Starting phenix.real_space_refine on Sun May 18 07:46:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz7_45055/05_2025/9bz7_45055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz7_45055/05_2025/9bz7_45055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz7_45055/05_2025/9bz7_45055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz7_45055/05_2025/9bz7_45055.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz7_45055/05_2025/9bz7_45055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz7_45055/05_2025/9bz7_45055.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 77 5.16 5 C 11382 2.51 5 N 2604 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16961 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.12, per 1000 atoms: 0.36 Number of scatterers: 16961 At special positions: 0 Unit cell: (107, 107, 123.05, 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 77 16.00 O 2898 8.00 N 2604 7.00 C 11382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " 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: 4.24 Conformation dependent library (CDL) restraints added in 2.1 seconds 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 7 sheets defined 71.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.654A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 240 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.820A pdb=" N LEU A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 298 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.528A pdb=" N VAL A 310 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.833A pdb=" N LEU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.250A pdb=" N PHE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.653A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 209 through 240 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.821A pdb=" N LEU B 255 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.527A pdb=" N VAL B 310 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.833A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.250A pdb=" N PHE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.654A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 196 through 206 Processing helix chain 'C' and resid 209 through 240 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.822A pdb=" N LEU C 255 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 Proline residue: C 291 - end of helix Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.527A pdb=" N VAL C 310 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.832A pdb=" N LEU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.249A pdb=" N PHE C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.653A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 196 through 206 Processing helix chain 'D' and resid 209 through 240 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.820A pdb=" N LEU D 255 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 298 Proline residue: D 291 - end of helix Processing helix chain 'D' and resid 306 through 311 removed outlier: 3.528A pdb=" N VAL D 310 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.832A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 4.250A pdb=" N PHE D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 86 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.653A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 158 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'E' and resid 209 through 240 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.820A pdb=" N LEU E 255 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 Proline residue: E 291 - end of helix Processing helix chain 'E' and resid 306 through 311 removed outlier: 3.528A pdb=" N VAL E 310 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 341 removed outlier: 3.832A pdb=" N LEU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 4.250A pdb=" N PHE E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.653A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 158 Processing helix chain 'F' and resid 196 through 206 Processing helix chain 'F' and resid 209 through 240 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.820A pdb=" N LEU F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 298 Proline residue: F 291 - end of helix Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.527A pdb=" N VAL F 310 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 341 removed outlier: 3.832A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 357 removed outlier: 4.250A pdb=" N PHE F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.654A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 158 Processing helix chain 'G' and resid 196 through 206 Processing helix chain 'G' and resid 209 through 240 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.820A pdb=" N LEU G 255 " --> pdb=" O THR G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 Proline residue: G 291 - end of helix Processing helix chain 'G' and resid 306 through 311 removed outlier: 3.527A pdb=" N VAL G 310 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 341 removed outlier: 3.831A pdb=" N LEU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 357 removed outlier: 4.250A pdb=" N PHE G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS G 357 " --> pdb=" O LEU G 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1099 hydrogen bonds defined for protein. 3192 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: 4.79 Time building geometry restraints manager: 4.94 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: 4956 1.34 - 1.46: 3834 1.46 - 1.58: 8507 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 17395 Sorted by residual: bond pdb=" CG ARG G 256 " pdb=" CD ARG G 256 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.48e-01 bond pdb=" CG ARG E 256 " pdb=" CD ARG E 256 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.43e-01 bond pdb=" CG ARG C 256 " pdb=" CD ARG C 256 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.40e-01 bond pdb=" CG ARG F 256 " pdb=" CD ARG F 256 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.39e-01 bond pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.24e-01 ... (remaining 17390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 22724 1.15 - 2.29: 698 2.29 - 3.44: 112 3.44 - 4.59: 90 4.59 - 5.73: 36 Bond angle restraints: 23660 Sorted by residual: angle pdb=" C GLN B 56 " pdb=" N GLU B 57 " pdb=" CA GLU B 57 " ideal model delta sigma weight residual 120.68 116.28 4.40 1.70e+00 3.46e-01 6.69e+00 angle pdb=" C GLN F 56 " pdb=" N GLU F 57 " pdb=" CA GLU F 57 " ideal model delta sigma weight residual 120.68 116.32 4.36 1.70e+00 3.46e-01 6.57e+00 angle pdb=" C GLN G 56 " pdb=" N GLU G 57 " pdb=" CA GLU G 57 " ideal model delta sigma weight residual 120.68 116.33 4.35 1.70e+00 3.46e-01 6.54e+00 angle pdb=" C GLN C 56 " pdb=" N GLU C 57 " pdb=" CA GLU C 57 " ideal model delta sigma weight residual 120.68 116.33 4.35 1.70e+00 3.46e-01 6.54e+00 angle pdb=" C GLN A 56 " pdb=" N GLU A 57 " pdb=" CA GLU A 57 " ideal model delta sigma weight residual 120.68 116.36 4.32 1.70e+00 3.46e-01 6.45e+00 ... (remaining 23655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 8729 15.02 - 30.04: 1225 30.04 - 45.05: 371 45.05 - 60.07: 42 60.07 - 75.09: 28 Dihedral angle restraints: 10395 sinusoidal: 4130 harmonic: 6265 Sorted by residual: dihedral pdb=" CG LYS B 140 " pdb=" CD LYS B 140 " pdb=" CE LYS B 140 " pdb=" NZ LYS B 140 " ideal model delta sinusoidal sigma weight residual 180.00 120.29 59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 140 " pdb=" CD LYS A 140 " pdb=" CE LYS A 140 " pdb=" NZ LYS A 140 " ideal model delta sinusoidal sigma weight residual 180.00 120.29 59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS C 140 " pdb=" CD LYS C 140 " pdb=" CE LYS C 140 " pdb=" NZ LYS C 140 " ideal model delta sinusoidal sigma weight residual 180.00 120.31 59.69 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 10392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1950 0.034 - 0.067: 576 0.067 - 0.101: 238 0.101 - 0.134: 29 0.134 - 0.168: 14 Chirality restraints: 2807 Sorted by residual: chirality pdb=" CB ILE D 50 " pdb=" CA ILE D 50 " pdb=" CG1 ILE D 50 " pdb=" CG2 ILE D 50 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE E 50 " pdb=" CA ILE E 50 " pdb=" CG1 ILE E 50 " pdb=" CG2 ILE E 50 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CB ILE F 50 " pdb=" CA ILE F 50 " pdb=" CG1 ILE F 50 " pdb=" CG2 ILE F 50 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 2804 not shown) Planarity restraints: 2842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 57 " 0.005 2.00e-02 2.50e+03 9.51e-03 9.05e-01 pdb=" CD GLU C 57 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU C 57 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU C 57 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 57 " 0.004 2.00e-02 2.50e+03 8.93e-03 7.97e-01 pdb=" CD GLU E 57 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLU E 57 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU E 57 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 57 " -0.004 2.00e-02 2.50e+03 8.92e-03 7.95e-01 pdb=" CD GLU A 57 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLU A 57 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU A 57 " -0.005 2.00e-02 2.50e+03 ... (remaining 2839 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 349 2.71 - 3.26: 17129 3.26 - 3.80: 27093 3.80 - 4.35: 33413 4.35 - 4.90: 57839 Nonbonded interactions: 135823 Sorted by model distance: nonbonded pdb=" O GLN D 56 " pdb=" OG1 THR D 59 " model vdw 2.159 3.040 nonbonded pdb=" O GLN F 56 " pdb=" OG1 THR F 59 " model vdw 2.159 3.040 nonbonded pdb=" O GLN C 56 " pdb=" OG1 THR C 59 " model vdw 2.159 3.040 nonbonded pdb=" O GLN E 56 " pdb=" OG1 THR E 59 " model vdw 2.159 3.040 nonbonded pdb=" O GLN A 56 " pdb=" OG1 THR A 59 " model vdw 2.159 3.040 ... (remaining 135818 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.160 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 0.026 17409 Z= 0.111 Angle : 0.544 5.733 23688 Z= 0.275 Chirality : 0.039 0.168 2807 Planarity : 0.003 0.030 2842 Dihedral : 15.789 75.091 6279 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.79 % Allowed : 26.52 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2044 helix: 2.38 (0.14), residues: 1421 sheet: -1.41 (0.49), residues: 84 loop : -1.82 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS A 330 PHE 0.010 0.001 PHE F 109 TYR 0.005 0.001 TYR B 236 ARG 0.008 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.12106 ( 1099) hydrogen bonds : angle 4.13323 ( 3192) SS BOND : bond 0.00128 ( 14) SS BOND : angle 0.66479 ( 28) covalent geometry : bond 0.00235 (17395) covalent geometry : angle 0.54427 (23660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 2.097 Fit side-chains REVERT: B 290 MET cc_start: 0.9241 (ttm) cc_final: 0.9026 (mtp) REVERT: C 213 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9138 (mm) REVERT: C 306 ASN cc_start: 0.8193 (t0) cc_final: 0.7665 (t160) REVERT: C 309 LYS cc_start: 0.8780 (tmmt) cc_final: 0.8304 (ptpp) REVERT: D 303 LYS cc_start: 0.7329 (mttt) cc_final: 0.7023 (mtmt) REVERT: F 338 GLU cc_start: 0.8677 (tt0) cc_final: 0.8471 (tt0) REVERT: G 256 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8496 (mtm110) REVERT: G 303 LYS cc_start: 0.7215 (mttt) cc_final: 0.6789 (mtpt) outliers start: 34 outliers final: 4 residues processed: 249 average time/residue: 1.5147 time to fit residues: 416.8145 Evaluate side-chains 168 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 282 ASN B 266 GLN B 355 ASN C 266 GLN D 266 GLN D 355 ASN E 266 GLN F 266 GLN G 266 GLN G 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.108798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076807 restraints weight = 29418.396| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.72 r_work: 0.2918 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17409 Z= 0.212 Angle : 0.601 6.032 23688 Z= 0.297 Chirality : 0.041 0.158 2807 Planarity : 0.004 0.039 2842 Dihedral : 3.490 28.720 2263 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.15 % Allowed : 22.16 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2044 helix: 2.41 (0.14), residues: 1428 sheet: -1.39 (0.51), residues: 84 loop : -1.87 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 74 HIS 0.002 0.001 HIS A 134 PHE 0.015 0.001 PHE C 333 TYR 0.014 0.001 TYR B 25 ARG 0.008 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1099) hydrogen bonds : angle 3.68475 ( 3192) SS BOND : bond 0.00205 ( 14) SS BOND : angle 1.14379 ( 28) covalent geometry : bond 0.00515 (17395) covalent geometry : angle 0.59998 (23660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 202 time to evaluate : 1.908 Fit side-chains REVERT: A 345 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8620 (tptm) REVERT: B 303 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6598 (mttt) REVERT: B 345 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8679 (tptm) REVERT: C 48 LEU cc_start: 0.8663 (mt) cc_final: 0.8451 (mm) REVERT: C 345 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8777 (tptm) REVERT: D 63 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8184 (tp40) REVERT: D 345 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8711 (tptm) REVERT: D 354 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8454 (tm-30) REVERT: D 355 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7794 (m-40) REVERT: F 37 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9020 (mt) REVERT: G 256 ARG cc_start: 0.8919 (mtm110) cc_final: 0.8654 (mtm110) REVERT: G 303 LYS cc_start: 0.7154 (mttt) cc_final: 0.6625 (mppt) outliers start: 98 outliers final: 31 residues processed: 275 average time/residue: 1.2848 time to fit residues: 393.5825 Evaluate side-chains 207 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 355 ASN B 206 ASN B 355 ASN C 63 GLN C 306 ASN E 63 GLN G 206 ASN G 306 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079043 restraints weight = 28928.735| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.72 r_work: 0.2958 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17409 Z= 0.121 Angle : 0.535 6.963 23688 Z= 0.263 Chirality : 0.039 0.163 2807 Planarity : 0.003 0.037 2842 Dihedral : 3.183 21.509 2256 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.25 % Allowed : 22.22 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 2044 helix: 2.60 (0.14), residues: 1428 sheet: -1.46 (0.51), residues: 84 loop : -1.90 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 74 HIS 0.001 0.000 HIS F 106 PHE 0.008 0.001 PHE B 109 TYR 0.016 0.001 TYR A 111 ARG 0.008 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1099) hydrogen bonds : angle 3.49176 ( 3192) SS BOND : bond 0.00138 ( 14) SS BOND : angle 0.96001 ( 28) covalent geometry : bond 0.00285 (17395) covalent geometry : angle 0.53416 (23660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 207 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8594 (tptm) REVERT: B 303 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6593 (mttt) REVERT: B 345 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8574 (tptm) REVERT: C 345 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8839 (tptm) REVERT: D 151 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8460 (m-40) REVERT: D 154 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8126 (tp) REVERT: D 345 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8661 (tptm) REVERT: E 339 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8042 (tm-30) REVERT: F 63 GLN cc_start: 0.8371 (mm110) cc_final: 0.8085 (tp-100) REVERT: G 256 ARG cc_start: 0.8931 (mtm110) cc_final: 0.8684 (mtm110) REVERT: G 303 LYS cc_start: 0.7041 (mttt) cc_final: 0.6565 (mppt) outliers start: 81 outliers final: 31 residues processed: 262 average time/residue: 1.3200 time to fit residues: 384.6398 Evaluate side-chains 209 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 158 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 206 ASN B 355 ASN C 306 ASN D 63 GLN D 355 ASN F 306 ASN G 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080378 restraints weight = 28936.510| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.69 r_work: 0.2981 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17409 Z= 0.109 Angle : 0.529 5.873 23688 Z= 0.258 Chirality : 0.038 0.172 2807 Planarity : 0.003 0.038 2842 Dihedral : 3.138 21.301 2256 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.78 % Allowed : 22.64 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 2044 helix: 2.62 (0.14), residues: 1442 sheet: -1.43 (0.52), residues: 84 loop : -2.09 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 74 HIS 0.001 0.000 HIS E 106 PHE 0.008 0.001 PHE G 333 TYR 0.009 0.001 TYR B 25 ARG 0.009 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 1099) hydrogen bonds : angle 3.39279 ( 3192) SS BOND : bond 0.00133 ( 14) SS BOND : angle 0.91300 ( 28) covalent geometry : bond 0.00249 (17395) covalent geometry : angle 0.52843 (23660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 1.929 Fit side-chains REVERT: A 151 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8411 (m-40) REVERT: A 345 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8613 (tptm) REVERT: B 303 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6578 (mttt) REVERT: B 345 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8605 (tptm) REVERT: B 355 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: C 345 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8815 (tptm) REVERT: D 151 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8444 (m-40) REVERT: D 154 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8139 (tp) REVERT: D 345 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8605 (tptm) REVERT: D 354 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8419 (tm-30) REVERT: D 355 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7863 (m-40) REVERT: F 63 GLN cc_start: 0.8440 (mm110) cc_final: 0.8216 (tp-100) REVERT: F 339 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8098 (tm-30) REVERT: G 256 ARG cc_start: 0.8891 (mtm110) cc_final: 0.8572 (mtm110) outliers start: 72 outliers final: 38 residues processed: 249 average time/residue: 1.4086 time to fit residues: 388.3229 Evaluate side-chains 223 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 108 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 355 ASN C 306 ASN D 63 GLN D 355 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078788 restraints weight = 29378.834| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.73 r_work: 0.2934 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17409 Z= 0.147 Angle : 0.563 6.878 23688 Z= 0.276 Chirality : 0.039 0.181 2807 Planarity : 0.004 0.038 2842 Dihedral : 3.170 20.783 2256 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.67 % Allowed : 22.64 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 2044 helix: 2.59 (0.14), residues: 1442 sheet: -1.46 (0.52), residues: 84 loop : -2.04 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.002 0.000 HIS B 134 PHE 0.010 0.001 PHE C 333 TYR 0.011 0.001 TYR B 25 ARG 0.010 0.001 ARG D 152 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1099) hydrogen bonds : angle 3.45588 ( 3192) SS BOND : bond 0.00186 ( 14) SS BOND : angle 1.02344 ( 28) covalent geometry : bond 0.00359 (17395) covalent geometry : angle 0.56188 (23660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 199 time to evaluate : 2.092 Fit side-chains REVERT: A 345 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8566 (tptm) REVERT: B 303 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6500 (mttt) REVERT: B 345 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8528 (tptm) REVERT: B 355 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8227 (m110) REVERT: C 345 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8748 (tptm) REVERT: D 154 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8096 (tp) REVERT: D 345 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8604 (tptm) REVERT: E 339 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8061 (tm-30) REVERT: F 37 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9049 (mt) REVERT: F 144 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8835 (mm-30) REVERT: F 339 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8089 (tm-30) REVERT: G 256 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8694 (mtm110) outliers start: 89 outliers final: 41 residues processed: 264 average time/residue: 1.3187 time to fit residues: 387.5504 Evaluate side-chains 231 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 200 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 355 ASN C 63 GLN C 306 ASN D 63 GLN D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 GLN G 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078793 restraints weight = 29391.974| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.73 r_work: 0.2936 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17409 Z= 0.142 Angle : 0.573 6.906 23688 Z= 0.281 Chirality : 0.040 0.184 2807 Planarity : 0.004 0.042 2842 Dihedral : 3.197 20.704 2256 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.46 % Allowed : 23.58 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.20), residues: 2044 helix: 2.62 (0.14), residues: 1442 sheet: -1.46 (0.52), residues: 84 loop : -2.02 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.001 0.000 HIS A 134 PHE 0.010 0.001 PHE C 333 TYR 0.016 0.001 TYR A 25 ARG 0.012 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1099) hydrogen bonds : angle 3.44432 ( 3192) SS BOND : bond 0.00180 ( 14) SS BOND : angle 1.01209 ( 28) covalent geometry : bond 0.00346 (17395) covalent geometry : angle 0.57242 (23660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 1.969 Fit side-chains REVERT: A 345 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8601 (tptm) REVERT: B 303 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6504 (mttt) REVERT: B 345 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8552 (tptm) REVERT: B 354 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 355 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7853 (m-40) REVERT: C 345 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8773 (tptm) REVERT: D 154 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8067 (tp) REVERT: D 354 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8351 (tm-30) REVERT: D 355 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7890 (m-40) REVERT: F 37 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9022 (mt) REVERT: F 339 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8149 (tm-30) REVERT: G 144 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8818 (mm-30) REVERT: G 256 ARG cc_start: 0.8901 (mtm110) cc_final: 0.8652 (mtm110) outliers start: 85 outliers final: 37 residues processed: 254 average time/residue: 1.3500 time to fit residues: 380.8980 Evaluate side-chains 230 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 21 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 355 ASN C 63 GLN C 306 ASN C 355 ASN D 63 GLN D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 GLN G 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078787 restraints weight = 28435.736| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.62 r_work: 0.2953 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17409 Z= 0.152 Angle : 0.594 7.061 23688 Z= 0.293 Chirality : 0.040 0.194 2807 Planarity : 0.004 0.049 2842 Dihedral : 3.232 20.321 2256 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.10 % Allowed : 24.63 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 2044 helix: 2.61 (0.14), residues: 1442 sheet: -1.80 (0.40), residues: 126 loop : -1.81 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.001 0.000 HIS A 134 PHE 0.010 0.001 PHE C 333 TYR 0.017 0.001 TYR A 25 ARG 0.011 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 1099) hydrogen bonds : angle 3.47416 ( 3192) SS BOND : bond 0.00191 ( 14) SS BOND : angle 1.02924 ( 28) covalent geometry : bond 0.00372 (17395) covalent geometry : angle 0.59353 (23660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 192 time to evaluate : 1.895 Fit side-chains REVERT: A 151 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8398 (m-40) REVERT: A 345 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8614 (tptm) REVERT: B 303 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6547 (mttt) REVERT: B 345 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8582 (tptm) REVERT: C 345 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8850 (tptm) REVERT: D 154 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8047 (tp) REVERT: E 339 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 37 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9030 (mt) REVERT: F 339 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8166 (tm-30) REVERT: G 144 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8861 (mm-30) REVERT: G 256 ARG cc_start: 0.8955 (mtm110) cc_final: 0.8667 (mtm110) outliers start: 78 outliers final: 38 residues processed: 247 average time/residue: 1.3779 time to fit residues: 379.1839 Evaluate side-chains 216 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN C 355 ASN D 56 GLN D 63 GLN D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079182 restraints weight = 28348.782| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.66 r_work: 0.2958 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17409 Z= 0.138 Angle : 0.608 7.262 23688 Z= 0.300 Chirality : 0.040 0.198 2807 Planarity : 0.004 0.059 2842 Dihedral : 3.249 20.064 2256 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.78 % Allowed : 25.42 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 2044 helix: 2.61 (0.14), residues: 1442 sheet: -1.76 (0.40), residues: 126 loop : -1.81 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 74 HIS 0.001 0.000 HIS A 134 PHE 0.009 0.001 PHE C 333 TYR 0.016 0.001 TYR A 25 ARG 0.013 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1099) hydrogen bonds : angle 3.44976 ( 3192) SS BOND : bond 0.00169 ( 14) SS BOND : angle 0.99255 ( 28) covalent geometry : bond 0.00338 (17395) covalent geometry : angle 0.60702 (23660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 1.901 Fit side-chains REVERT: A 345 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8585 (tptm) REVERT: B 152 ARG cc_start: 0.7435 (mtm110) cc_final: 0.7162 (mtm110) REVERT: B 303 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6524 (mttt) REVERT: B 345 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8573 (tptm) REVERT: B 354 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8484 (tm-30) REVERT: C 345 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8846 (tptm) REVERT: D 151 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8504 (m-40) REVERT: D 154 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7995 (tp) REVERT: D 354 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8548 (tm-30) REVERT: E 152 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7422 (mtm110) REVERT: E 339 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8090 (tm-30) REVERT: F 37 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9027 (mt) REVERT: F 63 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8136 (tp-100) REVERT: F 206 ASN cc_start: 0.8878 (t0) cc_final: 0.8646 (t0) REVERT: F 339 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8156 (tm-30) REVERT: F 350 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8832 (mm) REVERT: G 144 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8864 (mm-30) REVERT: G 256 ARG cc_start: 0.8961 (mtm110) cc_final: 0.8678 (mtm110) outliers start: 72 outliers final: 37 residues processed: 249 average time/residue: 1.3259 time to fit residues: 366.2623 Evaluate side-chains 240 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 63 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN D 56 GLN D 63 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN G 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077399 restraints weight = 28738.166| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.69 r_work: 0.2925 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17409 Z= 0.190 Angle : 0.654 11.046 23688 Z= 0.322 Chirality : 0.041 0.200 2807 Planarity : 0.004 0.061 2842 Dihedral : 3.328 21.122 2256 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.36 % Allowed : 26.52 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 2044 helix: 2.57 (0.14), residues: 1442 sheet: -1.76 (0.41), residues: 126 loop : -1.80 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 85 HIS 0.002 0.001 HIS A 134 PHE 0.013 0.001 PHE F 333 TYR 0.017 0.001 TYR A 25 ARG 0.015 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1099) hydrogen bonds : angle 3.55761 ( 3192) SS BOND : bond 0.00222 ( 14) SS BOND : angle 1.09128 ( 28) covalent geometry : bond 0.00468 (17395) covalent geometry : angle 0.65330 (23660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 2.126 Fit side-chains REVERT: A 151 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8429 (m-40) REVERT: A 345 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8582 (tptm) REVERT: B 303 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6544 (mttt) REVERT: B 345 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8647 (tptm) REVERT: B 354 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 345 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8889 (tptm) REVERT: D 151 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8480 (m-40) REVERT: D 154 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8071 (tp) REVERT: E 256 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.7966 (mtm-85) REVERT: E 339 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8090 (tm-30) REVERT: F 37 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9043 (mt) REVERT: F 63 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8160 (tp-100) REVERT: F 339 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8246 (tm-30) REVERT: G 31 GLU cc_start: 0.8552 (tt0) cc_final: 0.8330 (tt0) REVERT: G 144 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8863 (mm-30) REVERT: G 256 ARG cc_start: 0.8994 (mtm110) cc_final: 0.8718 (mtm110) outliers start: 64 outliers final: 41 residues processed: 235 average time/residue: 1.4437 time to fit residues: 374.9467 Evaluate side-chains 226 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 188 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN D 63 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 266 GLN G 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080102 restraints weight = 28483.222| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.67 r_work: 0.2971 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17409 Z= 0.129 Angle : 0.632 8.619 23688 Z= 0.312 Chirality : 0.040 0.211 2807 Planarity : 0.004 0.062 2842 Dihedral : 3.275 20.134 2256 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.84 % Allowed : 27.15 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 2044 helix: 2.62 (0.14), residues: 1442 sheet: -1.68 (0.41), residues: 126 loop : -1.77 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 74 HIS 0.001 0.000 HIS G 106 PHE 0.008 0.001 PHE C 109 TYR 0.013 0.001 TYR A 25 ARG 0.015 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 1099) hydrogen bonds : angle 3.43490 ( 3192) SS BOND : bond 0.00131 ( 14) SS BOND : angle 0.92156 ( 28) covalent geometry : bond 0.00310 (17395) covalent geometry : angle 0.63199 (23660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 1.860 Fit side-chains REVERT: A 151 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8433 (m-40) REVERT: A 345 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8582 (tptm) REVERT: B 152 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7197 (mtm110) REVERT: B 303 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6510 (mttt) REVERT: B 345 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8561 (tptm) REVERT: C 345 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8814 (tptm) REVERT: D 151 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8530 (m-40) REVERT: D 154 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7984 (tp) REVERT: E 256 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.7944 (mtm-85) REVERT: E 339 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8144 (tm-30) REVERT: F 339 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8167 (tm-30) REVERT: G 256 ARG cc_start: 0.8978 (mtm110) cc_final: 0.8736 (mtm110) outliers start: 54 outliers final: 34 residues processed: 238 average time/residue: 1.4279 time to fit residues: 374.9979 Evaluate side-chains 236 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 19 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 30.0000 chunk 185 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN D 56 GLN D 63 GLN D 266 GLN D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN F 306 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077018 restraints weight = 28547.140| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.70 r_work: 0.2917 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17409 Z= 0.199 Angle : 0.678 11.799 23688 Z= 0.335 Chirality : 0.042 0.201 2807 Planarity : 0.005 0.067 2842 Dihedral : 3.393 21.990 2256 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.05 % Allowed : 26.84 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 2044 helix: 2.45 (0.14), residues: 1449 sheet: -1.71 (0.41), residues: 126 loop : -1.67 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 85 HIS 0.002 0.001 HIS A 134 PHE 0.014 0.001 PHE C 333 TYR 0.016 0.001 TYR A 25 ARG 0.015 0.001 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1099) hydrogen bonds : angle 3.61808 ( 3192) SS BOND : bond 0.00232 ( 14) SS BOND : angle 1.12005 ( 28) covalent geometry : bond 0.00494 (17395) covalent geometry : angle 0.67744 (23660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9506.03 seconds wall clock time: 165 minutes 1.03 seconds (9901.03 seconds total)