Starting phenix.real_space_refine on Sun Oct 25 04:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t35_55484/10_2026/9t35_55484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t35_55484/10_2026/9t35_55484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t35_55484/10_2026/9t35_55484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t35_55484/10_2026/9t35_55484.map" model { file = "/net/cci-nas-00/data/ceres_data/9t35_55484/10_2026/9t35_55484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t35_55484/10_2026/9t35_55484.cif" } resolution = 2.78 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= 0.001 sd= 0.035 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 102 5.16 5 C 10164 2.51 5 N 2436 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.70, per 1000 atoms: 0.18 Number of scatterers: 15342 At special positions: 0 Unit cell: (97.65, 110.67, 122.388, 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 102 16.00 O 2640 8.00 N 2436 7.00 C 10164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " 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: 1.16 Conformation dependent library (CDL) restraints added in 577.4 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 7 sheets defined 78.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.662A pdb=" N ARG A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.650A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.513A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.829A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.582A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.091A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.662A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.649A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.513A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.828A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.582A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 383 through 394 removed outlier: 4.091A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.662A pdb=" N ARG C 18 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.649A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 169 through 179 removed outlier: 3.514A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.829A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 removed outlier: 3.582A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 383 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.092A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.662A pdb=" N ARG D 18 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 21 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.650A pdb=" N LYS D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 169 through 179 removed outlier: 3.513A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.829A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.582A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 383 Processing helix chain 'D' and resid 383 through 394 removed outlier: 4.092A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.662A pdb=" N ARG E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 21 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.649A pdb=" N LYS E 145 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.514A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.828A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.583A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 383 Processing helix chain 'E' and resid 383 through 394 removed outlier: 4.092A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 21 removed outlier: 3.662A pdb=" N ARG F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 141 Proline residue: F 126 - end of helix Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.650A pdb=" N LYS F 145 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 Processing helix chain 'F' and resid 169 through 179 removed outlier: 3.515A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.829A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.582A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 383 Processing helix chain 'F' and resid 383 through 394 removed outlier: 4.092A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 56 1058 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4524 1.34 - 1.46: 4243 1.46 - 1.58: 6869 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 15780 Sorted by residual: bond pdb=" CB PRO B 15 " pdb=" CG PRO B 15 " ideal model delta sigma weight residual 1.492 1.527 -0.035 5.00e-02 4.00e+02 4.83e-01 bond pdb=" CB PRO A 15 " pdb=" CG PRO A 15 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.72e-01 bond pdb=" CB PRO D 15 " pdb=" CG PRO D 15 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.53e-01 bond pdb=" CB PRO E 15 " pdb=" CG PRO E 15 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.52e-01 bond pdb=" CB PRO C 15 " pdb=" CG PRO C 15 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.50e-01 ... (remaining 15775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 21058 1.08 - 2.15: 241 2.15 - 3.23: 55 3.23 - 4.30: 0 4.30 - 5.38: 12 Bond angle restraints: 21366 Sorted by residual: angle pdb=" N LYS D 369 " pdb=" CA LYS D 369 " pdb=" C LYS D 369 " ideal model delta sigma weight residual 112.13 114.29 -2.16 1.37e+00 5.33e-01 2.48e+00 angle pdb=" N LYS F 369 " pdb=" CA LYS F 369 " pdb=" C LYS F 369 " ideal model delta sigma weight residual 112.13 114.27 -2.14 1.37e+00 5.33e-01 2.44e+00 angle pdb=" N LYS A 369 " pdb=" CA LYS A 369 " pdb=" C LYS A 369 " ideal model delta sigma weight residual 112.13 114.26 -2.13 1.37e+00 5.33e-01 2.42e+00 angle pdb=" N LYS B 369 " pdb=" CA LYS B 369 " pdb=" C LYS B 369 " ideal model delta sigma weight residual 112.13 114.26 -2.13 1.37e+00 5.33e-01 2.41e+00 angle pdb=" N LYS C 369 " pdb=" CA LYS C 369 " pdb=" C LYS C 369 " ideal model delta sigma weight residual 112.13 114.25 -2.12 1.37e+00 5.33e-01 2.40e+00 ... (remaining 21361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.71: 8472 11.71 - 23.42: 514 23.42 - 35.12: 198 35.12 - 46.83: 68 46.83 - 58.54: 18 Dihedral angle restraints: 9270 sinusoidal: 3786 harmonic: 5484 Sorted by residual: dihedral pdb=" CA LYS A 369 " pdb=" C LYS A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta harmonic sigma weight residual -180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LYS C 369 " pdb=" C LYS C 369 " pdb=" N ASN C 370 " pdb=" CA ASN C 370 " ideal model delta harmonic sigma weight residual -180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LYS E 369 " pdb=" C LYS E 369 " pdb=" N ASN E 370 " pdb=" CA ASN E 370 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1420 0.025 - 0.049: 549 0.049 - 0.074: 293 0.074 - 0.099: 48 0.099 - 0.123: 48 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CA ILE F 53 " pdb=" N ILE F 53 " pdb=" C ILE F 53 " pdb=" CB ILE F 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE E 53 " pdb=" N ILE E 53 " pdb=" C ILE E 53 " pdb=" CB ILE E 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 2355 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO D 22 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 21 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO C 22 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 22 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 22 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 21 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO B 22 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.014 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 11548 3.11 - 3.56: 16785 3.56 - 4.01: 23221 4.01 - 4.45: 29682 4.45 - 4.90: 43433 Nonbonded interactions: 124669 Sorted by model distance: nonbonded pdb=" O ARG B 346 " pdb=" OG SER B 347 " model vdw 2.664 3.040 nonbonded pdb=" O ARG F 346 " pdb=" OG SER F 347 " model vdw 2.664 3.040 nonbonded pdb=" O ARG D 346 " pdb=" OG SER D 347 " model vdw 2.664 3.040 nonbonded pdb=" O ARG A 346 " pdb=" OG SER A 347 " model vdw 2.665 3.040 nonbonded pdb=" O ARG C 346 " pdb=" OG SER C 347 " model vdw 2.665 3.040 ... (remaining 124664 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.120 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:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.002 0.035 15798 Z= 0.077 Angle : 0.353 5.381 21402 Z= 0.187 Chirality : 0.036 0.123 2358 Planarity : 0.002 0.026 2568 Dihedral : 9.947 58.541 5664 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.47 % Allowed : 8.48 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.19), residues: 1782 helix: 2.67 (0.14), residues: 1272 sheet: 3.21 (0.46), residues: 96 loop : -0.11 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.008 0.001 TYR D 332 PHE 0.006 0.001 PHE B 275 TRP 0.009 0.001 TRP C 24 HIS 0.002 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (15780) covalent geometry : angle 0.35275 / 0.19 (21366) SS BOND : bond 0.00053 / 0.03 ( 18) SS BOND : angle 0.47782 / 0.32 ( 36) hydrogen bonds : bond 0.11607 / 7.67 ( 1058) hydrogen bonds : angle 5.25290 / 3.74 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.414 Fit side-chains REVERT: A 17 TYR cc_start: 0.8873 (m-10) cc_final: 0.8642 (m-10) REVERT: A 25 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: A 29 ASP cc_start: 0.8732 (m-30) cc_final: 0.8429 (m-30) REVERT: A 46 GLN cc_start: 0.9157 (tp40) cc_final: 0.8887 (tp-100) REVERT: A 49 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8331 (mp10) REVERT: A 169 THR cc_start: 0.8690 (m) cc_final: 0.8445 (p) REVERT: A 324 PHE cc_start: 0.8467 (t80) cc_final: 0.7902 (m-80) REVERT: A 352 SER cc_start: 0.8818 (m) cc_final: 0.8459 (p) REVERT: A 370 ASN cc_start: 0.8641 (m-40) cc_final: 0.8227 (m-40) REVERT: B 25 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: B 46 GLN cc_start: 0.9075 (tp40) cc_final: 0.8872 (tp40) REVERT: B 49 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: B 51 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7728 (mttp) REVERT: B 163 CYS cc_start: 0.8871 (m) cc_final: 0.8445 (m) REVERT: B 233 ASP cc_start: 0.8798 (t70) cc_final: 0.8036 (t0) REVERT: B 236 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8572 (mp0) REVERT: B 238 GLU cc_start: 0.8384 (tp30) cc_final: 0.7926 (tp30) REVERT: B 324 PHE cc_start: 0.8345 (t80) cc_final: 0.7855 (m-80) REVERT: B 352 SER cc_start: 0.9067 (m) cc_final: 0.8666 (t) REVERT: C 49 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: C 159 ILE cc_start: 0.8595 (mm) cc_final: 0.8329 (mt) REVERT: C 324 PHE cc_start: 0.8647 (t80) cc_final: 0.8012 (m-80) REVERT: C 352 SER cc_start: 0.8847 (m) cc_final: 0.8346 (t) REVERT: D 25 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: D 29 ASP cc_start: 0.8463 (m-30) cc_final: 0.8064 (m-30) REVERT: D 46 GLN cc_start: 0.9247 (tp40) cc_final: 0.8819 (tp-100) REVERT: D 102 ASP cc_start: 0.8073 (p0) cc_final: 0.7643 (p0) REVERT: D 159 ILE cc_start: 0.8598 (mm) cc_final: 0.8318 (mt) REVERT: D 163 CYS cc_start: 0.8925 (m) cc_final: 0.8591 (m) REVERT: D 169 THR cc_start: 0.8167 (m) cc_final: 0.7937 (t) REVERT: D 233 ASP cc_start: 0.8859 (t70) cc_final: 0.7854 (t0) REVERT: D 236 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8782 (mp0) REVERT: D 238 GLU cc_start: 0.8067 (tp30) cc_final: 0.7718 (tp30) REVERT: D 275 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8457 (t80) REVERT: D 324 PHE cc_start: 0.8433 (t80) cc_final: 0.8063 (m-80) REVERT: D 352 SER cc_start: 0.8775 (m) cc_final: 0.8417 (p) REVERT: D 370 ASN cc_start: 0.8887 (m-40) cc_final: 0.8544 (m-40) REVERT: E 25 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: E 49 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: E 233 ASP cc_start: 0.8668 (t70) cc_final: 0.7726 (t0) REVERT: E 236 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8324 (mp0) REVERT: E 238 GLU cc_start: 0.8689 (tp30) cc_final: 0.8247 (tp30) REVERT: E 324 PHE cc_start: 0.8326 (t80) cc_final: 0.7716 (m-80) REVERT: E 352 SER cc_start: 0.8965 (m) cc_final: 0.8551 (t) REVERT: E 370 ASN cc_start: 0.8699 (m-40) cc_final: 0.8227 (m-40) REVERT: F 49 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8589 (mp10) REVERT: F 63 ASP cc_start: 0.8629 (m-30) cc_final: 0.8388 (p0) REVERT: F 352 SER cc_start: 0.8902 (m) cc_final: 0.8452 (t) REVERT: F 381 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7986 (mm-40) outliers start: 42 outliers final: 8 residues processed: 331 average time/residue: 0.5610 time to fit residues: 205.2092 Evaluate side-chains 170 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 275 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 105 GLN A 239 GLN A 288 ASN B 49 GLN B 105 GLN B 239 GLN C 49 GLN C 105 GLN C 267 GLN C 288 ASN D 49 GLN D 105 GLN D 155 HIS D 239 GLN E 49 GLN E 105 GLN E 239 GLN F 49 GLN F 105 GLN F 107 ASN F 288 ASN F 381 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073673 restraints weight = 26204.834| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.72 r_work: 0.2808 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15798 Z= 0.150 Angle : 0.472 5.796 21402 Z= 0.258 Chirality : 0.040 0.191 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.943 57.562 2068 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.53 % Allowed : 13.55 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.29 (0.19), residues: 1782 helix: 2.78 (0.14), residues: 1278 sheet: 3.18 (0.47), residues: 96 loop : -0.12 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 309 TYR 0.012 0.001 TYR E 30 PHE 0.010 0.001 PHE A 318 TRP 0.011 0.001 TRP D 168 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15780) covalent geometry : angle 0.47073 / 0.26 (21366) SS BOND : bond 0.00144 / 0.09 ( 18) SS BOND : angle 0.96871 / 0.56 ( 36) hydrogen bonds : bond 0.04283 / 2.81 ( 1058) hydrogen bonds : angle 4.22625 / 2.98 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 0.582 Fit side-chains REVERT: A 17 TYR cc_start: 0.8789 (m-10) cc_final: 0.8571 (m-10) REVERT: A 25 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: A 46 GLN cc_start: 0.9102 (tp40) cc_final: 0.8833 (tp-100) REVERT: A 49 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: A 104 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8171 (t70) REVERT: A 233 ASP cc_start: 0.8428 (t0) cc_final: 0.7051 (t0) REVERT: A 236 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8362 (mp0) REVERT: A 254 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 324 PHE cc_start: 0.8327 (t80) cc_final: 0.7598 (m-80) REVERT: A 327 SER cc_start: 0.8969 (t) cc_final: 0.8743 (p) REVERT: A 352 SER cc_start: 0.8784 (m) cc_final: 0.8339 (p) REVERT: A 380 ASP cc_start: 0.8445 (t0) cc_final: 0.8237 (m-30) REVERT: B 49 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: B 51 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7601 (mttp) REVERT: B 163 CYS cc_start: 0.8652 (m) cc_final: 0.8163 (m) REVERT: B 233 ASP cc_start: 0.8858 (t70) cc_final: 0.7866 (t0) REVERT: B 236 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8750 (mp0) REVERT: B 281 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7900 (p90) REVERT: B 324 PHE cc_start: 0.8221 (t80) cc_final: 0.7587 (m-80) REVERT: B 352 SER cc_start: 0.9009 (m) cc_final: 0.8503 (t) REVERT: B 381 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: C 49 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: C 104 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8243 (t70) REVERT: C 162 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8491 (mtmm) REVERT: C 281 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7940 (p90) REVERT: C 324 PHE cc_start: 0.8431 (t80) cc_final: 0.7895 (m-80) REVERT: D 25 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: D 29 ASP cc_start: 0.8360 (m-30) cc_final: 0.7870 (m-30) REVERT: D 46 GLN cc_start: 0.9144 (tp40) cc_final: 0.8845 (tp-100) REVERT: D 49 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: D 104 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8217 (t70) REVERT: D 275 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8153 (t80) REVERT: D 281 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8249 (p90) REVERT: D 324 PHE cc_start: 0.8308 (t80) cc_final: 0.7925 (m-80) REVERT: D 352 SER cc_start: 0.8728 (m) cc_final: 0.8305 (p) REVERT: E 49 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: E 163 CYS cc_start: 0.8638 (m) cc_final: 0.8165 (m) REVERT: E 233 ASP cc_start: 0.8699 (t70) cc_final: 0.7582 (t0) REVERT: E 235 LYS cc_start: 0.8995 (mtpm) cc_final: 0.8697 (mtpp) REVERT: E 236 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8592 (mp0) REVERT: E 281 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8005 (p90) REVERT: E 324 PHE cc_start: 0.8263 (t80) cc_final: 0.7437 (m-80) REVERT: E 352 SER cc_start: 0.8887 (m) cc_final: 0.8391 (t) REVERT: E 370 ASN cc_start: 0.8721 (m-40) cc_final: 0.8227 (m-40) REVERT: E 381 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: F 49 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: F 63 ASP cc_start: 0.8653 (m-30) cc_final: 0.8264 (p0) REVERT: F 155 HIS cc_start: 0.8685 (t-170) cc_final: 0.8294 (t-170) REVERT: F 236 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8434 (mp0) REVERT: F 254 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8647 (t) REVERT: F 381 GLN cc_start: 0.8229 (tp40) cc_final: 0.7906 (mm-40) outliers start: 77 outliers final: 14 residues processed: 230 average time/residue: 0.4781 time to fit residues: 124.1532 Evaluate side-chains 173 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [145, 20, 143, 124, 6, 138, 56, 59, 92, 112, 136] chunk 145 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 253 HIS D 239 GLN E 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.073028 restraints weight = 26245.495| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.72 r_work: 0.2814 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15798 Z= 0.119 Angle : 0.442 5.450 21402 Z= 0.240 Chirality : 0.040 0.208 2358 Planarity : 0.003 0.030 2568 Dihedral : 5.877 59.224 2064 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.59 % Allowed : 15.84 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.19), residues: 1782 helix: 2.98 (0.13), residues: 1248 sheet: 3.40 (0.47), residues: 96 loop : 0.04 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 309 TYR 0.012 0.001 TYR F 281 PHE 0.007 0.001 PHE C 318 TRP 0.011 0.001 TRP D 168 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15780) covalent geometry : angle 0.44124 / 0.24 (21366) SS BOND : bond 0.00147 / 0.09 ( 18) SS BOND : angle 0.66142 / 0.39 ( 36) hydrogen bonds : bond 0.03775 / 2.47 ( 1058) hydrogen bonds : angle 4.03920 / 2.86 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.450 Fit side-chains REVERT: A 17 TYR cc_start: 0.8752 (m-10) cc_final: 0.8494 (m-10) REVERT: A 25 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: A 29 ASP cc_start: 0.8205 (m-30) cc_final: 0.7931 (m-30) REVERT: A 46 GLN cc_start: 0.9038 (tp40) cc_final: 0.8767 (tp-100) REVERT: A 49 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: A 104 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8091 (t70) REVERT: A 233 ASP cc_start: 0.8689 (t0) cc_final: 0.7710 (t0) REVERT: A 236 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8247 (mp0) REVERT: A 281 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8073 (p90) REVERT: A 324 PHE cc_start: 0.8266 (t80) cc_final: 0.7576 (m-80) REVERT: A 352 SER cc_start: 0.8704 (m) cc_final: 0.8285 (p) REVERT: A 381 GLN cc_start: 0.8382 (tp40) cc_final: 0.7952 (mm-40) REVERT: B 49 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: B 163 CYS cc_start: 0.8537 (m) cc_final: 0.8046 (m) REVERT: B 233 ASP cc_start: 0.8890 (t70) cc_final: 0.7753 (t0) REVERT: B 236 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8758 (mp0) REVERT: B 281 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7887 (p90) REVERT: B 324 PHE cc_start: 0.8147 (t80) cc_final: 0.7412 (m-80) REVERT: B 352 SER cc_start: 0.8878 (m) cc_final: 0.8323 (t) REVERT: B 381 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: C 49 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: C 104 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8290 (t70) REVERT: C 281 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7819 (p90) REVERT: C 324 PHE cc_start: 0.8324 (t80) cc_final: 0.7810 (m-80) REVERT: C 380 ASP cc_start: 0.8572 (t0) cc_final: 0.8281 (m-30) REVERT: D 25 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: D 29 ASP cc_start: 0.8266 (m-30) cc_final: 0.7920 (m-30) REVERT: D 46 GLN cc_start: 0.9070 (tp40) cc_final: 0.8706 (tp-100) REVERT: D 49 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: D 104 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8161 (t70) REVERT: D 281 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8184 (p90) REVERT: D 324 PHE cc_start: 0.8178 (t80) cc_final: 0.7821 (m-80) REVERT: D 352 SER cc_start: 0.8771 (m) cc_final: 0.8336 (p) REVERT: E 49 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: E 163 CYS cc_start: 0.8563 (m) cc_final: 0.8069 (m) REVERT: E 233 ASP cc_start: 0.8827 (t70) cc_final: 0.7698 (t0) REVERT: E 235 LYS cc_start: 0.8915 (mtpm) cc_final: 0.8648 (mtpp) REVERT: E 236 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8667 (mp0) REVERT: E 281 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7988 (p90) REVERT: E 324 PHE cc_start: 0.7998 (t80) cc_final: 0.7469 (m-80) REVERT: E 352 SER cc_start: 0.8806 (m) cc_final: 0.8274 (t) REVERT: E 370 ASN cc_start: 0.8618 (m-40) cc_final: 0.8167 (m-40) REVERT: F 49 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: F 63 ASP cc_start: 0.8666 (m-30) cc_final: 0.8257 (p0) REVERT: F 155 HIS cc_start: 0.8600 (t-170) cc_final: 0.8198 (t-170) REVERT: F 236 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8392 (mp0) REVERT: F 254 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8511 (t) REVERT: F 281 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8067 (p90) outliers start: 61 outliers final: 16 residues processed: 211 average time/residue: 0.4643 time to fit residues: 110.6601 Evaluate side-chains 178 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [109, 141, 149, 165, 162, 44, 30, 62, 21, 65, 114] chunk 109 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN C 155 HIS D 239 GLN E 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.067893 restraints weight = 26642.789| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.70 r_work: 0.2715 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 15798 Z= 0.249 Angle : 0.542 5.720 21402 Z= 0.295 Chirality : 0.043 0.203 2358 Planarity : 0.003 0.032 2568 Dihedral : 6.261 59.737 2064 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.18 % Allowed : 15.96 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.19), residues: 1782 helix: 2.52 (0.14), residues: 1278 sheet: 2.43 (0.51), residues: 102 loop : -0.21 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 306 TYR 0.025 0.002 TYR E 30 PHE 0.016 0.002 PHE A 146 TRP 0.012 0.001 TRP D 168 HIS 0.004 0.001 HIS E 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (15780) covalent geometry : angle 0.54114 / 0.29 (21366) SS BOND : bond 0.00247 / 0.16 ( 18) SS BOND : angle 0.96143 / 0.60 ( 36) hydrogen bonds : bond 0.04667 / 3.04 ( 1058) hydrogen bonds : angle 4.22164 / 2.98 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 140 time to evaluate : 0.550 Fit side-chains REVERT: A 17 TYR cc_start: 0.8856 (m-10) cc_final: 0.8636 (m-10) REVERT: A 25 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: A 49 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: A 104 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.8517 (t70) REVERT: A 233 ASP cc_start: 0.8826 (t0) cc_final: 0.7539 (t0) REVERT: A 235 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8131 (mtpp) REVERT: A 236 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8475 (mp0) REVERT: A 281 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8147 (p90) REVERT: A 324 PHE cc_start: 0.8168 (t80) cc_final: 0.7708 (m-80) REVERT: B 49 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: B 163 CYS cc_start: 0.8635 (m) cc_final: 0.8187 (m) REVERT: B 233 ASP cc_start: 0.8782 (t70) cc_final: 0.7800 (t0) REVERT: B 236 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8718 (mp0) REVERT: B 238 GLU cc_start: 0.8266 (tp30) cc_final: 0.7920 (tp30) REVERT: B 324 PHE cc_start: 0.8083 (t80) cc_final: 0.7522 (m-80) REVERT: B 380 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: B 381 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: C 49 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: C 104 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8157 (t70) REVERT: C 324 PHE cc_start: 0.8523 (t80) cc_final: 0.7973 (m-80) REVERT: C 380 ASP cc_start: 0.8780 (t0) cc_final: 0.8487 (m-30) REVERT: D 25 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: D 46 GLN cc_start: 0.9100 (tp40) cc_final: 0.8809 (tp-100) REVERT: D 49 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: D 104 HIS cc_start: 0.9122 (OUTLIER) cc_final: 0.8487 (t70) REVERT: D 233 ASP cc_start: 0.8639 (t0) cc_final: 0.7269 (t0) REVERT: D 236 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: D 324 PHE cc_start: 0.8341 (t80) cc_final: 0.7847 (m-80) REVERT: E 49 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8345 (mp10) REVERT: E 163 CYS cc_start: 0.8504 (m) cc_final: 0.8064 (m) REVERT: E 233 ASP cc_start: 0.8786 (t70) cc_final: 0.7649 (t0) REVERT: E 235 LYS cc_start: 0.8980 (mtpm) cc_final: 0.8706 (mtpp) REVERT: E 236 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8637 (mp0) REVERT: E 324 PHE cc_start: 0.8113 (t80) cc_final: 0.7543 (m-80) REVERT: E 380 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: E 381 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: F 49 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: F 63 ASP cc_start: 0.8681 (m-30) cc_final: 0.8343 (p0) REVERT: F 104 HIS cc_start: 0.9038 (OUTLIER) cc_final: 0.8572 (t70) REVERT: F 235 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8597 (mmmm) REVERT: F 236 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8413 (mp0) REVERT: F 254 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8626 (t) REVERT: F 281 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7951 (p90) outliers start: 71 outliers final: 30 residues processed: 199 average time/residue: 0.5005 time to fit residues: 111.7756 Evaluate side-chains 181 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [121, 19, 33, 127, 13, 73, 0, 165, 133, 24, 178] chunk 121 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN D 239 GLN E 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070511 restraints weight = 26399.505| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.72 r_work: 0.2765 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15798 Z= 0.131 Angle : 0.452 5.454 21402 Z= 0.247 Chirality : 0.040 0.182 2358 Planarity : 0.003 0.033 2568 Dihedral : 6.149 59.742 2064 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.89 % Allowed : 17.20 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.27 (0.19), residues: 1782 helix: 2.81 (0.13), residues: 1248 sheet: 2.70 (0.51), residues: 102 loop : 0.02 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 389 TYR 0.014 0.001 TYR B 281 PHE 0.013 0.001 PHE A 353 TRP 0.016 0.001 TRP D 168 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15780) covalent geometry : angle 0.45177 / 0.25 (21366) SS BOND : bond 0.00154 / 0.10 ( 18) SS BOND : angle 0.60047 / 0.36 ( 36) hydrogen bonds : bond 0.03847 / 2.52 ( 1058) hydrogen bonds : angle 3.99818 / 2.83 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 0.505 Fit side-chains REVERT: A 17 TYR cc_start: 0.8756 (m-10) cc_final: 0.8466 (m-10) REVERT: A 25 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 46 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8599 (tp40) REVERT: A 49 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: A 104 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8091 (t70) REVERT: A 233 ASP cc_start: 0.8845 (t0) cc_final: 0.7511 (t0) REVERT: A 235 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8228 (mtpp) REVERT: A 236 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8380 (mp0) REVERT: A 281 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8113 (p90) REVERT: A 324 PHE cc_start: 0.8099 (t80) cc_final: 0.7677 (m-80) REVERT: A 351 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8701 (t80) REVERT: B 49 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: B 163 CYS cc_start: 0.8625 (m) cc_final: 0.8139 (m) REVERT: B 233 ASP cc_start: 0.8817 (t70) cc_final: 0.7580 (t0) REVERT: B 236 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8679 (mp0) REVERT: B 238 GLU cc_start: 0.8207 (tp30) cc_final: 0.7865 (tp30) REVERT: B 281 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8045 (p90) REVERT: B 324 PHE cc_start: 0.8040 (t80) cc_final: 0.7490 (m-80) REVERT: B 380 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: B 381 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8414 (mp10) REVERT: C 49 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: C 104 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8244 (t70) REVERT: C 155 HIS cc_start: 0.8638 (t-90) cc_final: 0.8199 (t-170) REVERT: C 281 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8008 (p90) REVERT: C 324 PHE cc_start: 0.8406 (t80) cc_final: 0.7884 (m-80) REVERT: C 351 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7946 (t80) REVERT: D 25 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: D 46 GLN cc_start: 0.9060 (tp40) cc_final: 0.8838 (tp-100) REVERT: D 49 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: D 104 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8245 (t70) REVERT: D 233 ASP cc_start: 0.8752 (t0) cc_final: 0.7432 (t0) REVERT: D 236 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8650 (mp0) REVERT: D 281 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8182 (p90) REVERT: D 324 PHE cc_start: 0.8275 (t80) cc_final: 0.7827 (m-80) REVERT: D 351 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (t80) REVERT: E 49 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: E 163 CYS cc_start: 0.8565 (m) cc_final: 0.8106 (m) REVERT: E 233 ASP cc_start: 0.8792 (t70) cc_final: 0.7565 (t0) REVERT: E 236 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8657 (mp0) REVERT: E 238 GLU cc_start: 0.8392 (tp30) cc_final: 0.8031 (tp30) REVERT: E 281 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7965 (p90) REVERT: E 324 PHE cc_start: 0.8064 (t80) cc_final: 0.7507 (m-80) REVERT: E 370 ASN cc_start: 0.8753 (m-40) cc_final: 0.8334 (m-40) REVERT: E 380 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: E 381 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: F 49 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: F 63 ASP cc_start: 0.8702 (m-30) cc_final: 0.8245 (p0) REVERT: F 236 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8244 (mp0) REVERT: F 281 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8027 (p90) REVERT: F 324 PHE cc_start: 0.8534 (t80) cc_final: 0.7930 (m-80) outliers start: 66 outliers final: 21 residues processed: 198 average time/residue: 0.4909 time to fit residues: 109.1148 Evaluate side-chains 184 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [74, 149, 122, 47, 45, 37, 83, 134, 69, 24, 99] chunk 74 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN D 239 GLN E 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.068236 restraints weight = 26345.706| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.69 r_work: 0.2722 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 15798 Z= 0.224 Angle : 0.517 5.645 21402 Z= 0.281 Chirality : 0.042 0.183 2358 Planarity : 0.003 0.034 2568 Dihedral : 6.270 59.882 2064 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.06 % Allowed : 17.31 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.19), residues: 1782 helix: 2.53 (0.14), residues: 1278 sheet: 2.51 (0.51), residues: 102 loop : -0.33 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 306 TYR 0.021 0.002 TYR C 30 PHE 0.013 0.002 PHE C 353 TRP 0.018 0.001 TRP D 168 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (15780) covalent geometry : angle 0.51606 / 0.28 (21366) SS BOND : bond 0.00235 / 0.15 ( 18) SS BOND : angle 0.82115 / 0.51 ( 36) hydrogen bonds : bond 0.04394 / 2.87 ( 1058) hydrogen bonds : angle 4.10900 / 2.91 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 132 time to evaluate : 0.585 Fit side-chains REVERT: A 17 TYR cc_start: 0.8871 (m-10) cc_final: 0.8617 (m-10) REVERT: A 25 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: A 49 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: A 104 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8446 (t70) REVERT: A 233 ASP cc_start: 0.8922 (t0) cc_final: 0.7662 (t0) REVERT: A 236 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8468 (mp0) REVERT: A 281 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8182 (p90) REVERT: A 324 PHE cc_start: 0.8225 (t80) cc_final: 0.7757 (m-80) REVERT: A 351 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8765 (t80) REVERT: B 49 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8328 (mp10) REVERT: B 163 CYS cc_start: 0.8622 (m) cc_final: 0.8171 (m) REVERT: B 233 ASP cc_start: 0.8834 (t70) cc_final: 0.7772 (t0) REVERT: B 236 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8699 (mp0) REVERT: B 238 GLU cc_start: 0.8237 (tp30) cc_final: 0.7933 (tp30) REVERT: B 281 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8010 (p90) REVERT: B 324 PHE cc_start: 0.8137 (t80) cc_final: 0.7574 (m-80) REVERT: B 380 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8415 (m-30) REVERT: B 381 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: C 49 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: C 104 HIS cc_start: 0.9117 (OUTLIER) cc_final: 0.8362 (t70) REVERT: C 155 HIS cc_start: 0.8793 (t-90) cc_final: 0.8374 (t-170) REVERT: C 281 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7997 (p90) REVERT: C 324 PHE cc_start: 0.8566 (t80) cc_final: 0.8030 (m-80) REVERT: D 25 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: D 49 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: D 104 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8448 (t70) REVERT: D 281 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8319 (p90) REVERT: D 324 PHE cc_start: 0.8395 (t80) cc_final: 0.7889 (m-80) REVERT: D 351 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8883 (t80) REVERT: E 49 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: E 163 CYS cc_start: 0.8559 (m) cc_final: 0.8080 (m) REVERT: E 233 ASP cc_start: 0.8730 (t70) cc_final: 0.7594 (t0) REVERT: E 236 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8640 (mp0) REVERT: E 238 GLU cc_start: 0.8396 (tp30) cc_final: 0.8098 (tp30) REVERT: E 324 PHE cc_start: 0.8160 (t80) cc_final: 0.7589 (m-80) REVERT: E 380 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: E 381 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (mp10) REVERT: F 49 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: F 63 ASP cc_start: 0.8675 (m-30) cc_final: 0.8360 (p0) REVERT: F 155 HIS cc_start: 0.8756 (t-170) cc_final: 0.8429 (t-170) REVERT: F 254 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8684 (t) REVERT: F 281 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8015 (p90) REVERT: F 324 PHE cc_start: 0.8648 (t80) cc_final: 0.8005 (m-80) outliers start: 69 outliers final: 26 residues processed: 188 average time/residue: 0.4930 time to fit residues: 104.2119 Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [34, 178, 127, 165, 63, 65, 0, 9, 132, 47, 83] chunk 34 optimal weight: 0.0980 chunk 178 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 GLN D 239 GLN E 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.072699 restraints weight = 26124.537| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.70 r_work: 0.2791 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15798 Z= 0.112 Angle : 0.439 5.192 21402 Z= 0.240 Chirality : 0.039 0.179 2358 Planarity : 0.003 0.033 2568 Dihedral : 6.131 59.712 2064 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.18 % Allowed : 18.37 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.19), residues: 1782 helix: 2.66 (0.14), residues: 1278 sheet: 2.81 (0.52), residues: 102 loop : -0.39 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 309 TYR 0.014 0.001 TYR E 281 PHE 0.008 0.001 PHE B 275 TRP 0.018 0.001 TRP D 168 HIS 0.002 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15780) covalent geometry : angle 0.43905 / 0.24 (21366) SS BOND : bond 0.00139 / 0.09 ( 18) SS BOND : angle 0.49637 / 0.30 ( 36) hydrogen bonds : bond 0.03575 / 2.34 ( 1058) hydrogen bonds : angle 3.92647 / 2.78 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.613 Fit side-chains REVERT: A 17 TYR cc_start: 0.8766 (m-10) cc_final: 0.8528 (m-10) REVERT: A 25 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: A 49 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: A 104 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8171 (t70) REVERT: A 233 ASP cc_start: 0.8956 (t0) cc_final: 0.7685 (t0) REVERT: A 236 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8444 (mp0) REVERT: A 281 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8199 (p90) REVERT: A 324 PHE cc_start: 0.8155 (t80) cc_final: 0.7747 (m-80) REVERT: A 351 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8656 (t80) REVERT: B 49 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8414 (mp10) REVERT: B 163 CYS cc_start: 0.8682 (m) cc_final: 0.8333 (m) REVERT: B 233 ASP cc_start: 0.8816 (t70) cc_final: 0.7768 (t0) REVERT: B 236 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8657 (mp0) REVERT: B 238 GLU cc_start: 0.8223 (tp30) cc_final: 0.7908 (tp30) REVERT: B 281 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8158 (p90) REVERT: B 324 PHE cc_start: 0.8126 (t80) cc_final: 0.7523 (m-80) REVERT: B 370 ASN cc_start: 0.8838 (m-40) cc_final: 0.8513 (m-40) REVERT: C 49 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 104 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8558 (t70) REVERT: C 155 HIS cc_start: 0.8708 (t-90) cc_final: 0.8293 (t-170) REVERT: C 281 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8136 (p90) REVERT: C 324 PHE cc_start: 0.8460 (t80) cc_final: 0.7948 (m-80) REVERT: C 381 GLN cc_start: 0.8572 (tp40) cc_final: 0.8283 (mm-40) REVERT: D 25 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: D 49 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: D 104 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8174 (t70) REVERT: D 281 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8257 (p90) REVERT: D 324 PHE cc_start: 0.8319 (t80) cc_final: 0.7866 (m-80) REVERT: D 351 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8762 (t80) REVERT: E 49 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: E 163 CYS cc_start: 0.8684 (m) cc_final: 0.8324 (m) REVERT: E 238 GLU cc_start: 0.8358 (tp30) cc_final: 0.8052 (tp30) REVERT: E 281 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8190 (p90) REVERT: E 324 PHE cc_start: 0.8150 (t80) cc_final: 0.7535 (m-80) REVERT: E 370 ASN cc_start: 0.8760 (m-40) cc_final: 0.8355 (m-40) REVERT: E 380 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: E 381 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: F 49 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: F 63 ASP cc_start: 0.8668 (m-30) cc_final: 0.8252 (p0) REVERT: F 155 HIS cc_start: 0.8669 (t-170) cc_final: 0.8287 (t-170) REVERT: F 281 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8007 (p90) REVERT: F 324 PHE cc_start: 0.8571 (t80) cc_final: 0.8020 (m-80) outliers start: 54 outliers final: 19 residues processed: 197 average time/residue: 0.4851 time to fit residues: 108.0105 Evaluate side-chains 179 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [57, 114, 71, 53, 162, 138, 111, 135, 106, 116, 171] chunk 57 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 GLN D 239 GLN F 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.072086 restraints weight = 26213.749| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.70 r_work: 0.2805 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15798 Z= 0.111 Angle : 0.445 5.913 21402 Z= 0.242 Chirality : 0.040 0.201 2358 Planarity : 0.003 0.034 2568 Dihedral : 6.067 59.444 2064 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.77 % Allowed : 19.08 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.19), residues: 1782 helix: 2.69 (0.14), residues: 1278 sheet: 2.82 (0.52), residues: 102 loop : -0.43 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 262 TYR 0.013 0.001 TYR B 281 PHE 0.009 0.001 PHE E 331 TRP 0.020 0.001 TRP C 168 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15780) covalent geometry : angle 0.44528 / 0.24 (21366) SS BOND : bond 0.00129 / 0.08 ( 18) SS BOND : angle 0.48483 / 0.30 ( 36) hydrogen bonds : bond 0.03549 / 2.32 ( 1058) hydrogen bonds : angle 3.91331 / 2.77 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.414 Fit side-chains REVERT: A 17 TYR cc_start: 0.8729 (m-10) cc_final: 0.8492 (m-10) REVERT: A 25 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: A 29 ASP cc_start: 0.8222 (m-30) cc_final: 0.7944 (m-30) REVERT: A 49 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: A 104 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8061 (t70) REVERT: A 233 ASP cc_start: 0.8948 (t0) cc_final: 0.7714 (t0) REVERT: A 236 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8479 (mp0) REVERT: A 281 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8124 (p90) REVERT: A 324 PHE cc_start: 0.8059 (t80) cc_final: 0.7654 (m-80) REVERT: A 351 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8632 (t80) REVERT: B 49 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: B 163 CYS cc_start: 0.8609 (m) cc_final: 0.8260 (m) REVERT: B 233 ASP cc_start: 0.8852 (t70) cc_final: 0.7705 (t0) REVERT: B 236 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8626 (mp0) REVERT: B 238 GLU cc_start: 0.8190 (tp30) cc_final: 0.7889 (tp30) REVERT: B 281 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8062 (p90) REVERT: B 324 PHE cc_start: 0.8027 (t80) cc_final: 0.7533 (m-80) REVERT: B 370 ASN cc_start: 0.8714 (m-40) cc_final: 0.8364 (m-40) REVERT: C 49 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 155 HIS cc_start: 0.8636 (t-90) cc_final: 0.8181 (t-170) REVERT: C 281 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8052 (p90) REVERT: C 324 PHE cc_start: 0.8387 (t80) cc_final: 0.7978 (m-80) REVERT: C 370 ASN cc_start: 0.8597 (m-40) cc_final: 0.8278 (m-40) REVERT: C 381 GLN cc_start: 0.8550 (tp40) cc_final: 0.8244 (mm-40) REVERT: D 25 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: D 49 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: D 104 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8079 (t70) REVERT: D 281 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8156 (p90) REVERT: D 324 PHE cc_start: 0.8247 (t80) cc_final: 0.7803 (m-80) REVERT: D 351 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8734 (t80) REVERT: E 49 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: E 163 CYS cc_start: 0.8611 (m) cc_final: 0.8253 (m) REVERT: E 236 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8606 (mp0) REVERT: E 238 GLU cc_start: 0.8349 (tp30) cc_final: 0.8042 (tp30) REVERT: E 281 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7975 (p90) REVERT: E 324 PHE cc_start: 0.8054 (t80) cc_final: 0.7541 (m-80) REVERT: E 370 ASN cc_start: 0.8639 (m-40) cc_final: 0.8206 (m-40) REVERT: E 380 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: E 381 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: F 49 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: F 63 ASP cc_start: 0.8662 (m-30) cc_final: 0.8248 (p0) REVERT: F 155 HIS cc_start: 0.8581 (t-170) cc_final: 0.8171 (t-170) REVERT: F 236 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8278 (mp0) REVERT: F 278 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7866 (pt) REVERT: F 281 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8068 (p90) REVERT: F 324 PHE cc_start: 0.8453 (t80) cc_final: 0.7921 (m-80) REVERT: F 370 ASN cc_start: 0.8634 (m-40) cc_final: 0.8326 (m-40) outliers start: 47 outliers final: 19 residues processed: 194 average time/residue: 0.4799 time to fit residues: 104.5298 Evaluate side-chains 189 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 281 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [158, 121, 119, 124, 173, 63, 26, 100, 27, 147, 92] chunk 158 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 147 optimal weight: 0.0170 chunk 92 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 GLN D 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.073569 restraints weight = 26021.063| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.70 r_work: 0.2828 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15798 Z= 0.099 Angle : 0.439 6.468 21402 Z= 0.237 Chirality : 0.040 0.273 2358 Planarity : 0.003 0.033 2568 Dihedral : 6.005 59.812 2064 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.47 % Allowed : 19.61 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.12 (0.19), residues: 1782 helix: 2.73 (0.14), residues: 1278 sheet: 2.81 (0.51), residues: 102 loop : -0.47 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 262 TYR 0.014 0.001 TYR E 281 PHE 0.008 0.001 PHE B 331 TRP 0.021 0.001 TRP C 168 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (15780) covalent geometry : angle 0.43862 / 0.24 (21366) SS BOND : bond 0.00125 / 0.08 ( 18) SS BOND : angle 0.40844 / 0.24 ( 36) hydrogen bonds : bond 0.03343 / 2.19 ( 1058) hydrogen bonds : angle 3.86944 / 2.74 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.585 Fit side-chains REVERT: A 17 TYR cc_start: 0.8726 (m-10) cc_final: 0.8494 (m-10) REVERT: A 25 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: A 29 ASP cc_start: 0.8304 (m-30) cc_final: 0.7960 (m-30) REVERT: A 49 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: A 104 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.7926 (t70) REVERT: A 233 ASP cc_start: 0.8921 (t0) cc_final: 0.7637 (t0) REVERT: A 236 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8426 (mp0) REVERT: A 281 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8187 (p90) REVERT: A 324 PHE cc_start: 0.8033 (t80) cc_final: 0.7654 (m-80) REVERT: A 375 MET cc_start: 0.9025 (mtm) cc_final: 0.8797 (mtm) REVERT: B 49 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: B 233 ASP cc_start: 0.8849 (t70) cc_final: 0.7688 (t0) REVERT: B 236 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8679 (mp0) REVERT: B 238 GLU cc_start: 0.8212 (tp30) cc_final: 0.7907 (tp30) REVERT: B 281 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7904 (p90) REVERT: B 324 PHE cc_start: 0.8029 (t80) cc_final: 0.7496 (m-80) REVERT: B 370 ASN cc_start: 0.8628 (m-40) cc_final: 0.8249 (m-40) REVERT: C 49 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: C 155 HIS cc_start: 0.8526 (t-90) cc_final: 0.8049 (t-170) REVERT: C 281 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8045 (p90) REVERT: C 324 PHE cc_start: 0.8361 (t80) cc_final: 0.7962 (m-80) REVERT: C 370 ASN cc_start: 0.8536 (m-40) cc_final: 0.8220 (m-40) REVERT: C 381 GLN cc_start: 0.8505 (tp40) cc_final: 0.8186 (mm-40) REVERT: D 25 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: D 29 ASP cc_start: 0.8527 (m-30) cc_final: 0.8204 (m-30) REVERT: D 49 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: D 104 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.7900 (t70) REVERT: D 281 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8144 (p90) REVERT: D 324 PHE cc_start: 0.8227 (t80) cc_final: 0.7807 (m-80) REVERT: D 351 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8689 (t80) REVERT: D 375 MET cc_start: 0.9011 (mtm) cc_final: 0.8804 (mtm) REVERT: E 49 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: E 236 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8579 (mp0) REVERT: E 238 GLU cc_start: 0.8310 (tp30) cc_final: 0.8017 (tp30) REVERT: E 281 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8015 (p90) REVERT: E 324 PHE cc_start: 0.8020 (t80) cc_final: 0.7555 (m-80) REVERT: E 370 ASN cc_start: 0.8543 (m-40) cc_final: 0.8123 (m-40) REVERT: E 380 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: E 381 GLN cc_start: 0.8714 (tp40) cc_final: 0.8387 (mp10) REVERT: F 49 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: F 63 ASP cc_start: 0.8645 (m-30) cc_final: 0.8250 (p0) REVERT: F 155 HIS cc_start: 0.8599 (t-170) cc_final: 0.8219 (t-170) REVERT: F 236 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8292 (mp0) REVERT: F 278 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7793 (pt) REVERT: F 281 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7856 (p90) REVERT: F 324 PHE cc_start: 0.8461 (t80) cc_final: 0.7744 (m-80) REVERT: F 370 ASN cc_start: 0.8564 (m-40) cc_final: 0.8257 (m-40) outliers start: 42 outliers final: 16 residues processed: 199 average time/residue: 0.5034 time to fit residues: 112.5936 Evaluate side-chains 187 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 281 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [144, 26, 33, 11, 50, 125, 35, 135, 116, 38, 62] chunk 144 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 GLN D 239 GLN F 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072714 restraints weight = 26308.419| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.72 r_work: 0.2791 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15798 Z= 0.134 Angle : 0.467 7.260 21402 Z= 0.251 Chirality : 0.041 0.256 2358 Planarity : 0.003 0.033 2568 Dihedral : 6.056 59.791 2064 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.30 % Allowed : 19.91 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.06 (0.19), residues: 1782 helix: 2.68 (0.14), residues: 1278 sheet: 2.75 (0.51), residues: 102 loop : -0.46 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 266 TYR 0.014 0.001 TYR E 281 PHE 0.008 0.001 PHE E 275 TRP 0.023 0.001 TRP F 168 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15780) covalent geometry : angle 0.46680 / 0.25 (21366) SS BOND : bond 0.00150 / 0.10 ( 18) SS BOND : angle 0.58392 / 0.36 ( 36) hydrogen bonds : bond 0.03687 / 2.42 ( 1058) hydrogen bonds : angle 3.93742 / 2.79 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.614 Fit side-chains REVERT: A 17 TYR cc_start: 0.8852 (m-10) cc_final: 0.8633 (m-10) REVERT: A 25 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: A 29 ASP cc_start: 0.8317 (m-30) cc_final: 0.8043 (m-30) REVERT: A 49 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: A 104 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8176 (t70) REVERT: A 233 ASP cc_start: 0.8947 (t0) cc_final: 0.7717 (t0) REVERT: A 235 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8632 (mmpt) REVERT: A 236 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8486 (mp0) REVERT: A 281 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8253 (p90) REVERT: A 324 PHE cc_start: 0.8080 (t80) cc_final: 0.7672 (m-80) REVERT: B 49 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: B 233 ASP cc_start: 0.8845 (t70) cc_final: 0.7805 (t0) REVERT: B 236 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8610 (mp0) REVERT: B 238 GLU cc_start: 0.8210 (tp30) cc_final: 0.7898 (tp30) REVERT: B 281 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7996 (p90) REVERT: B 324 PHE cc_start: 0.7983 (t80) cc_final: 0.7503 (m-80) REVERT: B 370 ASN cc_start: 0.8711 (m-40) cc_final: 0.8350 (m-40) REVERT: C 49 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: C 155 HIS cc_start: 0.8579 (t-90) cc_final: 0.8127 (t-170) REVERT: C 281 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8011 (p90) REVERT: C 324 PHE cc_start: 0.8413 (t80) cc_final: 0.8000 (m-80) REVERT: C 370 ASN cc_start: 0.8603 (m-40) cc_final: 0.8246 (m-40) REVERT: C 381 GLN cc_start: 0.8564 (tp40) cc_final: 0.8243 (mm-40) REVERT: D 25 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: D 49 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: D 104 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8253 (t70) REVERT: D 281 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8205 (p90) REVERT: D 324 PHE cc_start: 0.8276 (t80) cc_final: 0.7827 (m-80) REVERT: D 351 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8653 (t80) REVERT: E 49 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: E 236 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8623 (mp0) REVERT: E 238 GLU cc_start: 0.8372 (tp30) cc_final: 0.8073 (tp30) REVERT: E 281 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7996 (p90) REVERT: E 324 PHE cc_start: 0.8083 (t80) cc_final: 0.7581 (m-80) REVERT: E 370 ASN cc_start: 0.8659 (m-40) cc_final: 0.8250 (m-40) REVERT: E 380 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: E 381 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: F 49 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: F 63 ASP cc_start: 0.8651 (m-30) cc_final: 0.8243 (p0) REVERT: F 155 HIS cc_start: 0.8643 (t-170) cc_final: 0.8245 (t-170) REVERT: F 233 ASP cc_start: 0.8594 (t0) cc_final: 0.7713 (t0) REVERT: F 236 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8219 (mp0) REVERT: F 278 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (pt) REVERT: F 281 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8061 (p90) REVERT: F 324 PHE cc_start: 0.8430 (t80) cc_final: 0.7911 (m-80) REVERT: F 370 ASN cc_start: 0.8600 (m-40) cc_final: 0.8292 (m-40) outliers start: 39 outliers final: 17 residues processed: 177 average time/residue: 0.5329 time to fit residues: 105.3013 Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 281 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [15, 94, 35, 125, 33, 152, 166, 148, 164, 100, 60] chunk 15 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 0.0870 chunk 60 optimal weight: 0.3980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073968 restraints weight = 25923.048| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.72 r_work: 0.2819 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15798 Z= 0.106 Angle : 0.451 7.674 21402 Z= 0.241 Chirality : 0.040 0.264 2358 Planarity : 0.003 0.033 2568 Dihedral : 6.008 59.324 2064 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.36 % Allowed : 19.85 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.10 (0.19), residues: 1782 helix: 2.73 (0.14), residues: 1278 sheet: 2.69 (0.50), residues: 102 loop : -0.49 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 262 TYR 0.014 0.001 TYR E 281 PHE 0.008 0.001 PHE B 275 TRP 0.025 0.001 TRP F 168 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15780) covalent geometry : angle 0.45142 / 0.24 (21366) SS BOND : bond 0.00130 / 0.08 ( 18) SS BOND : angle 0.45109 / 0.27 ( 36) hydrogen bonds : bond 0.03435 / 2.26 ( 1058) hydrogen bonds : angle 3.88668 / 2.75 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.51 seconds wall clock time: 68 minutes 5.75 seconds (4085.75 seconds total)