Starting phenix.real_space_refine on Wed Sep 17 22:40:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq3_61721/09_2025/9jq3_61721_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq3_61721/09_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_61721/09_2025/9jq3_61721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq3_61721/09_2025/9jq3_61721.map" model { file = "/net/cci-nas-00/data/ceres_data/9jq3_61721/09_2025/9jq3_61721_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq3_61721/09_2025/9jq3_61721_trim.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.13, per 1000 atoms: 0.26 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: 1.06 Conformation dependent library (CDL) restraints added in 585.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 2.03 Time building geometry restraints manager: 1.41 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: 0.01 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.19), 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 ARG 0.001 0.000 ARG B 366 TYR 0.004 0.000 TYR C 97 PHE 0.006 0.000 PHE D 165 TRP 0.002 0.000 TRP A 52 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00471 (12276) covalent geometry : angle 0.77200 (16580) SS BOND : bond 0.11018 ( 4) SS BOND : angle 18.45923 ( 8) hydrogen bonds : bond 0.16631 ( 670) hydrogen bonds : angle 6.54159 ( 1923) *********************** 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 : 0.490 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: 0.7290 time to fit residues: 208.4610 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 : 0.476 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.146087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119607 restraints weight = 13328.598| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.58 r_work: 0.3263 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2366 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= 0.191 Angle : 0.617 8.081 16588 Z= 0.319 Chirality : 0.046 0.353 1804 Planarity : 0.004 0.049 2132 Dihedral : 9.834 141.488 1868 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 4.22 % Allowed : 17.69 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1540 helix: 0.36 (0.18), residues: 836 sheet: -0.86 (0.38), residues: 140 loop : -1.64 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 18 TYR 0.012 0.002 TYR D 69 PHE 0.011 0.001 PHE D 27 TRP 0.015 0.002 TRP C 166 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00447 (12276) covalent geometry : angle 0.61658 (16580) SS BOND : bond 0.00907 ( 4) SS BOND : angle 1.65110 ( 8) hydrogen bonds : bond 0.05385 ( 670) hydrogen bonds : angle 4.87378 ( 1923) *********************** 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 244 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8103 (tp) cc_final: 0.7808 (tm) REVERT: A 135 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.5526 (pp-130) REVERT: A 227 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 249 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7955 (p) REVERT: A 382 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8402 (mtt180) REVERT: C 18 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7687 (mtt90) REVERT: C 165 PHE cc_start: 0.7521 (m-80) cc_final: 0.7298 (m-80) REVERT: C 208 SER cc_start: 0.8592 (m) cc_final: 0.8122 (p) REVERT: C 230 LYS cc_start: 0.8253 (tttt) cc_final: 0.7848 (tttm) REVERT: D 22 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: D 53 LYS cc_start: 0.7179 (mtmm) cc_final: 0.6624 (mttt) REVERT: D 367 ASP cc_start: 0.8330 (m-30) cc_final: 0.8015 (m-30) outliers start: 52 outliers final: 21 residues processed: 229 average time/residue: 0.6151 time to fit residues: 152.1404 Evaluate side-chains 196 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 22 GLN 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 54 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 A 390 ASN B 19 GLN B 43 ASN B 106 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 37 GLN C 163 ASN D 54 GLN D 57 ASN D 390 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117973 restraints weight = 13555.337| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.57 r_work: 0.3253 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12280 Z= 0.174 Angle : 0.583 8.220 16588 Z= 0.301 Chirality : 0.044 0.315 1804 Planarity : 0.004 0.043 2132 Dihedral : 9.478 145.719 1868 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 4.06 % Allowed : 18.26 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.20), residues: 1540 helix: 0.79 (0.18), residues: 840 sheet: -0.63 (0.37), residues: 140 loop : -1.42 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.011 0.001 TYR C 76 PHE 0.011 0.001 PHE D 226 TRP 0.014 0.002 TRP A 166 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00409 (12276) covalent geometry : angle 0.58082 (16580) SS BOND : bond 0.00668 ( 4) SS BOND : angle 2.14220 ( 8) hydrogen bonds : bond 0.05067 ( 670) hydrogen bonds : angle 4.66817 ( 1923) *********************** 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 230 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.5529 (pp-130) REVERT: A 154 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7081 (mmtm) REVERT: A 157 HIS cc_start: 0.6832 (m90) cc_final: 0.6397 (m-70) REVERT: A 227 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 249 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 382 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8372 (mtt90) REVERT: B 19 GLN cc_start: 0.7526 (mt0) cc_final: 0.6650 (mp-120) REVERT: B 157 HIS cc_start: 0.7074 (p90) cc_final: 0.6665 (p90) REVERT: C 165 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: C 208 SER cc_start: 0.8581 (m) cc_final: 0.8168 (p) REVERT: C 230 LYS cc_start: 0.8279 (tttt) cc_final: 0.7856 (tttm) REVERT: D 10 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7547 (mt) REVERT: D 21 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.5968 (ttp-170) REVERT: D 53 LYS cc_start: 0.7263 (mtmm) cc_final: 0.6821 (mttt) REVERT: D 54 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: D 337 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: D 367 ASP cc_start: 0.8423 (m-30) cc_final: 0.7853 (m-30) outliers start: 50 outliers final: 22 residues processed: 215 average time/residue: 0.6526 time to fit residues: 151.3346 Evaluate side-chains 199 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 A residue 269 VAL Chi-restraints excluded: chain A residue 287 ILE 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 193 ILE Chi-restraints excluded: chain B residue 230 LYS 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 237 LEU Chi-restraints excluded: chain C residue 269 VAL 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 54 GLN 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 337 GLU 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 69 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118291 restraints weight = 13453.534| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.57 r_work: 0.3259 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12280 Z= 0.150 Angle : 0.551 8.472 16588 Z= 0.285 Chirality : 0.042 0.302 1804 Planarity : 0.004 0.044 2132 Dihedral : 9.261 146.649 1868 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 3.98 % Allowed : 18.91 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.20), residues: 1540 helix: 1.07 (0.18), residues: 840 sheet: -0.54 (0.37), residues: 140 loop : -1.27 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.010 0.001 TYR C 76 PHE 0.008 0.001 PHE D 226 TRP 0.013 0.001 TRP A 166 HIS 0.004 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00351 (12276) covalent geometry : angle 0.54966 (16580) SS BOND : bond 0.00683 ( 4) SS BOND : angle 1.71554 ( 8) hydrogen bonds : bond 0.04664 ( 670) hydrogen bonds : angle 4.51206 ( 1923) *********************** 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 224 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7102 (mmtm) REVERT: A 157 HIS cc_start: 0.6830 (m90) cc_final: 0.6391 (m-70) REVERT: A 227 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 249 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7904 (p) REVERT: A 271 ASP cc_start: 0.8681 (m-30) cc_final: 0.8479 (m-30) REVERT: A 382 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8346 (mtt90) REVERT: B 19 GLN cc_start: 0.7529 (mt0) cc_final: 0.6659 (mp-120) REVERT: B 152 GLU cc_start: 0.7500 (pt0) cc_final: 0.7265 (pt0) REVERT: B 157 HIS cc_start: 0.7099 (p90) cc_final: 0.6705 (p-80) REVERT: C 18 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7785 (mtt90) REVERT: C 165 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: C 208 SER cc_start: 0.8590 (m) cc_final: 0.8193 (p) REVERT: C 230 LYS cc_start: 0.8290 (tttt) cc_final: 0.7837 (tttp) REVERT: D 21 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.6145 (ttp-170) REVERT: D 53 LYS cc_start: 0.7183 (mtmm) cc_final: 0.6817 (mttt) REVERT: D 147 MET cc_start: 0.6772 (mtt) cc_final: 0.6369 (mtt) REVERT: D 337 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7593 (mp0) outliers start: 49 outliers final: 24 residues processed: 210 average time/residue: 0.6760 time to fit residues: 152.6203 Evaluate side-chains 200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 237 LEU Chi-restraints excluded: chain C residue 269 VAL 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 172 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 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 84 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.144847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118585 restraints weight = 13474.260| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.58 r_work: 0.3263 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12280 Z= 0.138 Angle : 0.538 8.490 16588 Z= 0.277 Chirality : 0.042 0.315 1804 Planarity : 0.004 0.044 2132 Dihedral : 9.036 145.918 1865 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 3.17 % Allowed : 20.13 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.20), residues: 1540 helix: 1.26 (0.18), residues: 840 sheet: -0.43 (0.37), residues: 140 loop : -1.15 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.010 0.001 TYR C 76 PHE 0.007 0.001 PHE D 226 TRP 0.012 0.001 TRP A 166 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00321 (12276) covalent geometry : angle 0.53746 (16580) SS BOND : bond 0.00466 ( 4) SS BOND : angle 1.43033 ( 8) hydrogen bonds : bond 0.04384 ( 670) hydrogen bonds : angle 4.40747 ( 1923) *********************** 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 215 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7111 (mmtm) REVERT: A 157 HIS cc_start: 0.6863 (m90) cc_final: 0.6413 (m-70) REVERT: A 227 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 249 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 271 ASP cc_start: 0.8695 (m-30) cc_final: 0.8473 (m-30) REVERT: A 300 MET cc_start: 0.8896 (mtp) cc_final: 0.8532 (mtm) REVERT: A 382 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8335 (mtt90) REVERT: B 19 GLN cc_start: 0.7522 (mt0) cc_final: 0.6640 (mp-120) REVERT: B 152 GLU cc_start: 0.7498 (pt0) cc_final: 0.7293 (pt0) REVERT: C 18 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7799 (mtt90) REVERT: C 47 ASN cc_start: 0.8242 (m-40) cc_final: 0.7970 (t0) REVERT: C 165 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: C 208 SER cc_start: 0.8572 (m) cc_final: 0.8199 (p) REVERT: C 230 LYS cc_start: 0.8216 (tttt) cc_final: 0.7770 (tttm) REVERT: C 269 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8629 (t) REVERT: D 10 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7724 (mt) REVERT: D 21 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6104 (ttp-170) REVERT: D 53 LYS cc_start: 0.7239 (mtmm) cc_final: 0.6833 (mttt) REVERT: D 68 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.5925 (pm20) REVERT: D 150 LYS cc_start: 0.7970 (mttt) cc_final: 0.7315 (mptt) REVERT: D 337 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7640 (mp0) outliers start: 39 outliers final: 21 residues processed: 205 average time/residue: 0.6672 time to fit residues: 147.0378 Evaluate side-chains 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 269 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 28 LEU 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 244 VAL 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 49 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** C 163 ASN C 348 GLN D 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116567 restraints weight = 13438.711| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.57 r_work: 0.3236 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3125 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= 0.180 Angle : 0.580 8.773 16588 Z= 0.299 Chirality : 0.044 0.307 1804 Planarity : 0.004 0.046 2132 Dihedral : 8.983 145.579 1863 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 3.98 % Allowed : 19.40 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1540 helix: 1.22 (0.18), residues: 840 sheet: -0.38 (0.37), residues: 140 loop : -1.10 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.013 0.001 TYR C 76 PHE 0.007 0.001 PHE D 226 TRP 0.014 0.002 TRP A 166 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00426 (12276) covalent geometry : angle 0.57873 (16580) SS BOND : bond 0.00638 ( 4) SS BOND : angle 1.83160 ( 8) hydrogen bonds : bond 0.04978 ( 670) hydrogen bonds : angle 4.49114 ( 1923) *********************** 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 221 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8014 (tp) cc_final: 0.7776 (tm) REVERT: A 147 MET cc_start: 0.7513 (ptp) cc_final: 0.7225 (ptp) REVERT: A 154 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7162 (mmtm) REVERT: A 157 HIS cc_start: 0.6873 (m90) cc_final: 0.6424 (m-70) REVERT: A 227 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 249 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7928 (p) REVERT: A 271 ASP cc_start: 0.8717 (m-30) cc_final: 0.8433 (m-30) REVERT: A 382 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8337 (mtt90) REVERT: B 19 GLN cc_start: 0.7509 (mt0) cc_final: 0.6647 (mp-120) REVERT: B 20 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 152 GLU cc_start: 0.7540 (pt0) cc_final: 0.7273 (pt0) REVERT: C 165 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: C 208 SER cc_start: 0.8591 (m) cc_final: 0.8220 (p) REVERT: C 230 LYS cc_start: 0.8257 (tttt) cc_final: 0.7795 (tttm) REVERT: C 269 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8641 (t) REVERT: D 21 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6159 (ttp-170) REVERT: D 53 LYS cc_start: 0.7236 (mtmm) cc_final: 0.6835 (mttt) REVERT: D 68 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.5922 (pm20) REVERT: D 137 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5650 (tt0) REVERT: D 150 LYS cc_start: 0.7913 (mttt) cc_final: 0.7271 (mptt) REVERT: D 253 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7996 (mm) REVERT: D 337 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7667 (mp0) outliers start: 49 outliers final: 28 residues processed: 207 average time/residue: 0.6995 time to fit residues: 155.3962 Evaluate side-chains 206 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 16 GLU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 64 THR 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 269 VAL 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 137 GLU 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 269 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 32 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 124 optimal weight: 0.0570 chunk 9 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.144857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118557 restraints weight = 13459.068| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.58 r_work: 0.3264 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12280 Z= 0.134 Angle : 0.553 8.397 16588 Z= 0.283 Chirality : 0.041 0.281 1804 Planarity : 0.004 0.044 2132 Dihedral : 8.878 144.557 1863 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 3.81 % Allowed : 20.29 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.21), residues: 1540 helix: 1.39 (0.18), residues: 840 sheet: -0.32 (0.38), residues: 140 loop : -1.03 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.009 0.001 TYR C 76 PHE 0.006 0.001 PHE D 226 TRP 0.012 0.001 TRP A 166 HIS 0.007 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00312 (12276) covalent geometry : angle 0.54914 (16580) SS BOND : bond 0.00674 ( 4) SS BOND : angle 3.12554 ( 8) hydrogen bonds : bond 0.04236 ( 670) hydrogen bonds : angle 4.35476 ( 1923) *********************** 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 216 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7900 (tp) cc_final: 0.7655 (tm) REVERT: A 147 MET cc_start: 0.7505 (ptp) cc_final: 0.7190 (ptp) REVERT: A 154 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7183 (mmtm) REVERT: A 157 HIS cc_start: 0.6855 (m90) cc_final: 0.6403 (m-70) REVERT: A 227 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 249 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 382 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8323 (mtt90) REVERT: B 19 GLN cc_start: 0.7527 (mt0) cc_final: 0.6684 (mp-120) REVERT: B 152 GLU cc_start: 0.7488 (pt0) cc_final: 0.7225 (pt0) REVERT: B 157 HIS cc_start: 0.7122 (p-80) cc_final: 0.6772 (p-80) REVERT: C 47 ASN cc_start: 0.8240 (m-40) cc_final: 0.7967 (t0) REVERT: C 135 MET cc_start: 0.6635 (pp-130) cc_final: 0.6408 (tmm) REVERT: C 165 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: C 208 SER cc_start: 0.8577 (m) cc_final: 0.8209 (p) REVERT: C 230 LYS cc_start: 0.8236 (tttt) cc_final: 0.7784 (tttm) REVERT: D 21 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6118 (ttp-170) REVERT: D 53 LYS cc_start: 0.7245 (mtmm) cc_final: 0.6829 (mppt) REVERT: D 68 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.5931 (pm20) REVERT: D 137 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5519 (tt0) REVERT: D 324 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6789 (p) REVERT: D 337 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7598 (mp0) outliers start: 47 outliers final: 21 residues processed: 201 average time/residue: 0.6799 time to fit residues: 146.6735 Evaluate side-chains 194 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 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 28 LEU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 137 GLU 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 244 VAL Chi-restraints excluded: chain D residue 324 THR 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 22 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 51 optimal weight: 0.0470 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- 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 C 37 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118220 restraints weight = 13395.966| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.57 r_work: 0.3257 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12280 Z= 0.141 Angle : 0.557 8.280 16588 Z= 0.284 Chirality : 0.041 0.285 1804 Planarity : 0.004 0.045 2132 Dihedral : 8.830 143.470 1862 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 2.84 % Allowed : 21.35 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.21), residues: 1540 helix: 1.44 (0.18), residues: 840 sheet: -0.25 (0.38), residues: 140 loop : -0.97 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 18 TYR 0.011 0.001 TYR C 76 PHE 0.006 0.001 PHE D 226 TRP 0.012 0.001 TRP A 166 HIS 0.009 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00331 (12276) covalent geometry : angle 0.55361 (16580) SS BOND : bond 0.00581 ( 4) SS BOND : angle 2.74592 ( 8) hydrogen bonds : bond 0.04348 ( 670) hydrogen bonds : angle 4.33550 ( 1923) *********************** 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 202 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7930 (tp) cc_final: 0.7679 (tm) REVERT: A 147 MET cc_start: 0.7491 (ptp) cc_final: 0.7159 (ptp) REVERT: A 150 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7779 (mmtt) REVERT: A 154 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7169 (mmtm) REVERT: A 157 HIS cc_start: 0.6875 (m90) cc_final: 0.6427 (m-70) REVERT: A 227 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 249 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 271 ASP cc_start: 0.8591 (m-30) cc_final: 0.8124 (m-30) REVERT: A 382 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8336 (mtt90) REVERT: B 19 GLN cc_start: 0.7512 (mt0) cc_final: 0.6650 (mp-120) REVERT: B 150 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7824 (ptpp) REVERT: B 152 GLU cc_start: 0.7473 (pt0) cc_final: 0.7205 (pt0) REVERT: B 157 HIS cc_start: 0.7064 (p-80) cc_final: 0.6785 (p-80) REVERT: C 7 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8326 (OUTLIER) REVERT: C 165 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: C 208 SER cc_start: 0.8562 (m) cc_final: 0.8207 (p) REVERT: C 230 LYS cc_start: 0.8220 (tttt) cc_final: 0.7764 (tttm) REVERT: D 21 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6110 (ttp-170) REVERT: D 53 LYS cc_start: 0.7244 (mtmm) cc_final: 0.6823 (mppt) REVERT: D 68 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: D 137 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5569 (tt0) REVERT: D 337 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7604 (mp0) outliers start: 35 outliers final: 26 residues processed: 194 average time/residue: 0.7023 time to fit residues: 146.1369 Evaluate side-chains 200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 16 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 150 LYS 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 7 ASP 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 137 GLU 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 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 149 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115835 restraints weight = 13349.253| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.57 r_work: 0.3227 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12280 Z= 0.209 Angle : 0.624 9.122 16588 Z= 0.319 Chirality : 0.045 0.324 1804 Planarity : 0.004 0.046 2132 Dihedral : 8.970 143.589 1862 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 3.00 % Allowed : 21.10 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1540 helix: 1.23 (0.18), residues: 840 sheet: -0.24 (0.39), residues: 140 loop : -1.02 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.015 0.002 TYR C 76 PHE 0.008 0.001 PHE D 27 TRP 0.013 0.002 TRP A 166 HIS 0.010 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00501 (12276) covalent geometry : angle 0.62083 (16580) SS BOND : bond 0.00823 ( 4) SS BOND : angle 2.98583 ( 8) hydrogen bonds : bond 0.05255 ( 670) hydrogen bonds : angle 4.51314 ( 1923) *********************** 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 202 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7522 (ptp) cc_final: 0.7244 (ptp) REVERT: A 150 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7807 (mmtt) REVERT: A 157 HIS cc_start: 0.6892 (m90) cc_final: 0.6439 (m-70) REVERT: A 227 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 19 GLN cc_start: 0.7570 (mt0) cc_final: 0.6658 (mp-120) REVERT: B 150 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7869 (ptpp) REVERT: B 152 GLU cc_start: 0.7534 (pt0) cc_final: 0.7262 (pt0) REVERT: C 47 ASN cc_start: 0.8267 (m-40) cc_final: 0.7895 (t0) REVERT: C 135 MET cc_start: 0.6641 (pp-130) cc_final: 0.6415 (tmm) REVERT: C 165 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: C 208 SER cc_start: 0.8658 (m) cc_final: 0.8274 (p) REVERT: C 230 LYS cc_start: 0.8231 (tttt) cc_final: 0.7773 (tttm) REVERT: D 21 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6198 (ttp-170) REVERT: D 53 LYS cc_start: 0.7289 (mtmm) cc_final: 0.6904 (mttt) REVERT: D 68 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: D 137 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5567 (tt0) REVERT: D 337 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7687 (mp0) outliers start: 37 outliers final: 25 residues processed: 193 average time/residue: 0.6978 time to fit residues: 144.6244 Evaluate side-chains 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 287 ILE 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 150 LYS 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 7 ASP 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 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 137 GLU 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 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 44 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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** C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120301 restraints weight = 13424.416| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.58 r_work: 0.3284 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3230 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= 0.107 Angle : 0.532 8.238 16588 Z= 0.270 Chirality : 0.040 0.285 1804 Planarity : 0.004 0.043 2132 Dihedral : 8.673 141.899 1862 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 2.27 % Allowed : 22.00 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1540 helix: 1.63 (0.18), residues: 840 sheet: -0.14 (0.39), residues: 140 loop : -0.90 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 41 TYR 0.008 0.001 TYR D 129 PHE 0.006 0.001 PHE D 226 TRP 0.010 0.001 TRP A 166 HIS 0.007 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00239 (12276) covalent geometry : angle 0.52995 (16580) SS BOND : bond 0.00383 ( 4) SS BOND : angle 2.03594 ( 8) hydrogen bonds : bond 0.03738 ( 670) hydrogen bonds : angle 4.24411 ( 1923) ********************** 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 198 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7810 (tp) cc_final: 0.7573 (tm) REVERT: A 147 MET cc_start: 0.7491 (ptp) cc_final: 0.7185 (ptp) REVERT: A 157 HIS cc_start: 0.6895 (m90) cc_final: 0.6425 (m-70) REVERT: A 227 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 382 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8307 (mtt90) REVERT: B 16 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: B 19 GLN cc_start: 0.7586 (mt0) cc_final: 0.6712 (mp-120) REVERT: B 150 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7818 (ptpp) REVERT: B 152 GLU cc_start: 0.7478 (pt0) cc_final: 0.7205 (pt0) REVERT: B 157 HIS cc_start: 0.7077 (p-80) cc_final: 0.6846 (p-80) REVERT: C 47 ASN cc_start: 0.8232 (m-40) cc_final: 0.7969 (t0) REVERT: C 165 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: C 184 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4992 (pt) REVERT: C 208 SER cc_start: 0.8598 (m) cc_final: 0.8226 (p) REVERT: D 16 GLU cc_start: 0.7371 (mp0) cc_final: 0.6813 (mm-30) REVERT: D 21 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6101 (ttp-170) REVERT: D 53 LYS cc_start: 0.7202 (mtmm) cc_final: 0.6802 (mppt) REVERT: D 68 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.5887 (pm20) REVERT: D 137 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5348 (tt0) REVERT: D 337 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7577 (mp0) outliers start: 28 outliers final: 17 residues processed: 192 average time/residue: 0.7108 time to fit residues: 146.4761 Evaluate side-chains 191 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 ASP 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 150 LYS 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 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 28 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 137 GLU 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 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 11 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 131 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- 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 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119272 restraints weight = 13411.832| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.58 r_work: 0.3266 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3251 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= 0.131 Angle : 0.554 8.013 16588 Z= 0.281 Chirality : 0.041 0.288 1804 Planarity : 0.004 0.044 2132 Dihedral : 8.667 141.316 1862 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 2.44 % Allowed : 21.59 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1540 helix: 1.63 (0.18), residues: 840 sheet: -0.12 (0.39), residues: 140 loop : -0.89 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.010 0.001 TYR C 76 PHE 0.006 0.001 PHE D 226 TRP 0.010 0.001 TRP A 166 HIS 0.007 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00306 (12276) covalent geometry : angle 0.55173 (16580) SS BOND : bond 0.00503 ( 4) SS BOND : angle 2.15234 ( 8) hydrogen bonds : bond 0.04136 ( 670) hydrogen bonds : angle 4.26668 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4832.82 seconds wall clock time: 83 minutes 8.04 seconds (4988.04 seconds total)