Starting phenix.real_space_refine on Sun Jun 15 00:08:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz7_45055/06_2025/9bz7_45055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz7_45055/06_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_45055/06_2025/9bz7_45055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz7_45055/06_2025/9bz7_45055.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz7_45055/06_2025/9bz7_45055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz7_45055/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.06, 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: 4.23 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: 1.44 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: 4.76 Time building geometry restraints manager: 5.03 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 33.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- 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 : 1.905 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: 1.4838 time to fit residues: 406.0534 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 : 2.089 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.108755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076803 restraints weight = 29411.955| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.70 r_work: 0.2917 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 : 0.005 0.038 17409 Z= 0.212 Angle : 0.601 6.030 23688 Z= 0.297 Chirality : 0.041 0.157 2807 Planarity : 0.004 0.039 2842 Dihedral : 3.491 28.714 2263 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.15 % Allowed : 22.22 % Favored : 72.64 % 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: 1.82 (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 0.04147 ( 1099) hydrogen bonds : angle 3.68560 ( 3192) SS BOND : bond 0.00206 ( 14) SS BOND : angle 1.14624 ( 28) covalent geometry : bond 0.00515 (17395) covalent geometry : angle 0.59993 (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 : 1.906 Fit side-chains REVERT: A 345 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: B 303 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6598 (mttt) REVERT: B 345 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8678 (tptm) REVERT: C 48 LEU cc_start: 0.8663 (mt) cc_final: 0.8453 (mm) REVERT: C 345 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8777 (tptm) REVERT: D 63 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8187 (tp40) REVERT: D 345 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8711 (tptm) REVERT: D 354 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 355 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7794 (m-40) REVERT: F 37 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9019 (mt) REVERT: G 256 ARG cc_start: 0.8920 (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: 1.3349 time to fit residues: 407.3370 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 : 2.072 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 198 optimal weight: 0.2980 chunk 112 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 306 ASN E 63 GLN G 206 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 = 0.3642 r_free = 0.3642 target = 0.110772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079028 restraints weight = 28930.174| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.71 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: 0.8412 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17409 Z= 0.119 Angle : 0.534 6.966 23688 Z= 0.262 Chirality : 0.039 0.165 2807 Planarity : 0.003 0.033 2842 Dihedral : 3.178 21.446 2256 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.25 % Allowed : 22.16 % 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: 2.03 (0.20), residues: 2044 helix: 2.61 (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 0.006 0.001 TRP E 74 HIS 0.001 0.000 HIS F 106 PHE 0.008 0.001 PHE B 109 TYR 0.015 0.001 TYR A 111 ARG 0.008 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1099) hydrogen bonds : angle 3.48886 ( 3192) SS BOND : bond 0.00147 ( 14) SS BOND : angle 0.98958 ( 28) covalent geometry : bond 0.00278 (17395) covalent geometry : angle 0.53304 (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 286 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 2.278 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8592 (tptm) REVERT: B 303 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6593 (mttt) REVERT: B 345 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8572 (tptm) REVERT: C 345 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8836 (tptm) REVERT: D 63 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8206 (tp40) REVERT: D 151 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8455 (m-40) REVERT: D 154 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8130 (tp) REVERT: D 345 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8658 (tptm) REVERT: E 339 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8065 (tm-30) REVERT: F 63 GLN cc_start: 0.8371 (mm110) cc_final: 0.8085 (tp-100) REVERT: G 256 ARG cc_start: 0.8933 (mtm110) cc_final: 0.8713 (mtm110) REVERT: G 303 LYS cc_start: 0.7039 (mttt) cc_final: 0.6559 (mppt) outliers start: 81 outliers final: 29 residues processed: 260 average time/residue: 1.7315 time to fit residues: 500.2251 Evaluate side-chains 204 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 3.791 ------------------------------------------------------------------------------- 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 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 331 SER 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 307 VAL Chi-restraints excluded: chain G residue 331 SER 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: 5.9990 chunk 81 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 355 ASN F 306 ASN G 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079459 restraints weight = 28994.654| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.69 r_work: 0.2964 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17409 Z= 0.119 Angle : 0.535 5.805 23688 Z= 0.261 Chirality : 0.039 0.171 2807 Planarity : 0.003 0.039 2842 Dihedral : 3.164 21.239 2256 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.62 % Allowed : 22.74 % Favored : 73.63 % 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: 1.99 (0.20), residues: 2044 helix: 2.60 (0.14), residues: 1442 sheet: -1.46 (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 C 330 PHE 0.008 0.001 PHE C 333 TYR 0.010 0.001 TYR B 25 ARG 0.009 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1099) hydrogen bonds : angle 3.43482 ( 3192) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.93140 ( 28) covalent geometry : bond 0.00283 (17395) covalent geometry : angle 0.53403 (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 273 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 1.914 Fit side-chains REVERT: A 151 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8420 (m-40) REVERT: A 345 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8625 (tptm) REVERT: B 303 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6596 (mttt) REVERT: B 345 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8623 (tptm) REVERT: B 355 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8143 (m-40) REVERT: C 345 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8810 (tptm) REVERT: D 151 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8450 (m-40) REVERT: D 154 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8150 (tp) REVERT: D 345 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8624 (tptm) REVERT: D 354 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 355 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: F 63 GLN cc_start: 0.8441 (mm110) cc_final: 0.8222 (tp-100) REVERT: F 144 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8727 (mm-30) REVERT: F 339 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 256 ARG cc_start: 0.8895 (mtm110) cc_final: 0.8579 (mtm110) REVERT: G 303 LYS cc_start: 0.7108 (mttt) cc_final: 0.6616 (mtpt) outliers start: 69 outliers final: 38 residues processed: 248 average time/residue: 1.4353 time to fit residues: 392.4503 Evaluate side-chains 231 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain A residue 345 LYS 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 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 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 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 308 LEU Chi-restraints excluded: chain G residue 338 GLU 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: 6.9990 chunk 180 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 189 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 355 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077869 restraints weight = 29416.753| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.72 r_work: 0.2920 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.004 0.032 17409 Z= 0.165 Angle : 0.572 6.372 23688 Z= 0.281 Chirality : 0.040 0.177 2807 Planarity : 0.004 0.039 2842 Dihedral : 3.223 21.114 2256 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.88 % Allowed : 22.90 % Favored : 72.22 % 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: 1.97 (0.20), residues: 2044 helix: 2.57 (0.14), residues: 1442 sheet: -1.49 (0.52), residues: 84 loop : -2.07 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.002 0.001 HIS A 134 PHE 0.011 0.001 PHE C 333 TYR 0.011 0.001 TYR B 25 ARG 0.010 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1099) hydrogen bonds : angle 3.50487 ( 3192) SS BOND : bond 0.00195 ( 14) SS BOND : angle 1.04149 ( 28) covalent geometry : bond 0.00406 (17395) covalent geometry : angle 0.57170 (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 293 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 1.946 Fit side-chains REVERT: A 151 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8348 (m-40) REVERT: A 345 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8591 (tptm) REVERT: B 303 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6609 (mttt) REVERT: B 345 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8549 (tptm) REVERT: C 345 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8738 (tptm) REVERT: D 154 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8112 (tp) REVERT: D 345 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8620 (tptm) REVERT: E 339 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8069 (tm-30) REVERT: F 37 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9014 (mt) REVERT: F 56 GLN cc_start: 0.8141 (pp30) cc_final: 0.7703 (pp30) REVERT: F 144 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8775 (mm-30) REVERT: F 339 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8125 (tm-30) REVERT: G 256 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8686 (mtm110) outliers start: 93 outliers final: 41 residues processed: 268 average time/residue: 1.3629 time to fit residues: 404.4746 Evaluate side-chains 225 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 341 VAL 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 C residue 37 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 207 ASN 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 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: 8.9990 chunk 97 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077218 restraints weight = 29385.883| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.70 r_work: 0.2909 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17409 Z= 0.171 Angle : 0.594 6.764 23688 Z= 0.292 Chirality : 0.040 0.181 2807 Planarity : 0.004 0.040 2842 Dihedral : 3.294 20.718 2256 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.20 % Allowed : 24.58 % Favored : 71.22 % 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: 1.99 (0.20), residues: 2044 helix: 2.57 (0.14), residues: 1442 sheet: -1.83 (0.40), residues: 126 loop : -1.86 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 85 HIS 0.002 0.001 HIS A 134 PHE 0.011 0.001 PHE C 333 TYR 0.014 0.001 TYR D 25 ARG 0.012 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1099) hydrogen bonds : angle 3.55031 ( 3192) SS BOND : bond 0.00215 ( 14) SS BOND : angle 1.10930 ( 28) covalent geometry : bond 0.00420 (17395) covalent geometry : angle 0.59301 (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 273 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 2.339 Fit side-chains REVERT: A 345 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8662 (tptm) REVERT: B 303 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6533 (mttt) REVERT: B 345 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8558 (tptm) REVERT: B 354 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 355 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7933 (m-40) REVERT: C 345 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8766 (tptm) REVERT: D 154 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8016 (tp) REVERT: D 345 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8621 (tptm) REVERT: D 354 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 355 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7793 (m-40) REVERT: F 37 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9025 (mt) REVERT: F 339 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8122 (tm-30) REVERT: G 144 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8800 (mm-30) REVERT: G 256 ARG cc_start: 0.8997 (mtm110) cc_final: 0.8744 (mtm110) outliers start: 80 outliers final: 34 residues processed: 251 average time/residue: 1.5391 time to fit residues: 428.6597 Evaluate side-chains 207 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 2.725 ------------------------------------------------------------------------------- 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 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 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 207 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER 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 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 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 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: 1.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 136 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 266 GLN C 306 ASN D 355 ASN 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 = 0.3654 r_free = 0.3654 target = 0.111848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080115 restraints weight = 28227.005| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.67 r_work: 0.2968 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17409 Z= 0.118 Angle : 0.576 6.996 23688 Z= 0.284 Chirality : 0.039 0.203 2807 Planarity : 0.004 0.049 2842 Dihedral : 3.224 20.782 2256 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.83 % Allowed : 24.84 % Favored : 71.32 % 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 (0.19), residues: 2044 helix: 2.61 (0.14), residues: 1442 sheet: -1.43 (0.52), residues: 84 loop : -2.06 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 74 HIS 0.001 0.000 HIS C 106 PHE 0.009 0.001 PHE E 109 TYR 0.014 0.001 TYR A 25 ARG 0.012 0.001 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1099) hydrogen bonds : angle 3.41269 ( 3192) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.92936 ( 28) covalent geometry : bond 0.00276 (17395) covalent geometry : angle 0.57530 (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: 73 poor density : 197 time to evaluate : 1.963 Fit side-chains REVERT: A 151 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8401 (m-40) REVERT: A 152 ARG cc_start: 0.7373 (mtm110) cc_final: 0.7116 (mtm110) REVERT: A 345 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8588 (tptm) REVERT: B 152 ARG cc_start: 0.7464 (mtm110) cc_final: 0.7174 (mtm110) REVERT: B 303 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6511 (mttt) REVERT: B 345 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8552 (tptm) REVERT: B 355 ASN cc_start: 0.8189 (m-40) cc_final: 0.7825 (m110) REVERT: C 345 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8797 (tptm) REVERT: D 151 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: D 154 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8100 (tp) REVERT: E 339 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8126 (tm-30) REVERT: F 206 ASN cc_start: 0.8860 (t0) cc_final: 0.8649 (t0) REVERT: F 339 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8168 (tm-30) REVERT: F 350 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8852 (mm) REVERT: G 144 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8812 (mm-30) REVERT: G 152 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7218 (mtm110) REVERT: G 256 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8693 (mtm110) outliers start: 73 outliers final: 34 residues processed: 250 average time/residue: 1.3383 time to fit residues: 371.5100 Evaluate side-chains 229 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 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 C residue 113 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 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 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 242 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 133 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 199 optimal weight: 0.0770 chunk 128 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 266 GLN C 306 ASN C 355 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.110598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078748 restraints weight = 28478.932| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.67 r_work: 0.2949 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17409 Z= 0.148 Angle : 0.613 10.696 23688 Z= 0.300 Chirality : 0.040 0.201 2807 Planarity : 0.004 0.059 2842 Dihedral : 3.195 13.632 2254 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.73 % Allowed : 25.89 % Favored : 70.38 % 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: 2.03 (0.19), residues: 2044 helix: 2.54 (0.14), residues: 1449 sheet: -1.77 (0.41), residues: 126 loop : -1.73 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 74 HIS 0.002 0.000 HIS A 134 PHE 0.010 0.001 PHE C 333 TYR 0.016 0.001 TYR A 25 ARG 0.013 0.001 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1099) hydrogen bonds : angle 3.48013 ( 3192) SS BOND : bond 0.00178 ( 14) SS BOND : angle 1.00115 ( 28) covalent geometry : bond 0.00363 (17395) covalent geometry : angle 0.61219 (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: 71 poor density : 203 time to evaluate : 2.122 Fit side-chains REVERT: A 151 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8441 (m-40) REVERT: A 345 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: B 303 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6522 (mttt) REVERT: B 345 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8567 (tptm) REVERT: C 345 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8809 (tptm) REVERT: D 151 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8487 (m-40) REVERT: D 154 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8058 (tp) REVERT: E 339 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8103 (tm-30) REVERT: F 37 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9032 (mt) REVERT: F 339 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8179 (tm-30) REVERT: F 350 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8881 (mm) REVERT: G 144 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8848 (mm-30) REVERT: G 256 ARG cc_start: 0.8979 (mtm110) cc_final: 0.8697 (mtm110) outliers start: 71 outliers final: 34 residues processed: 255 average time/residue: 1.5246 time to fit residues: 426.7988 Evaluate side-chains 234 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 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 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 C residue 355 ASN Chi-restraints excluded: chain D residue 30 LEU 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 242 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 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 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 308 LEU 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: 9.9990 chunk 72 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 overall best weight: 2.1704 ------------------------------------------------------------------------------- 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 ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN F 63 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 = 0.3630 r_free = 0.3630 target = 0.110133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078054 restraints weight = 28703.303| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.70 r_work: 0.2934 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17409 Z= 0.165 Angle : 0.655 8.995 23688 Z= 0.324 Chirality : 0.041 0.203 2807 Planarity : 0.004 0.060 2842 Dihedral : 3.246 13.656 2254 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.20 % Allowed : 27.31 % Favored : 69.49 % 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: 1.99 (0.19), residues: 2044 helix: 2.50 (0.14), residues: 1449 sheet: -1.74 (0.41), residues: 126 loop : -1.72 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 74 HIS 0.002 0.001 HIS A 134 PHE 0.011 0.001 PHE C 333 TYR 0.015 0.001 TYR A 25 ARG 0.014 0.001 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1099) hydrogen bonds : angle 3.51690 ( 3192) SS BOND : bond 0.00202 ( 14) SS BOND : angle 1.03591 ( 28) covalent geometry : bond 0.00411 (17395) covalent geometry : angle 0.65478 (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 253 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 2.164 Fit side-chains REVERT: A 151 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8437 (m-40) REVERT: A 152 ARG cc_start: 0.7385 (mtm110) cc_final: 0.7106 (mtm110) REVERT: A 345 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8632 (tptm) REVERT: B 152 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7207 (mtm110) REVERT: B 303 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6541 (mttt) REVERT: B 345 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8585 (tptm) REVERT: C 345 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8820 (tptm) REVERT: D 151 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8484 (m-40) REVERT: D 154 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8037 (tp) REVERT: E 256 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.7932 (mtm-85) REVERT: E 339 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8089 (tm-30) REVERT: F 37 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9031 (mt) REVERT: F 151 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: F 339 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8183 (tm-30) REVERT: F 350 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8878 (mm) REVERT: G 144 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8861 (mm-30) outliers start: 61 outliers final: 33 residues processed: 240 average time/residue: 1.4336 time to fit residues: 379.0715 Evaluate side-chains 218 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 207 ASN Chi-restraints excluded: chain C residue 242 LEU 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 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 E residue 37 LEU Chi-restraints excluded: chain E residue 242 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 113 LEU Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 331 SER 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 308 LEU 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: 4.9990 chunk 10 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 C 355 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 266 GLN F 63 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.111442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079726 restraints weight = 28512.593| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.68 r_work: 0.2966 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1926 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= 0.134 Angle : 0.647 9.017 23688 Z= 0.319 Chirality : 0.040 0.216 2807 Planarity : 0.004 0.059 2842 Dihedral : 3.228 13.522 2254 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.68 % Allowed : 27.89 % Favored : 69.43 % 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 (0.19), residues: 2044 helix: 2.53 (0.14), residues: 1449 sheet: -1.70 (0.41), residues: 126 loop : -1.71 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 74 HIS 0.001 0.000 HIS A 134 PHE 0.008 0.001 PHE E 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 0.03286 ( 1099) hydrogen bonds : angle 3.44687 ( 3192) SS BOND : bond 0.00140 ( 14) SS BOND : angle 0.92662 ( 28) covalent geometry : bond 0.00328 (17395) covalent geometry : angle 0.64670 (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 248 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 2.017 Fit side-chains REVERT: A 151 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8426 (m-40) REVERT: A 152 ARG cc_start: 0.7368 (mtm110) cc_final: 0.7084 (mtm110) REVERT: A 345 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8600 (tptm) REVERT: B 152 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7271 (mtm110) REVERT: B 303 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6520 (mttt) REVERT: B 339 GLU cc_start: 0.8690 (tp30) cc_final: 0.8455 (tm-30) REVERT: B 345 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8548 (tptm) REVERT: C 345 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8826 (tptm) REVERT: D 151 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: D 154 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8026 (tp) REVERT: E 256 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7939 (mtm-85) REVERT: E 339 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8135 (tm-30) REVERT: F 37 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9023 (mt) REVERT: F 339 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8172 (tm-30) REVERT: F 350 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8849 (mm) outliers start: 51 outliers final: 32 residues processed: 232 average time/residue: 1.4498 time to fit residues: 370.1685 Evaluate side-chains 218 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 207 ASN Chi-restraints excluded: chain C residue 242 LEU 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 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 E residue 37 LEU Chi-restraints excluded: chain E residue 242 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 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 56 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 19 optimal weight: 0.0170 chunk 183 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.9822 ------------------------------------------------------------------------------- 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 C 355 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.110463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078581 restraints weight = 28360.144| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.68 r_work: 0.2946 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17409 Z= 0.160 Angle : 0.660 8.775 23688 Z= 0.326 Chirality : 0.041 0.212 2807 Planarity : 0.004 0.065 2842 Dihedral : 3.249 13.568 2254 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.73 % Allowed : 27.68 % Favored : 69.59 % 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: 1.98 (0.19), residues: 2044 helix: 2.52 (0.14), residues: 1449 sheet: -1.42 (0.52), residues: 84 loop : -1.93 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 134 PHE 0.011 0.001 PHE C 333 TYR 0.022 0.001 TYR C 111 ARG 0.014 0.001 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 1099) hydrogen bonds : angle 3.50217 ( 3192) SS BOND : bond 0.00180 ( 14) SS BOND : angle 1.00258 ( 28) covalent geometry : bond 0.00395 (17395) covalent geometry : angle 0.65961 (23660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10493.81 seconds wall clock time: 183 minutes 42.13 seconds (11022.13 seconds total)