0.001 HIS A 239 PHE 0.007 0.001 PHE D 226 TYR 0.006 0.001 TYR A 76 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 670) hydrogen bonds : angle 4.24345 ( 1923) SS BOND : bond 0.00338 ( 4) SS BOND : angle 2.05094 ( 8) covalent geometry : bond 0.00227 (12276) covalent geometry : angle 0.49781 (16580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7204 (mm-40) REVERT: A 133 LEU cc_start: 0.7841 (tp) cc_final: 0.7552 (tm) REVERT: A 135 MET cc_start: 0.6815 (ptm) cc_final: 0.5458 (pp-130) REVERT: A 154 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7104 (mmtm) REVERT: A 157 HIS cc_start: 0.6876 (m90) cc_final: 0.6286 (m-70) REVERT: A 227 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 249 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 300 MET cc_start: 0.8700 (mtp) cc_final: 0.8411 (mtm) REVERT: A 382 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8338 (mtt180) REVERT: B 19 GLN cc_start: 0.7446 (mt0) cc_final: 0.6556 (mp-120) REVERT: B 157 HIS cc_start: 0.6994 (p-80) cc_final: 0.6596 (p90) REVERT: C 47 ASN cc_start: 0.8207 (m-40) cc_final: 0.7884 (t0) REVERT: C 165 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: C 208 SER cc_start: 0.8603 (m) cc_final: 0.8210 (p) REVERT: C 230 LYS cc_start: 0.8245 (tttt) cc_final: 0.7802 (tttp) REVERT: C 348 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8566 (tp40) REVERT: D 16 GLU cc_start: 0.7386 (mp0) cc_final: 0.6831 (mm-30) REVERT: D 21 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6027 (ttp-170) REVERT: D 50 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: D 53 LYS cc_start: 0.7202 (mtmm) cc_final: 0.6783 (mttt) REVERT: D 68 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.5905 (pm20) REVERT: D 165 PHE cc_start: 0.5030 (OUTLIER) cc_final: 0.4812 (t80) REVERT: D 337 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7543 (mp0) outliers start: 38 outliers final: 16 residues processed: 210 average time/residue: 1.4164 time to fit residues: 320.1748 Evaluate side-chains 201 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 278 HIS C 37 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN D 107 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118408 restraints weight = 13427.828| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.58 r_work: 0.3256 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12280 Z= 0.160 Angle : 0.560 7.861 16588 Z= 0.288 Chirality : 0.043 0.297 1804 Planarity : 0.004 0.045 2132 Dihedral : 8.865 143.421 1862 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 3.25 % Allowed : 19.72 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1540 helix: 1.40 (0.18), residues: 840 sheet: -0.33 (0.37), residues: 140 loop : -1.02 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 166 HIS 0.004 0.001 HIS A 272 PHE 0.007 0.001 PHE D 27 TYR 0.012 0.001 TYR B 334 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 670) hydrogen bonds : angle 4.36810 ( 1923) SS BOND : bond 0.00656 ( 4) SS BOND : angle 2.81568 ( 8) covalent geometry : bond 0.00376 (12276) covalent geometry : angle 0.55713 (16580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.6802 (ptm) cc_final: 0.5439 (pp-130) REVERT: A 154 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7145 (mmtm) REVERT: A 157 HIS cc_start: 0.6873 (m90) cc_final: 0.6423 (m-70) REVERT: A 227 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 249 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7892 (p) REVERT: A 300 MET cc_start: 0.8838 (mtp) cc_final: 0.8535 (mtm) REVERT: A 382 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8389 (mtt90) REVERT: B 19 GLN cc_start: 0.7480 (mt0) cc_final: 0.6609 (mp-120) REVERT: C 18 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7825 (mtt90) REVERT: C 165 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 208 SER cc_start: 0.8618 (m) cc_final: 0.8242 (p) REVERT: C 230 LYS cc_start: 0.8234 (tttt) cc_final: 0.7788 (tttp) REVERT: C 271 ASP cc_start: 0.8777 (m-30) cc_final: 0.8550 (m-30) REVERT: D 21 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6172 (ttp-170) REVERT: D 24 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: D 53 LYS cc_start: 0.7248 (mtmm) cc_final: 0.6854 (mttt) REVERT: D 68 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: D 337 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7604 (mp0) outliers start: 40 outliers final: 24 residues processed: 208 average time/residue: 1.4145 time to fit residues: 316.4872 Evaluate side-chains 199 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 278 HIS C 37 GLN ** C 157 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 = 0.3679 r_free = 0.3679 target = 0.144922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118697 restraints weight = 13363.263| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.57 r_work: 0.3261 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12280 Z= 0.151 Angle : 0.559 7.865 16588 Z= 0.286 Chirality : 0.042 0.295 1804 Planarity : 0.004 0.044 2132 Dihedral : 8.826 143.012 1862 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 3.33 % Allowed : 20.13 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1540 helix: 1.44 (0.18), residues: 840 sheet: -0.29 (0.37), residues: 140 loop : -0.98 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 166 HIS 0.003 0.001 HIS A 239 PHE 0.006 0.001 PHE D 226 TYR 0.010 0.001 TYR C 76 ARG 0.005 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 670) hydrogen bonds : angle 4.35929 ( 1923) SS BOND : bond 0.00669 ( 4) SS BOND : angle 3.21807 ( 8) covalent geometry : bond 0.00355 (12276) covalent geometry : angle 0.55478 (16580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7957 (tp) cc_final: 0.7695 (tm) REVERT: A 135 MET cc_start: 0.6813 (ptm) cc_final: 0.5451 (pp-130) REVERT: A 147 MET cc_start: 0.7438 (ptp) cc_final: 0.7148 (ptp) REVERT: A 154 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7209 (mmtm) REVERT: A 157 HIS cc_start: 0.6880 (m90) cc_final: 0.6443 (m-70) REVERT: A 227 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 249 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7955 (p) REVERT: A 300 MET cc_start: 0.8848 (mtp) cc_final: 0.8552 (mtm) REVERT: A 382 ARG cc_start: 0.8675 (mtm-85) cc_final: 0.8340 (mtt90) REVERT: B 19 GLN cc_start: 0.7486 (mt0) cc_final: 0.6656 (mp-120) REVERT: B 20 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8109 (tp) REVERT: B 157 HIS cc_start: 0.7181 (p90) cc_final: 0.6853 (p-80) REVERT: C 47 ASN cc_start: 0.8236 (m-40) cc_final: 0.7955 (t0) REVERT: C 165 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: C 208 SER cc_start: 0.8582 (m) cc_final: 0.8206 (p) REVERT: C 230 LYS cc_start: 0.8239 (tttt) cc_final: 0.7796 (tttp) REVERT: C 271 ASP cc_start: 0.8747 (m-30) cc_final: 0.8511 (m-30) REVERT: D 21 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6134 (ttp-170) REVERT: D 24 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8298 (mmm) REVERT: D 53 LYS cc_start: 0.7248 (mtmm) cc_final: 0.6842 (mttt) REVERT: D 68 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: D 253 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7627 (mm) REVERT: D 337 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7606 (mp0) outliers start: 41 outliers final: 23 residues processed: 200 average time/residue: 1.4316 time to fit residues: 308.4577 Evaluate side-chains 198 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 120 optimal weight: 0.0870 chunk 44 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 157 HIS C 37 GLN ** C 157 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 = 0.3683 r_free = 0.3683 target = 0.145325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119039 restraints weight = 13456.949| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.58 r_work: 0.3267 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12280 Z= 0.136 Angle : 0.549 7.819 16588 Z= 0.280 Chirality : 0.041 0.281 1804 Planarity : 0.004 0.044 2132 Dihedral : 8.762 141.949 1862 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.84 % Allowed : 20.86 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1540 helix: 1.54 (0.18), residues: 840 sheet: -0.22 (0.38), residues: 140 loop : -0.92 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 166 HIS 0.003 0.001 HIS A 322 PHE 0.006 0.001 PHE D 226 TYR 0.009 0.001 TYR C 76 ARG 0.003 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 670) hydrogen bonds : angle 4.30253 ( 1923) SS BOND : bond 0.00642 ( 4) SS BOND : angle 2.42397 ( 8) covalent geometry : bond 0.00318 (12276) covalent geometry : angle 0.54644 (16580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7900 (tp) cc_final: 0.7624 (tm) REVERT: A 135 MET cc_start: 0.6882 (ptm) cc_final: 0.5557 (pp-130) REVERT: A 147 MET cc_start: 0.7511 (ptp) cc_final: 0.7188 (ptp) REVERT: A 154 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7201 (mmtm) REVERT: A 157 HIS cc_start: 0.6897 (m90) cc_final: 0.6324 (m-70) REVERT: A 227 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 249 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7887 (p) REVERT: A 300 MET cc_start: 0.8841 (mtp) cc_final: 0.8550 (mtm) REVERT: A 382 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8337 (mtt90) REVERT: B 19 GLN cc_start: 0.7395 (mt0) cc_final: 0.6569 (mp10) REVERT: B 157 HIS cc_start: 0.7055 (p-80) cc_final: 0.6791 (p-80) REVERT: C 47 ASN cc_start: 0.8236 (m-40) cc_final: 0.7954 (t0) REVERT: C 135 MET cc_start: 0.6600 (pp-130) cc_final: 0.6369 (tmm) REVERT: C 165 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: C 208 SER cc_start: 0.8560 (m) cc_final: 0.8188 (p) REVERT: C 230 LYS cc_start: 0.8265 (tttt) cc_final: 0.8044 (tmtp) REVERT: C 271 ASP cc_start: 0.8725 (m-30) cc_final: 0.8418 (m-30) REVERT: D 21 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6144 (ttp-170) REVERT: D 24 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (mmm) REVERT: D 53 LYS cc_start: 0.7248 (mtmm) cc_final: 0.6847 (mttt) REVERT: D 68 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.5934 (pm20) REVERT: D 110 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7475 (ttp80) REVERT: D 337 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7599 (mp0) outliers start: 35 outliers final: 24 residues processed: 196 average time/residue: 1.4333 time to fit residues: 302.1063 Evaluate side-chains 196 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN C 37 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116735 restraints weight = 13367.184| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.57 r_work: 0.3236 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12280 Z= 0.187 Angle : 0.596 8.454 16588 Z= 0.305 Chirality : 0.044 0.313 1804 Planarity : 0.004 0.046 2132 Dihedral : 8.878 141.978 1862 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.92 % Allowed : 20.78 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1540 helix: 1.38 (0.18), residues: 840 sheet: -0.17 (0.38), residues: 140 loop : -0.94 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 166 HIS 0.004 0.001 HIS A 272 PHE 0.008 0.001 PHE D 27 TYR 0.014 0.002 TYR C 76 ARG 0.003 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 670) hydrogen bonds : angle 4.43639 ( 1923) SS BOND : bond 0.00826 ( 4) SS BOND : angle 2.60158 ( 8) covalent geometry : bond 0.00447 (12276) covalent geometry : angle 0.59379 (16580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5433 (pp-130) REVERT: A 147 MET cc_start: 0.7520 (ptp) cc_final: 0.7235 (ptp) REVERT: A 154 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7213 (mmtm) REVERT: A 157 HIS cc_start: 0.6895 (m90) cc_final: 0.6424 (m-70) REVERT: A 227 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 249 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7899 (p) REVERT: B 19 GLN cc_start: 0.7524 (mt0) cc_final: 0.6619 (mp-120) REVERT: B 152 GLU cc_start: 0.7500 (pt0) cc_final: 0.7279 (pt0) REVERT: C 107 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8357 (tp-100) REVERT: C 165 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: C 208 SER cc_start: 0.8631 (m) cc_final: 0.8255 (p) REVERT: C 230 LYS cc_start: 0.8230 (tttt) cc_final: 0.7796 (tttm) REVERT: D 21 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6249 (ttp-170) REVERT: D 24 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (mmm) REVERT: D 53 LYS cc_start: 0.7289 (mtmm) cc_final: 0.6884 (mttt) REVERT: D 68 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.5898 (pm20) REVERT: D 110 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7491 (ttp80) REVERT: D 147 MET cc_start: 0.6584 (ptp) cc_final: 0.6080 (ptm) REVERT: D 152 GLU cc_start: 0.5636 (mm-30) cc_final: 0.5251 (pt0) REVERT: D 337 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7678 (mp0) outliers start: 36 outliers final: 22 residues processed: 197 average time/residue: 1.4552 time to fit residues: 308.0206 Evaluate side-chains 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 157 HIS C 37 GLN ** C 157 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 = 0.3686 r_free = 0.3686 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119685 restraints weight = 13393.463| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.57 r_work: 0.3269 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12280 Z= 0.128 Angle : 0.549 8.135 16588 Z= 0.278 Chirality : 0.041 0.294 1804 Planarity : 0.004 0.044 2132 Dihedral : 8.734 141.000 1862 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 21.10 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1540 helix: 1.54 (0.18), residues: 840 sheet: -0.12 (0.38), residues: 140 loop : -0.89 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 166 HIS 0.005 0.001 HIS D 322 PHE 0.006 0.001 PHE D 226 TYR 0.009 0.001 TYR C 76 ARG 0.002 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 670) hydrogen bonds : angle 4.28842 ( 1923) SS BOND : bond 0.00504 ( 4) SS BOND : angle 2.57701 ( 8) covalent geometry : bond 0.00295 (12276) covalent geometry : angle 0.54572 (16580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7905 (tp) cc_final: 0.7641 (tm) REVERT: A 135 MET cc_start: 0.6845 (ptm) cc_final: 0.5402 (pp-130) REVERT: A 147 MET cc_start: 0.7488 (ptp) cc_final: 0.7245 (ptp) REVERT: A 154 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7187 (mmtm) REVERT: A 157 HIS cc_start: 0.6863 (m90) cc_final: 0.6293 (m-70) REVERT: A 227 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 249 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.7937 (p) REVERT: A 382 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8320 (mtt90) REVERT: B 19 GLN cc_start: 0.7595 (mt0) cc_final: 0.7058 (tm-30) REVERT: B 152 GLU cc_start: 0.7473 (pt0) cc_final: 0.7174 (pt0) REVERT: C 47 ASN cc_start: 0.8234 (m-40) cc_final: 0.7956 (t0) REVERT: C 165 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: C 184 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.4877 (pt) REVERT: C 208 SER cc_start: 0.8554 (m) cc_final: 0.8171 (p) REVERT: C 230 LYS cc_start: 0.8243 (tttt) cc_final: 0.8028 (tmtp) REVERT: D 16 GLU cc_start: 0.7394 (mp0) cc_final: 0.6852 (mm-30) REVERT: D 21 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6167 (ttp-170) REVERT: D 24 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: D 53 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6822 (mppt) REVERT: D 68 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.5975 (pm20) REVERT: D 110 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7522 (ttp80) REVERT: D 147 MET cc_start: 0.6633 (ptp) cc_final: 0.6144 (ptm) REVERT: D 337 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7612 (mp0) outliers start: 32 outliers final: 20 residues processed: 197 average time/residue: 1.4251 time to fit residues: 302.1978 Evaluate side-chains 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 157 HIS C 37 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121958 restraints weight = 13443.502| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.58 r_work: 0.3303 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12280 Z= 0.104 Angle : 0.513 7.473 16588 Z= 0.260 Chirality : 0.039 0.267 1804 Planarity : 0.004 0.042 2132 Dihedral : 8.532 138.795 1862 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 21.92 % Favored : 76.06 % 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: 1.09 (0.21), residues: 1540 helix: 1.80 (0.18), residues: 844 sheet: -0.06 (0.38), residues: 140 loop : -0.73 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.003 0.001 HIS A 272 PHE 0.006 0.001 PHE D 226 TYR 0.008 0.001 TYR D 129 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 670) hydrogen bonds : angle 4.11334 ( 1923) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.88004 ( 8) covalent geometry : bond 0.00236 (12276) covalent geometry : angle 0.51172 (16580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10041.63 seconds wall clock time: 172 minutes 13.98 seconds (10333.98 seconds total)