Starting phenix.real_space_refine on Wed Feb 4 11:17:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye3_39188/02_2026/8ye3_39188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye3_39188/02_2026/8ye3_39188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ye3_39188/02_2026/8ye3_39188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye3_39188/02_2026/8ye3_39188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ye3_39188/02_2026/8ye3_39188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye3_39188/02_2026/8ye3_39188.map" } resolution = 3.4 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= 0.003 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6627 2.51 5 N 1725 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10491 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3497 Classifications: {'peptide': 452} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 438} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.67, per 1000 atoms: 0.25 Number of scatterers: 10491 At special positions: 0 Unit cell: (92.112, 89.688, 122.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2073 8.00 N 1725 7.00 C 6627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 464.2 milliseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 35.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 removed outlier: 3.596A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 195 through 203 removed outlier: 4.137A pdb=" N LYS A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 216 through 226 removed outlier: 4.302A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.213A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.582A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.503A pdb=" N PHE A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 513 Processing helix chain 'B' and resid 73 through 96 removed outlier: 3.597A pdb=" N LEU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 195 through 203 removed outlier: 4.137A pdb=" N LYS B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 226 removed outlier: 4.302A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.214A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.582A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.503A pdb=" N PHE B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 513 Processing helix chain 'C' and resid 73 through 96 removed outlier: 3.597A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 195 through 203 removed outlier: 4.136A pdb=" N LYS C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 216 through 226 removed outlier: 4.303A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.213A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.582A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.503A pdb=" N PHE C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 513 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 5.709A pdb=" N THR A 29 " --> pdb=" O LYS A 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 186 through 194 current: chain 'A' and resid 286 through 293 removed outlier: 7.088A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 352 current: chain 'A' and resid 364 through 368 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.597A pdb=" N GLY A 411 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 442 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.209A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 449 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 33 removed outlier: 5.709A pdb=" N THR B 29 " --> pdb=" O LYS B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 186 through 194 current: chain 'B' and resid 286 through 293 removed outlier: 7.087A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 349 through 352 current: chain 'B' and resid 364 through 368 Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AA7, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.597A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 442 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.208A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 33 removed outlier: 5.709A pdb=" N THR C 29 " --> pdb=" O LYS C 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 186 through 194 current: chain 'C' and resid 286 through 293 removed outlier: 7.087A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 349 through 352 current: chain 'C' and resid 364 through 368 Processing sheet with id=AB1, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.598A pdb=" N GLY C 411 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 442 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 430 through 434 removed outlier: 5.209A pdb=" N ILE C 431 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN C 426 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 449 " --> pdb=" O SER C 425 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3369 1.35 - 1.46: 2329 1.46 - 1.58: 4853 1.58 - 1.70: 3 1.70 - 1.82: 90 Bond restraints: 10644 Sorted by residual: bond pdb=" CB PRO B 101 " pdb=" CG PRO B 101 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" CB PRO A 101 " pdb=" CG PRO A 101 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.64e+00 bond pdb=" CB PRO C 101 " pdb=" CG PRO C 101 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.62e+00 bond pdb=" CG PRO C 265 " pdb=" CD PRO C 265 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.37e+00 bond pdb=" CG PRO B 265 " pdb=" CD PRO B 265 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.31e+00 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 14249 2.08 - 4.16: 136 4.16 - 6.24: 33 6.24 - 8.32: 0 8.32 - 10.40: 3 Bond angle restraints: 14421 Sorted by residual: angle pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 112.00 106.11 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" CA PRO B 265 " pdb=" N PRO B 265 " pdb=" CD PRO B 265 " ideal model delta sigma weight residual 112.00 106.11 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" CA PRO C 265 " pdb=" N PRO C 265 " pdb=" CD PRO C 265 " ideal model delta sigma weight residual 112.00 106.13 5.87 1.40e+00 5.10e-01 1.76e+01 angle pdb=" CA PRO B 101 " pdb=" N PRO B 101 " pdb=" CD PRO B 101 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" CA PRO C 101 " pdb=" N PRO C 101 " pdb=" CD PRO C 101 " ideal model delta sigma weight residual 112.00 106.59 5.41 1.40e+00 5.10e-01 1.49e+01 ... (remaining 14416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5526 17.66 - 35.33: 740 35.33 - 52.99: 258 52.99 - 70.66: 40 70.66 - 88.32: 15 Dihedral angle restraints: 6579 sinusoidal: 2598 harmonic: 3981 Sorted by residual: dihedral pdb=" CB CYS C 416 " pdb=" SG CYS C 416 " pdb=" SG CYS C 422 " pdb=" CB CYS C 422 " ideal model delta sinusoidal sigma weight residual -86.00 -156.78 70.78 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 422 " pdb=" CB CYS A 422 " ideal model delta sinusoidal sigma weight residual -86.00 -156.74 70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 422 " pdb=" CB CYS B 422 " ideal model delta sinusoidal sigma weight residual -86.00 -156.73 70.73 1 1.00e+01 1.00e-02 6.43e+01 ... (remaining 6576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1489 0.058 - 0.116: 238 0.116 - 0.173: 13 0.173 - 0.231: 0 0.231 - 0.289: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CB ILE B 292 " pdb=" CA ILE B 292 " pdb=" CG1 ILE B 292 " pdb=" CG2 ILE B 292 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE C 292 " pdb=" CA ILE C 292 " pdb=" CG1 ILE C 292 " pdb=" CG2 ILE C 292 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE A 292 " pdb=" CA ILE A 292 " pdb=" CG1 ILE A 292 " pdb=" CG2 ILE A 292 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1740 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 264 " 0.059 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO C 265 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 264 " -0.059 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 265 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 264 " -0.059 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO A 265 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.047 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 277 2.69 - 3.24: 9963 3.24 - 3.80: 16167 3.80 - 4.35: 20986 4.35 - 4.90: 35406 Nonbonded interactions: 82799 Sorted by model distance: nonbonded pdb=" OG1 THR A 36 " pdb=" OG SER A 38 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR B 36 " pdb=" OG SER B 38 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR C 36 " pdb=" OG SER C 38 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OD1 ASN B 331 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OD1 ASN A 331 " model vdw 2.194 3.040 ... (remaining 82794 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 : 0.003 0.108 10665 Z= 0.118 Angle : 0.534 10.396 14463 Z= 0.285 Chirality : 0.042 0.289 1743 Planarity : 0.005 0.087 1812 Dihedral : 17.687 88.319 3936 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.89 % Allowed : 31.88 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1344 helix: 0.68 (0.26), residues: 435 sheet: 0.22 (0.29), residues: 333 loop : -1.11 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 507 TYR 0.014 0.001 TYR A 417 PHE 0.011 0.001 PHE B 351 TRP 0.003 0.001 TRP A 52 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00329 (10644) covalent geometry : angle 0.53379 (14421) SS BOND : bond 0.00159 ( 21) SS BOND : angle 0.73609 ( 42) hydrogen bonds : bond 0.18257 ( 411) hydrogen bonds : angle 7.07384 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 352 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 338 ASP cc_start: 0.7102 (p0) cc_final: 0.6800 (p0) REVERT: A 370 MET cc_start: 0.8408 (ttm) cc_final: 0.8129 (ttm) REVERT: A 444 ASN cc_start: 0.7834 (p0) cc_final: 0.7107 (p0) REVERT: A 445 LYS cc_start: 0.7024 (mmtm) cc_final: 0.6768 (mmtm) REVERT: B 163 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6253 (mm-30) REVERT: B 236 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 238 SER cc_start: 0.7774 (t) cc_final: 0.7202 (m) REVERT: B 259 SER cc_start: 0.7724 (t) cc_final: 0.7305 (p) REVERT: B 263 ASP cc_start: 0.7149 (m-30) cc_final: 0.6894 (m-30) REVERT: B 272 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7466 (ttpp) REVERT: B 293 LYS cc_start: 0.7425 (mtpp) cc_final: 0.6982 (mtmm) REVERT: B 338 ASP cc_start: 0.7057 (p0) cc_final: 0.6620 (p0) REVERT: B 357 THR cc_start: 0.7594 (p) cc_final: 0.7285 (t) REVERT: B 399 LYS cc_start: 0.7350 (pttm) cc_final: 0.7094 (pttm) REVERT: B 414 VAL cc_start: 0.7865 (t) cc_final: 0.7462 (p) REVERT: B 488 PHE cc_start: 0.7885 (t80) cc_final: 0.7547 (t80) REVERT: C 351 PHE cc_start: 0.8043 (t80) cc_final: 0.7820 (t80) REVERT: C 357 THR cc_start: 0.7759 (p) cc_final: 0.7444 (t) outliers start: 11 outliers final: 10 residues processed: 353 average time/residue: 0.0825 time to fit residues: 42.1361 Evaluate side-chains 342 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 332 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 270 GLN B 302 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113089 restraints weight = 14912.772| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10665 Z= 0.146 Angle : 0.536 8.373 14463 Z= 0.276 Chirality : 0.042 0.215 1743 Planarity : 0.003 0.027 1812 Dihedral : 5.259 57.157 1454 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.53 % Allowed : 28.16 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1344 helix: 1.09 (0.26), residues: 432 sheet: 0.58 (0.30), residues: 327 loop : -1.18 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.013 0.001 TYR A 342 PHE 0.017 0.001 PHE C 32 TRP 0.006 0.001 TRP B 314 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00341 (10644) covalent geometry : angle 0.53441 (14421) SS BOND : bond 0.00357 ( 21) SS BOND : angle 0.87247 ( 42) hydrogen bonds : bond 0.03850 ( 411) hydrogen bonds : angle 5.24059 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8038 (tp30) cc_final: 0.7782 (tp30) REVERT: A 152 VAL cc_start: 0.8688 (m) cc_final: 0.8385 (t) REVERT: A 166 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8333 (mtmt) REVERT: A 198 TYR cc_start: 0.8427 (t80) cc_final: 0.8083 (t80) REVERT: A 218 GLU cc_start: 0.7970 (mp0) cc_final: 0.7769 (mp0) REVERT: A 232 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 263 ASP cc_start: 0.7481 (m-30) cc_final: 0.6990 (m-30) REVERT: A 289 MET cc_start: 0.8119 (mmm) cc_final: 0.7873 (tmm) REVERT: A 318 THR cc_start: 0.8629 (m) cc_final: 0.8316 (p) REVERT: A 378 GLU cc_start: 0.8086 (mp0) cc_final: 0.7882 (mp0) REVERT: A 444 ASN cc_start: 0.7905 (p0) cc_final: 0.7516 (p0) REVERT: A 454 ASN cc_start: 0.7786 (t0) cc_final: 0.7529 (m-40) REVERT: B 82 GLU cc_start: 0.8041 (tp30) cc_final: 0.7773 (tp30) REVERT: B 95 LEU cc_start: 0.8664 (tp) cc_final: 0.8462 (tp) REVERT: B 160 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7470 (mm) REVERT: B 174 THR cc_start: 0.7904 (t) cc_final: 0.7552 (p) REVERT: B 222 GLU cc_start: 0.7729 (tp30) cc_final: 0.7159 (tp30) REVERT: B 232 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: B 236 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 238 SER cc_start: 0.8649 (t) cc_final: 0.8231 (m) REVERT: B 251 MET cc_start: 0.7847 (mtt) cc_final: 0.7621 (mtt) REVERT: B 263 ASP cc_start: 0.7511 (m-30) cc_final: 0.7057 (m-30) REVERT: B 289 MET cc_start: 0.8184 (mmm) cc_final: 0.7888 (tpp) REVERT: B 293 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7292 (mtmm) REVERT: B 338 ASP cc_start: 0.7248 (p0) cc_final: 0.6871 (p0) REVERT: B 399 LYS cc_start: 0.7954 (pttm) cc_final: 0.7294 (pttm) REVERT: B 428 ASN cc_start: 0.8435 (t0) cc_final: 0.8216 (t0) REVERT: B 478 TYR cc_start: 0.7896 (m-10) cc_final: 0.7594 (m-10) REVERT: B 505 PHE cc_start: 0.7472 (t80) cc_final: 0.7181 (t80) REVERT: C 34 GLN cc_start: 0.8500 (tt0) cc_final: 0.8271 (tt0) REVERT: C 82 GLU cc_start: 0.7890 (tp30) cc_final: 0.7663 (tp30) REVERT: C 410 LEU cc_start: 0.8252 (mp) cc_final: 0.8001 (mt) REVERT: C 478 TYR cc_start: 0.7779 (m-10) cc_final: 0.7495 (m-10) outliers start: 56 outliers final: 26 residues processed: 392 average time/residue: 0.0805 time to fit residues: 46.2147 Evaluate side-chains 384 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 355 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 44 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 302 GLN A 345 ASN A 437 ASN A 454 ASN B 34 GLN B 224 GLN B 270 GLN B 345 ASN B 437 ASN C 240 ASN C 437 ASN C 454 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110915 restraints weight = 14502.778| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.04 r_work: 0.3117 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10665 Z= 0.253 Angle : 0.615 7.685 14463 Z= 0.316 Chirality : 0.045 0.318 1743 Planarity : 0.003 0.032 1812 Dihedral : 5.013 51.673 1434 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.66 % Allowed : 29.21 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1344 helix: 0.94 (0.26), residues: 432 sheet: 0.48 (0.30), residues: 327 loop : -1.27 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 229 TYR 0.015 0.002 TYR A 342 PHE 0.014 0.001 PHE B 483 TRP 0.010 0.002 TRP B 314 HIS 0.005 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00574 (10644) covalent geometry : angle 0.61311 (14421) SS BOND : bond 0.00353 ( 21) SS BOND : angle 1.12202 ( 42) hydrogen bonds : bond 0.04357 ( 411) hydrogen bonds : angle 5.25959 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 376 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.7555 (mt) cc_final: 0.7344 (mt) REVERT: A 152 VAL cc_start: 0.8822 (m) cc_final: 0.8454 (t) REVERT: A 218 GLU cc_start: 0.8001 (mp0) cc_final: 0.7630 (mp0) REVERT: A 222 GLU cc_start: 0.7863 (tp30) cc_final: 0.7395 (tp30) REVERT: A 225 GLN cc_start: 0.8203 (mt0) cc_final: 0.7940 (mt0) REVERT: A 232 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 236 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 289 MET cc_start: 0.8240 (mmm) cc_final: 0.8001 (tmm) REVERT: A 509 PHE cc_start: 0.7018 (t80) cc_final: 0.6716 (m-80) REVERT: B 78 LEU cc_start: 0.8473 (mt) cc_final: 0.8148 (mp) REVERT: B 82 GLU cc_start: 0.7896 (tp30) cc_final: 0.7670 (tp30) REVERT: B 160 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7402 (mm) REVERT: B 174 THR cc_start: 0.8083 (t) cc_final: 0.7835 (p) REVERT: B 222 GLU cc_start: 0.7985 (tp30) cc_final: 0.7744 (tp30) REVERT: B 236 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7415 (mt-10) REVERT: B 238 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 289 MET cc_start: 0.8229 (tmm) cc_final: 0.7881 (tmm) REVERT: B 338 ASP cc_start: 0.7255 (p0) cc_final: 0.6920 (p0) REVERT: B 393 CYS cc_start: 0.7450 (m) cc_final: 0.7210 (m) REVERT: B 399 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7752 (pttm) REVERT: B 428 ASN cc_start: 0.8489 (t0) cc_final: 0.8248 (t0) REVERT: B 478 TYR cc_start: 0.7956 (m-10) cc_final: 0.7720 (m-10) REVERT: C 34 GLN cc_start: 0.8787 (tt0) cc_final: 0.8540 (tt0) REVERT: C 82 GLU cc_start: 0.7785 (tp30) cc_final: 0.7561 (tp30) REVERT: C 222 GLU cc_start: 0.7999 (tp30) cc_final: 0.7411 (tp30) REVERT: C 232 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: C 236 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7396 (mt-10) REVERT: C 263 ASP cc_start: 0.7688 (m-30) cc_final: 0.7478 (m-30) REVERT: C 289 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7791 (tmm) REVERT: C 338 ASP cc_start: 0.7134 (p0) cc_final: 0.6814 (p0) REVERT: C 343 CYS cc_start: 0.7435 (m) cc_final: 0.7189 (m) REVERT: C 393 CYS cc_start: 0.7519 (m) cc_final: 0.7305 (m) REVERT: C 399 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7654 (pttm) REVERT: C 509 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6766 (m-80) outliers start: 70 outliers final: 34 residues processed: 398 average time/residue: 0.0840 time to fit residues: 48.2107 Evaluate side-chains 418 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 376 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN B 270 GLN ** B 317 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 = 0.3538 r_free = 0.3538 target = 0.126513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112831 restraints weight = 14497.237| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.04 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10665 Z= 0.147 Angle : 0.536 6.936 14463 Z= 0.277 Chirality : 0.042 0.286 1743 Planarity : 0.003 0.028 1812 Dihedral : 4.543 48.874 1432 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.50 % Allowed : 28.40 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1344 helix: 1.28 (0.27), residues: 414 sheet: 0.42 (0.29), residues: 327 loop : -1.20 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.012 0.001 TYR A 342 PHE 0.024 0.001 PHE A 32 TRP 0.008 0.001 TRP A 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00335 (10644) covalent geometry : angle 0.53381 (14421) SS BOND : bond 0.00298 ( 21) SS BOND : angle 0.96668 ( 42) hydrogen bonds : bond 0.03558 ( 411) hydrogen bonds : angle 5.02655 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 377 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.7530 (mt) cc_final: 0.7270 (mt) REVERT: A 152 VAL cc_start: 0.8774 (m) cc_final: 0.8404 (t) REVERT: A 163 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6222 (mm-30) REVERT: A 218 GLU cc_start: 0.8055 (mp0) cc_final: 0.7646 (mp0) REVERT: A 222 GLU cc_start: 0.7805 (tp30) cc_final: 0.7267 (tp30) REVERT: A 232 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: A 289 MET cc_start: 0.8163 (tmm) cc_final: 0.7917 (tmm) REVERT: A 509 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: B 38 SER cc_start: 0.8682 (p) cc_final: 0.8454 (m) REVERT: B 82 GLU cc_start: 0.7914 (tp30) cc_final: 0.7693 (tp30) REVERT: B 160 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7332 (mm) REVERT: B 174 THR cc_start: 0.8103 (t) cc_final: 0.7870 (p) REVERT: B 222 GLU cc_start: 0.7914 (tp30) cc_final: 0.7553 (tp30) REVERT: B 236 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 238 SER cc_start: 0.8643 (t) cc_final: 0.8284 (p) REVERT: B 289 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7880 (tmm) REVERT: B 296 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7863 (m) REVERT: B 338 ASP cc_start: 0.7236 (p0) cc_final: 0.6926 (p0) REVERT: B 393 CYS cc_start: 0.7439 (m) cc_final: 0.7160 (m) REVERT: B 399 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7743 (pttm) REVERT: B 419 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7614 (mtmt) REVERT: B 428 ASN cc_start: 0.8419 (t0) cc_final: 0.8188 (t0) REVERT: B 478 TYR cc_start: 0.7919 (m-10) cc_final: 0.7665 (m-10) REVERT: B 509 PHE cc_start: 0.7299 (t80) cc_final: 0.6778 (m-80) REVERT: C 34 GLN cc_start: 0.8742 (tt0) cc_final: 0.8458 (tt0) REVERT: C 82 GLU cc_start: 0.7820 (tp30) cc_final: 0.7597 (tp30) REVERT: C 163 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6398 (mm-30) REVERT: C 171 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 222 GLU cc_start: 0.7943 (tp30) cc_final: 0.7460 (tp30) REVERT: C 236 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7464 (mt-10) REVERT: C 289 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7679 (tmm) REVERT: C 338 ASP cc_start: 0.7139 (p0) cc_final: 0.6759 (p0) REVERT: C 343 CYS cc_start: 0.7474 (m) cc_final: 0.7240 (m) REVERT: C 361 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: C 393 CYS cc_start: 0.7532 (m) cc_final: 0.7331 (m) REVERT: C 399 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7616 (pttm) REVERT: C 509 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6417 (m-80) outliers start: 68 outliers final: 40 residues processed: 399 average time/residue: 0.0845 time to fit residues: 48.0271 Evaluate side-chains 433 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 382 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 52 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 270 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113497 restraints weight = 14428.054| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.04 r_work: 0.3205 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10665 Z= 0.121 Angle : 0.511 6.776 14463 Z= 0.264 Chirality : 0.042 0.306 1743 Planarity : 0.003 0.024 1812 Dihedral : 4.186 43.413 1430 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.61 % Allowed : 30.58 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.23), residues: 1344 helix: 1.36 (0.26), residues: 414 sheet: 0.48 (0.30), residues: 324 loop : -1.15 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 282 TYR 0.011 0.001 TYR A 417 PHE 0.028 0.001 PHE A 32 TRP 0.007 0.001 TRP B 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00276 (10644) covalent geometry : angle 0.50794 (14421) SS BOND : bond 0.00288 ( 21) SS BOND : angle 1.10991 ( 42) hydrogen bonds : bond 0.03278 ( 411) hydrogen bonds : angle 4.88316 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 369 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8521 (t80) cc_final: 0.8309 (t80) REVERT: A 40 VAL cc_start: 0.8369 (m) cc_final: 0.8090 (t) REVERT: A 152 VAL cc_start: 0.8748 (m) cc_final: 0.8384 (t) REVERT: A 163 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6253 (mm-30) REVERT: A 218 GLU cc_start: 0.8011 (mp0) cc_final: 0.7717 (mp0) REVERT: A 222 GLU cc_start: 0.7787 (tp30) cc_final: 0.7226 (tp30) REVERT: A 232 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: A 289 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7862 (tpp) REVERT: A 461 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8106 (mmtt) REVERT: A 509 PHE cc_start: 0.7004 (t80) cc_final: 0.6550 (m-80) REVERT: B 38 SER cc_start: 0.8576 (p) cc_final: 0.8331 (m) REVERT: B 160 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7302 (mm) REVERT: B 174 THR cc_start: 0.8083 (t) cc_final: 0.7850 (p) REVERT: B 236 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7457 (mt-10) REVERT: B 238 SER cc_start: 0.8607 (t) cc_final: 0.8215 (p) REVERT: B 289 MET cc_start: 0.8125 (tmm) cc_final: 0.7866 (tmm) REVERT: B 296 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7922 (m) REVERT: B 338 ASP cc_start: 0.7215 (p0) cc_final: 0.6900 (p0) REVERT: B 393 CYS cc_start: 0.7400 (m) cc_final: 0.7105 (m) REVERT: B 399 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7570 (pttm) REVERT: B 428 ASN cc_start: 0.8416 (t0) cc_final: 0.8159 (t0) REVERT: B 478 TYR cc_start: 0.7879 (m-10) cc_final: 0.7613 (m-10) REVERT: B 509 PHE cc_start: 0.7314 (t80) cc_final: 0.6595 (m-80) REVERT: C 34 GLN cc_start: 0.8690 (tt0) cc_final: 0.8394 (tt0) REVERT: C 42 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7546 (mtmm) REVERT: C 82 GLU cc_start: 0.7810 (tp30) cc_final: 0.7582 (tp30) REVERT: C 163 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6297 (mm-30) REVERT: C 222 GLU cc_start: 0.7918 (tp30) cc_final: 0.7410 (tp30) REVERT: C 236 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 289 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7689 (tmm) REVERT: C 338 ASP cc_start: 0.7077 (p0) cc_final: 0.6658 (p0) REVERT: C 343 CYS cc_start: 0.7476 (m) cc_final: 0.7275 (m) REVERT: C 393 CYS cc_start: 0.7516 (m) cc_final: 0.7300 (m) REVERT: C 399 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7576 (pttm) REVERT: C 509 PHE cc_start: 0.6962 (t80) cc_final: 0.6403 (m-80) outliers start: 57 outliers final: 39 residues processed: 390 average time/residue: 0.0919 time to fit residues: 51.6864 Evaluate side-chains 410 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 364 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.0970 chunk 53 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114519 restraints weight = 14628.511| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.07 r_work: 0.3240 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10665 Z= 0.103 Angle : 0.497 6.565 14463 Z= 0.257 Chirality : 0.041 0.322 1743 Planarity : 0.003 0.022 1812 Dihedral : 3.911 18.135 1428 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.77 % Allowed : 30.02 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1344 helix: 1.49 (0.27), residues: 414 sheet: 0.54 (0.30), residues: 327 loop : -1.10 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 282 TYR 0.010 0.001 TYR B 417 PHE 0.021 0.001 PHE A 351 TRP 0.006 0.001 TRP C 314 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00237 (10644) covalent geometry : angle 0.49422 (14421) SS BOND : bond 0.00196 ( 21) SS BOND : angle 1.07401 ( 42) hydrogen bonds : bond 0.03141 ( 411) hydrogen bonds : angle 4.81682 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 366 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 VAL cc_start: 0.8731 (m) cc_final: 0.8369 (t) REVERT: A 163 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6175 (mm-30) REVERT: A 222 GLU cc_start: 0.7782 (tp30) cc_final: 0.7219 (tp30) REVERT: A 232 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 378 GLU cc_start: 0.8165 (mp0) cc_final: 0.7955 (mp0) REVERT: A 461 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8085 (mmtt) REVERT: A 509 PHE cc_start: 0.6971 (t80) cc_final: 0.6658 (m-80) REVERT: B 38 SER cc_start: 0.8567 (p) cc_final: 0.8340 (m) REVERT: B 160 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7385 (mm) REVERT: B 174 THR cc_start: 0.8040 (t) cc_final: 0.7796 (p) REVERT: B 236 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7466 (mt-10) REVERT: B 238 SER cc_start: 0.8519 (t) cc_final: 0.8149 (p) REVERT: B 296 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7877 (m) REVERT: B 308 VAL cc_start: 0.8887 (t) cc_final: 0.8663 (t) REVERT: B 393 CYS cc_start: 0.7389 (m) cc_final: 0.7081 (m) REVERT: B 399 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7552 (pttm) REVERT: B 428 ASN cc_start: 0.8423 (t0) cc_final: 0.8158 (t0) REVERT: B 478 TYR cc_start: 0.7870 (m-10) cc_final: 0.7606 (m-10) REVERT: C 34 GLN cc_start: 0.8677 (tt0) cc_final: 0.8358 (tt0) REVERT: C 42 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7421 (mtmm) REVERT: C 82 GLU cc_start: 0.7852 (tp30) cc_final: 0.7611 (tp30) REVERT: C 163 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6384 (mm-30) REVERT: C 222 GLU cc_start: 0.7891 (tp30) cc_final: 0.7367 (tp30) REVERT: C 236 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 289 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7568 (tmm) REVERT: C 338 ASP cc_start: 0.7104 (p0) cc_final: 0.6691 (p0) REVERT: C 361 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: C 393 CYS cc_start: 0.7543 (m) cc_final: 0.7319 (m) REVERT: C 399 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7534 (pttm) REVERT: C 509 PHE cc_start: 0.6913 (t80) cc_final: 0.6441 (m-80) outliers start: 59 outliers final: 40 residues processed: 391 average time/residue: 0.0947 time to fit residues: 53.7891 Evaluate side-chains 406 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 359 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 0.0050 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114802 restraints weight = 14447.995| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.02 r_work: 0.3253 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10665 Z= 0.101 Angle : 0.506 6.948 14463 Z= 0.260 Chirality : 0.042 0.360 1743 Planarity : 0.003 0.022 1812 Dihedral : 3.835 17.460 1428 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.77 % Allowed : 29.61 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.23), residues: 1344 helix: 1.38 (0.26), residues: 432 sheet: 0.51 (0.29), residues: 333 loop : -1.07 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.013 0.001 TYR B 417 PHE 0.021 0.001 PHE C 32 TRP 0.007 0.001 TRP C 314 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00234 (10644) covalent geometry : angle 0.50340 (14421) SS BOND : bond 0.00335 ( 21) SS BOND : angle 1.09711 ( 42) hydrogen bonds : bond 0.03067 ( 411) hydrogen bonds : angle 4.73633 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 364 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8698 (m) cc_final: 0.8368 (p) REVERT: A 152 VAL cc_start: 0.8702 (m) cc_final: 0.8340 (t) REVERT: A 163 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6144 (mm-30) REVERT: A 222 GLU cc_start: 0.7797 (tp30) cc_final: 0.7235 (tp30) REVERT: A 232 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: A 461 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8066 (mmtt) REVERT: A 509 PHE cc_start: 0.7050 (t80) cc_final: 0.6746 (m-80) REVERT: B 38 SER cc_start: 0.8532 (p) cc_final: 0.8320 (m) REVERT: B 160 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7383 (mm) REVERT: B 174 THR cc_start: 0.8013 (t) cc_final: 0.7768 (p) REVERT: B 222 GLU cc_start: 0.7848 (tp30) cc_final: 0.7355 (tp30) REVERT: B 236 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 238 SER cc_start: 0.8505 (t) cc_final: 0.8148 (p) REVERT: B 272 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7525 (ttpp) REVERT: B 296 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7956 (m) REVERT: B 308 VAL cc_start: 0.8863 (t) cc_final: 0.8626 (t) REVERT: B 399 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7506 (pttm) REVERT: B 428 ASN cc_start: 0.8388 (t0) cc_final: 0.8122 (t0) REVERT: B 478 TYR cc_start: 0.7808 (m-10) cc_final: 0.7589 (m-10) REVERT: C 34 GLN cc_start: 0.8666 (tt0) cc_final: 0.8338 (tt0) REVERT: C 82 GLU cc_start: 0.7814 (tp30) cc_final: 0.7585 (tp30) REVERT: C 163 GLU cc_start: 0.6501 (mm-30) cc_final: 0.6256 (mm-30) REVERT: C 222 GLU cc_start: 0.7859 (tp30) cc_final: 0.7298 (tp30) REVERT: C 236 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 289 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7640 (tmm) REVERT: C 351 PHE cc_start: 0.8509 (t80) cc_final: 0.8143 (t80) REVERT: C 361 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: C 393 CYS cc_start: 0.7494 (m) cc_final: 0.7268 (m) REVERT: C 399 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7490 (pttm) REVERT: C 509 PHE cc_start: 0.6936 (t80) cc_final: 0.6477 (m-80) outliers start: 59 outliers final: 44 residues processed: 388 average time/residue: 0.0963 time to fit residues: 53.7577 Evaluate side-chains 411 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 360 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 454 ASN B 270 GLN B 454 ASN C 70 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112506 restraints weight = 14383.087| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.02 r_work: 0.3199 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10665 Z= 0.163 Angle : 0.557 6.563 14463 Z= 0.285 Chirality : 0.043 0.344 1743 Planarity : 0.003 0.024 1812 Dihedral : 4.111 18.264 1428 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.94 % Allowed : 29.85 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1344 helix: 1.28 (0.26), residues: 432 sheet: 0.44 (0.29), residues: 327 loop : -1.09 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.013 0.001 TYR B 417 PHE 0.025 0.001 PHE A 351 TRP 0.007 0.001 TRP B 314 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00373 (10644) covalent geometry : angle 0.55383 (14421) SS BOND : bond 0.00294 ( 21) SS BOND : angle 1.16402 ( 42) hydrogen bonds : bond 0.03558 ( 411) hydrogen bonds : angle 4.84772 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 381 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8615 (m) cc_final: 0.8330 (p) REVERT: A 80 LYS cc_start: 0.8447 (tptt) cc_final: 0.8175 (tptm) REVERT: A 152 VAL cc_start: 0.8768 (m) cc_final: 0.8426 (t) REVERT: A 163 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6241 (mm-30) REVERT: A 222 GLU cc_start: 0.7855 (tp30) cc_final: 0.7319 (tp30) REVERT: A 232 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: A 289 MET cc_start: 0.8238 (mmm) cc_final: 0.7966 (tmm) REVERT: A 338 ASP cc_start: 0.7318 (p0) cc_final: 0.6961 (p0) REVERT: A 351 PHE cc_start: 0.8519 (t80) cc_final: 0.8228 (t80) REVERT: A 393 CYS cc_start: 0.7498 (m) cc_final: 0.7236 (m) REVERT: A 461 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8101 (mmtt) REVERT: A 509 PHE cc_start: 0.7086 (t80) cc_final: 0.6542 (m-80) REVERT: B 38 SER cc_start: 0.8586 (p) cc_final: 0.8311 (m) REVERT: B 160 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7339 (mm) REVERT: B 174 THR cc_start: 0.8030 (t) cc_final: 0.7815 (p) REVERT: B 236 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 238 SER cc_start: 0.8575 (t) cc_final: 0.8209 (p) REVERT: B 289 MET cc_start: 0.8134 (mmm) cc_final: 0.7851 (tmm) REVERT: B 296 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8013 (m) REVERT: B 393 CYS cc_start: 0.7323 (m) cc_final: 0.7044 (m) REVERT: B 399 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7718 (pttm) REVERT: B 428 ASN cc_start: 0.8402 (t0) cc_final: 0.8162 (t0) REVERT: B 478 TYR cc_start: 0.7956 (m-10) cc_final: 0.7711 (m-10) REVERT: B 509 PHE cc_start: 0.7440 (t80) cc_final: 0.6622 (m-80) REVERT: C 34 GLN cc_start: 0.8760 (tt0) cc_final: 0.8515 (tt0) REVERT: C 42 LYS cc_start: 0.7797 (mtpp) cc_final: 0.7438 (mtmm) REVERT: C 82 GLU cc_start: 0.7815 (tp30) cc_final: 0.7594 (tp30) REVERT: C 163 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6342 (mm-30) REVERT: C 222 GLU cc_start: 0.7923 (tp30) cc_final: 0.7447 (tp30) REVERT: C 236 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7417 (mt-10) REVERT: C 289 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7694 (tmm) REVERT: C 338 ASP cc_start: 0.7036 (p0) cc_final: 0.6629 (p0) REVERT: C 361 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6869 (tt0) REVERT: C 393 CYS cc_start: 0.7573 (m) cc_final: 0.7324 (m) REVERT: C 399 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7534 (pttm) REVERT: C 509 PHE cc_start: 0.6972 (t80) cc_final: 0.6386 (m-80) outliers start: 61 outliers final: 46 residues processed: 401 average time/residue: 0.0957 time to fit residues: 55.5572 Evaluate side-chains 422 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 345 ASN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 454 ASN C 225 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112777 restraints weight = 14396.238| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.01 r_work: 0.3144 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10665 Z= 0.151 Angle : 0.553 6.928 14463 Z= 0.284 Chirality : 0.043 0.377 1743 Planarity : 0.003 0.023 1812 Dihedral : 4.111 18.347 1428 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.45 % Allowed : 30.66 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1344 helix: 1.28 (0.26), residues: 432 sheet: 0.43 (0.29), residues: 327 loop : -1.11 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.014 0.001 TYR B 417 PHE 0.028 0.002 PHE A 351 TRP 0.008 0.001 TRP C 314 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00348 (10644) covalent geometry : angle 0.54911 (14421) SS BOND : bond 0.00394 ( 21) SS BOND : angle 1.27041 ( 42) hydrogen bonds : bond 0.03479 ( 411) hydrogen bonds : angle 4.84516 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8584 (m) cc_final: 0.8307 (p) REVERT: A 42 LYS cc_start: 0.7555 (mtmm) cc_final: 0.7339 (mtmm) REVERT: A 80 LYS cc_start: 0.8451 (tptt) cc_final: 0.8177 (tptm) REVERT: A 152 VAL cc_start: 0.8744 (m) cc_final: 0.8388 (t) REVERT: A 163 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6171 (mm-30) REVERT: A 218 GLU cc_start: 0.7977 (mp0) cc_final: 0.7445 (mp0) REVERT: A 222 GLU cc_start: 0.7840 (tp30) cc_final: 0.7310 (tp30) REVERT: A 232 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 289 MET cc_start: 0.8231 (mmm) cc_final: 0.7955 (tmm) REVERT: A 351 PHE cc_start: 0.8552 (t80) cc_final: 0.8266 (t80) REVERT: A 393 CYS cc_start: 0.7530 (m) cc_final: 0.7290 (m) REVERT: A 461 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8101 (mmtt) REVERT: A 509 PHE cc_start: 0.7059 (t80) cc_final: 0.6475 (m-80) REVERT: B 38 SER cc_start: 0.8559 (p) cc_final: 0.8292 (m) REVERT: B 174 THR cc_start: 0.8043 (t) cc_final: 0.7823 (p) REVERT: B 236 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 238 SER cc_start: 0.8581 (t) cc_final: 0.8213 (p) REVERT: B 289 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7756 (tmm) REVERT: B 352 PHE cc_start: 0.8294 (m-80) cc_final: 0.7989 (m-80) REVERT: B 393 CYS cc_start: 0.7479 (m) cc_final: 0.7178 (m) REVERT: B 399 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7579 (pttm) REVERT: B 428 ASN cc_start: 0.8412 (t0) cc_final: 0.8170 (t0) REVERT: B 478 TYR cc_start: 0.7941 (m-10) cc_final: 0.7734 (m-10) REVERT: B 509 PHE cc_start: 0.7397 (t80) cc_final: 0.6688 (m-80) REVERT: C 34 GLN cc_start: 0.8747 (tt0) cc_final: 0.8442 (tt0) REVERT: C 82 GLU cc_start: 0.7789 (tp30) cc_final: 0.7579 (tp30) REVERT: C 163 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6301 (mm-30) REVERT: C 222 GLU cc_start: 0.7915 (tp30) cc_final: 0.7378 (tp30) REVERT: C 236 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 289 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7670 (tmm) REVERT: C 338 ASP cc_start: 0.7044 (p0) cc_final: 0.6630 (p0) REVERT: C 361 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: C 393 CYS cc_start: 0.7610 (m) cc_final: 0.7364 (m) REVERT: C 399 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7455 (pttm) REVERT: C 509 PHE cc_start: 0.6995 (t80) cc_final: 0.6463 (m-80) outliers start: 55 outliers final: 43 residues processed: 388 average time/residue: 0.0958 time to fit residues: 53.7617 Evaluate side-chains 426 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 454 ASN B 270 GLN B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113854 restraints weight = 14354.652| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.02 r_work: 0.3238 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10665 Z= 0.113 Angle : 0.532 7.214 14463 Z= 0.274 Chirality : 0.042 0.401 1743 Planarity : 0.003 0.022 1812 Dihedral : 4.010 18.396 1428 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.37 % Allowed : 30.50 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1344 helix: 1.34 (0.26), residues: 432 sheet: 0.45 (0.29), residues: 333 loop : -1.08 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 364 TYR 0.015 0.001 TYR B 417 PHE 0.026 0.001 PHE A 351 TRP 0.009 0.001 TRP C 314 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00261 (10644) covalent geometry : angle 0.52811 (14421) SS BOND : bond 0.00240 ( 21) SS BOND : angle 1.36497 ( 42) hydrogen bonds : bond 0.03251 ( 411) hydrogen bonds : angle 4.76855 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 371 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8579 (m) cc_final: 0.8314 (p) REVERT: A 80 LYS cc_start: 0.8477 (tptt) cc_final: 0.8206 (tptm) REVERT: A 152 VAL cc_start: 0.8702 (m) cc_final: 0.8331 (t) REVERT: A 163 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6184 (mm-30) REVERT: A 218 GLU cc_start: 0.7993 (mp0) cc_final: 0.7478 (mp0) REVERT: A 222 GLU cc_start: 0.7843 (tp30) cc_final: 0.7294 (tp30) REVERT: A 232 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 289 MET cc_start: 0.8175 (mmm) cc_final: 0.7925 (tmm) REVERT: A 351 PHE cc_start: 0.8540 (t80) cc_final: 0.8259 (t80) REVERT: A 461 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8090 (mmtt) REVERT: A 509 PHE cc_start: 0.7028 (t80) cc_final: 0.6434 (m-80) REVERT: B 38 SER cc_start: 0.8571 (p) cc_final: 0.8346 (m) REVERT: B 174 THR cc_start: 0.8028 (t) cc_final: 0.7808 (p) REVERT: B 222 GLU cc_start: 0.7901 (tp30) cc_final: 0.7463 (tp30) REVERT: B 236 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 238 SER cc_start: 0.8513 (t) cc_final: 0.8157 (p) REVERT: B 289 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7823 (tmm) REVERT: B 296 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.7910 (m) REVERT: B 393 CYS cc_start: 0.7431 (m) cc_final: 0.7137 (m) REVERT: B 399 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7504 (pttm) REVERT: B 428 ASN cc_start: 0.8364 (t0) cc_final: 0.8124 (t0) REVERT: B 509 PHE cc_start: 0.7357 (t80) cc_final: 0.6685 (m-80) REVERT: C 34 GLN cc_start: 0.8675 (tt0) cc_final: 0.8366 (tt0) REVERT: C 82 GLU cc_start: 0.7779 (tp30) cc_final: 0.7549 (tp30) REVERT: C 163 GLU cc_start: 0.6494 (mm-30) cc_final: 0.6249 (mm-30) REVERT: C 222 GLU cc_start: 0.7836 (tp30) cc_final: 0.7263 (tp30) REVERT: C 236 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 289 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7661 (tmm) REVERT: C 361 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: C 393 CYS cc_start: 0.7571 (m) cc_final: 0.7338 (m) REVERT: C 399 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7389 (pttm) REVERT: C 509 PHE cc_start: 0.6992 (t80) cc_final: 0.6467 (m-80) outliers start: 54 outliers final: 43 residues processed: 390 average time/residue: 0.1033 time to fit residues: 57.3459 Evaluate side-chains 416 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 366 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 454 ASN C 225 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113291 restraints weight = 14516.561| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.04 r_work: 0.3225 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10665 Z= 0.134 Angle : 0.552 7.259 14463 Z= 0.283 Chirality : 0.043 0.394 1743 Planarity : 0.003 0.022 1812 Dihedral : 4.066 18.641 1428 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.61 % Allowed : 30.26 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1344 helix: 1.34 (0.26), residues: 432 sheet: 0.48 (0.29), residues: 333 loop : -1.06 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.016 0.001 TYR B 417 PHE 0.026 0.001 PHE A 351 TRP 0.007 0.001 TRP B 314 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00309 (10644) covalent geometry : angle 0.54497 (14421) SS BOND : bond 0.00419 ( 21) SS BOND : angle 1.67110 ( 42) hydrogen bonds : bond 0.03360 ( 411) hydrogen bonds : angle 4.76601 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.75 seconds wall clock time: 41 minutes 27.96 seconds (2487.96 seconds total)