Starting phenix.real_space_refine on Tue Jan 21 10:47:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz7_45055/01_2025/9bz7_45055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz7_45055/01_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_45055/01_2025/9bz7_45055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz7_45055/01_2025/9bz7_45055.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz7_45055/01_2025/9bz7_45055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz7_45055/01_2025/9bz7_45055.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 11382 2.51 5 N 2604 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.76, per 1000 atoms: 0.34 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=2, 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 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: 3.93 Conformation dependent library (CDL) restraints added in 2.3 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: 1.32 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: 4.58 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 8705 15.02 - 30.04: 1213 30.04 - 45.05: 371 45.05 - 60.07: 42 60.07 - 75.09: 28 Dihedral angle restraints: 10359 sinusoidal: 4094 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 10356 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: 2.03 - 2.60: 131 2.60 - 3.18: 14569 3.18 - 3.75: 26671 3.75 - 4.33: 34454 4.33 - 4.90: 60034 Nonbonded interactions: 135859 Sorted by model distance: nonbonded pdb=" SG CYS F 84 " pdb=" SG CYS F 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 84 " pdb=" SG CYS E 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 84 " pdb=" SG CYS D 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 84 " pdb=" SG CYS C 248 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS G 84 " pdb=" SG CYS G 248 " model vdw 2.030 3.760 ... (remaining 135854 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: 0.410 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.060 ------------------------------------------------------------------------------- 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 17395 Z= 0.146 Angle : 0.544 5.733 23660 Z= 0.275 Chirality : 0.039 0.168 2807 Planarity : 0.003 0.030 2842 Dihedral : 15.789 75.091 6279 Min Nonbonded Distance : 2.029 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 *********************** 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 : 1.954 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: 1.5258 time to fit residues: 417.2131 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 : 2.127 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.108307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.076357 restraints weight = 29596.783| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.72 r_work: 0.2911 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17395 Z= 0.332 Angle : 0.597 5.946 23660 Z= 0.296 Chirality : 0.042 0.154 2807 Planarity : 0.004 0.035 2842 Dihedral : 3.509 28.707 2263 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.15 % Allowed : 22.48 % Favored : 72.37 % 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: 1.79 (0.19), residues: 2044 helix: 2.37 (0.14), residues: 1428 sheet: -1.37 (0.49), residues: 84 loop : -1.80 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.006 0.001 ARG C 152 *********************** 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 306 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 208 time to evaluate : 1.942 Fit side-chains REVERT: A 345 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8631 (tptm) REVERT: B 303 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6604 (mttt) REVERT: B 345 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8678 (tptm) REVERT: C 48 LEU cc_start: 0.8664 (mt) cc_final: 0.8455 (mm) REVERT: C 345 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8778 (tptm) REVERT: D 63 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8187 (tp40) REVERT: D 345 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8715 (tptm) REVERT: D 354 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8448 (tm-30) REVERT: D 355 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7777 (m-40) REVERT: E 339 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 354 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8553 (tm-30) REVERT: F 37 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9020 (mt) REVERT: G 206 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8259 (m-40) REVERT: G 256 ARG cc_start: 0.8922 (mtm110) cc_final: 0.8663 (mtm110) REVERT: G 303 LYS cc_start: 0.7158 (mttt) cc_final: 0.6628 (mppt) outliers start: 98 outliers final: 33 residues processed: 281 average time/residue: 1.3996 time to fit residues: 437.6043 Evaluate side-chains 211 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 A residue 355 ASN 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 154 ILE Chi-restraints excluded: chain G residue 206 ASN 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: 7.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 151 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 206 ASN B 355 ASN C 63 GLN C 306 ASN E 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 = 0.3635 r_free = 0.3635 target = 0.110352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078672 restraints weight = 29063.027| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.71 r_work: 0.2955 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17395 Z= 0.175 Angle : 0.532 6.538 23660 Z= 0.262 Chirality : 0.039 0.183 2807 Planarity : 0.003 0.035 2842 Dihedral : 3.200 21.469 2256 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.31 % Allowed : 22.90 % Favored : 72.79 % 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: 2.58 (0.14), residues: 1428 sheet: -1.32 (0.52), residues: 84 loop : -1.81 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 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 *********************** 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 293 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 211 time to evaluate : 2.033 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8610 (tptm) REVERT: B 303 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6610 (mttt) REVERT: B 345 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8593 (tptm) REVERT: C 345 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8854 (tptm) REVERT: D 63 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8145 (tp40) REVERT: D 154 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8154 (tp) REVERT: D 345 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8705 (tptm) REVERT: F 63 GLN cc_start: 0.8374 (mm110) cc_final: 0.8064 (tp-100) REVERT: G 256 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8712 (mtm110) REVERT: G 303 LYS cc_start: 0.7064 (mttt) cc_final: 0.6576 (mppt) outliers start: 82 outliers final: 31 residues processed: 267 average time/residue: 1.4095 time to fit residues: 416.8919 Evaluate side-chains 208 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 A residue 355 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 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: 7.9990 chunk 81 optimal weight: 4.9990 chunk 187 optimal weight: 0.4980 chunk 101 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN 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 = 0.3637 r_free = 0.3637 target = 0.110830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079152 restraints weight = 29196.172| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.71 r_work: 0.2945 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17395 Z= 0.182 Angle : 0.535 5.713 23660 Z= 0.262 Chirality : 0.039 0.172 2807 Planarity : 0.003 0.039 2842 Dihedral : 3.179 21.349 2256 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.62 % Allowed : 23.42 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 2044 helix: 2.58 (0.14), residues: 1442 sheet: -1.35 (0.53), residues: 84 loop : -2.01 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 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 A 256 *********************** 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 284 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 1.856 Fit side-chains REVERT: A 151 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: A 345 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8589 (tptm) REVERT: B 303 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6580 (mttt) REVERT: B 345 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8520 (tptm) REVERT: B 355 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: C 345 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8789 (tptm) REVERT: D 154 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8095 (tp) REVERT: D 345 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8687 (tptm) REVERT: E 339 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8068 (tm-30) REVERT: F 63 GLN cc_start: 0.8532 (mm110) cc_final: 0.8292 (tp-100) REVERT: G 256 ARG cc_start: 0.8918 (mtm110) cc_final: 0.8614 (mtm110) outliers start: 69 outliers final: 31 residues processed: 258 average time/residue: 1.4826 time to fit residues: 420.8123 Evaluate side-chains 216 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL 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 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 E residue 37 LEU Chi-restraints excluded: chain E residue 254 ILE 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 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: 10.0000 chunk 124 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075372 restraints weight = 29711.010| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.71 r_work: 0.2878 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 17395 Z= 0.358 Angle : 0.618 6.498 23660 Z= 0.304 Chirality : 0.042 0.172 2807 Planarity : 0.004 0.041 2842 Dihedral : 3.347 21.185 2256 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.99 % Allowed : 23.69 % 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: 1.89 (0.19), residues: 2044 helix: 2.48 (0.14), residues: 1442 sheet: -1.37 (0.53), residues: 84 loop : -2.01 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.003 0.001 HIS A 134 PHE 0.015 0.001 PHE C 333 TYR 0.016 0.001 TYR A 25 ARG 0.010 0.001 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 193 time to evaluate : 2.195 Fit side-chains REVERT: A 345 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8572 (tptm) REVERT: B 303 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6630 (mttt) REVERT: B 345 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8601 (tptm) REVERT: B 355 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8201 (m110) REVERT: C 345 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8766 (tptm) REVERT: D 154 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8074 (tp) REVERT: D 345 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8811 (tptm) REVERT: F 37 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9034 (mt) REVERT: F 63 GLN cc_start: 0.8467 (mm110) cc_final: 0.8257 (tp-100) REVERT: G 256 ARG cc_start: 0.8945 (mtm110) cc_final: 0.8688 (mtm110) outliers start: 95 outliers final: 44 residues processed: 265 average time/residue: 1.3599 time to fit residues: 399.9384 Evaluate side-chains 227 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 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 113 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 114 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 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 154 ILE 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 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: 7.9990 chunk 97 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 = 0.3588 r_free = 0.3588 target = 0.107456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.075822 restraints weight = 29666.771| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.72 r_work: 0.2887 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17395 Z= 0.291 Angle : 0.606 7.418 23660 Z= 0.297 Chirality : 0.041 0.167 2807 Planarity : 0.004 0.046 2842 Dihedral : 3.377 20.709 2256 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.31 % Allowed : 25.21 % Favored : 70.48 % 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: 2.51 (0.14), residues: 1442 sheet: -1.31 (0.44), residues: 126 loop : -1.88 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 74 HIS 0.002 0.001 HIS A 134 PHE 0.011 0.001 PHE C 333 TYR 0.018 0.001 TYR A 25 ARG 0.011 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 199 time to evaluate : 2.080 Fit side-chains REVERT: A 345 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8597 (tptm) REVERT: B 303 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6557 (mttt) REVERT: B 345 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8603 (tptm) REVERT: B 354 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 355 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7959 (m-40) REVERT: C 345 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8787 (tptm) REVERT: D 151 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8432 (m-40) REVERT: D 154 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8048 (tp) REVERT: D 345 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8798 (tptm) REVERT: E 339 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8071 (tm-30) REVERT: F 37 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9038 (mt) REVERT: F 63 GLN cc_start: 0.8469 (mm110) cc_final: 0.8204 (tp-100) REVERT: G 31 GLU cc_start: 0.8620 (tt0) cc_final: 0.8394 (tt0) REVERT: G 256 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8752 (mtm110) REVERT: G 338 GLU cc_start: 0.8945 (tt0) cc_final: 0.8734 (tt0) outliers start: 82 outliers final: 37 residues processed: 263 average time/residue: 1.3720 time to fit residues: 399.9162 Evaluate side-chains 228 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 272 VAL 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 207 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 151 ASN 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 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: 0.6980 chunk 170 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 355 ASN C 63 GLN C 306 ASN D 355 ASN E 355 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 = 0.3625 r_free = 0.3625 target = 0.109836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077789 restraints weight = 28551.754| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.68 r_work: 0.2931 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17395 Z= 0.210 Angle : 0.600 7.189 23660 Z= 0.296 Chirality : 0.040 0.185 2807 Planarity : 0.004 0.046 2842 Dihedral : 3.330 20.877 2256 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.20 % Allowed : 25.79 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 2044 helix: 2.59 (0.14), residues: 1442 sheet: -1.23 (0.44), residues: 126 loop : -1.85 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS F 106 PHE 0.008 0.001 PHE C 333 TYR 0.015 0.001 TYR A 25 ARG 0.012 0.001 ARG G 152 *********************** 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 272 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 192 time to evaluate : 1.836 Fit side-chains REVERT: A 151 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8403 (m-40) REVERT: A 345 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8629 (tptm) REVERT: B 303 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6563 (mttt) REVERT: B 345 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8591 (tptm) REVERT: C 345 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8869 (tptm) REVERT: D 151 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8488 (m-40) REVERT: D 154 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8057 (tp) REVERT: E 144 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8764 (mt-10) REVERT: E 339 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8099 (tm-30) REVERT: F 37 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9019 (mt) REVERT: F 63 GLN cc_start: 0.8493 (mm110) cc_final: 0.8234 (tp-100) REVERT: F 350 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8844 (mm) REVERT: G 144 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8831 (mm-30) REVERT: G 152 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7225 (mtm110) REVERT: G 256 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8727 (mtm110) REVERT: G 338 GLU cc_start: 0.8900 (tt0) cc_final: 0.8696 (tt0) outliers start: 80 outliers final: 35 residues processed: 252 average time/residue: 1.3713 time to fit residues: 383.6767 Evaluate side-chains 214 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 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 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 331 SER 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 272 VAL 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: 6.9990 chunk 159 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 128 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN C 355 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076338 restraints weight = 28807.460| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.68 r_work: 0.2910 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17395 Z= 0.299 Angle : 0.641 7.773 23660 Z= 0.315 Chirality : 0.041 0.195 2807 Planarity : 0.005 0.058 2842 Dihedral : 3.411 20.804 2256 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.89 % Allowed : 26.79 % Favored : 69.33 % 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: 2.00 (0.20), residues: 2044 helix: 2.51 (0.14), residues: 1442 sheet: -1.16 (0.45), residues: 126 loop : -1.85 (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 0.013 0.001 PHE C 333 TYR 0.016 0.001 TYR A 25 ARG 0.013 0.001 ARG A 152 *********************** 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 254 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 180 time to evaluate : 1.777 Fit side-chains REVERT: A 63 GLN cc_start: 0.8467 (mm110) cc_final: 0.8264 (tp40) REVERT: A 151 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8452 (m-40) REVERT: A 345 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8629 (tptm) REVERT: A 355 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8191 (m-40) REVERT: B 303 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6571 (mttt) REVERT: B 345 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8625 (tptm) REVERT: B 354 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8385 (tm-30) REVERT: C 345 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8910 (tptm) REVERT: D 151 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8471 (m-40) REVERT: D 154 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8074 (tp) REVERT: E 339 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 37 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9043 (mt) REVERT: F 63 GLN cc_start: 0.8470 (mm110) cc_final: 0.8239 (tp-100) REVERT: G 144 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8863 (mm-30) outliers start: 74 outliers final: 41 residues processed: 234 average time/residue: 1.3987 time to fit residues: 362.8892 Evaluate side-chains 224 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 242 LEU 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 A residue 355 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 272 VAL 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 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 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 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 63 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 83 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN E 355 ASN F 355 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 = 0.3639 r_free = 0.3639 target = 0.111129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079242 restraints weight = 28740.436| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.66 r_work: 0.2947 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17395 Z= 0.201 Angle : 0.638 11.408 23660 Z= 0.312 Chirality : 0.040 0.206 2807 Planarity : 0.005 0.062 2842 Dihedral : 3.360 20.504 2256 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.15 % Allowed : 27.73 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 2044 helix: 2.56 (0.14), residues: 1442 sheet: -1.13 (0.45), residues: 126 loop : -1.83 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.001 0.000 HIS F 106 PHE 0.008 0.001 PHE B 109 TYR 0.014 0.001 TYR A 25 ARG 0.014 0.001 ARG C 152 *********************** 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 268 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 1.967 Fit side-chains REVERT: A 63 GLN cc_start: 0.8470 (mm110) cc_final: 0.8266 (tp40) REVERT: A 345 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8603 (tptm) REVERT: B 303 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6533 (mttt) REVERT: B 345 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8621 (tptm) REVERT: B 354 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 345 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8879 (tptm) REVERT: D 151 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8498 (m-40) REVERT: D 154 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7981 (tp) REVERT: D 204 THR cc_start: 0.9255 (p) cc_final: 0.8997 (p) REVERT: E 339 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8147 (tm-30) REVERT: F 37 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9023 (mt) REVERT: F 63 GLN cc_start: 0.8482 (mm110) cc_final: 0.8248 (tp-100) REVERT: F 350 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8852 (mm) REVERT: G 144 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8890 (mm-30) REVERT: G 152 ARG cc_start: 0.7436 (mtm110) cc_final: 0.7205 (mtm110) REVERT: G 338 GLU cc_start: 0.8921 (tt0) cc_final: 0.8667 (tt0) outliers start: 60 outliers final: 32 residues processed: 246 average time/residue: 1.4595 time to fit residues: 395.7829 Evaluate side-chains 212 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 154 ILE 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 207 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 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 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 58 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN E 63 GLN F 306 ASN F 355 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077389 restraints weight = 28887.530| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.71 r_work: 0.2931 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17395 Z= 0.249 Angle : 0.652 8.787 23660 Z= 0.321 Chirality : 0.041 0.210 2807 Planarity : 0.005 0.063 2842 Dihedral : 3.362 21.009 2256 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.57 % Allowed : 28.31 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 2044 helix: 2.54 (0.14), residues: 1442 sheet: -1.07 (0.45), residues: 126 loop : -1.77 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.002 0.000 HIS A 134 PHE 0.010 0.001 PHE C 333 TYR 0.015 0.001 TYR A 25 ARG 0.015 0.001 ARG C 152 ********************** 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 231 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.894 Fit side-chains REVERT: A 345 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8612 (tptm) REVERT: B 303 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6549 (mttt) REVERT: B 339 GLU cc_start: 0.8712 (tp30) cc_final: 0.8431 (tm-30) REVERT: B 345 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8557 (tptm) REVERT: C 345 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8849 (tptm) REVERT: D 151 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8486 (m-40) REVERT: D 154 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8041 (tp) REVERT: D 204 THR cc_start: 0.9351 (p) cc_final: 0.9128 (p) REVERT: E 256 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: E 339 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8142 (tm-30) REVERT: E 354 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8551 (tm-30) REVERT: F 37 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9037 (mt) REVERT: F 63 GLN cc_start: 0.8466 (mm110) cc_final: 0.8224 (tp-100) REVERT: F 350 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8862 (mm) outliers start: 49 outliers final: 30 residues processed: 216 average time/residue: 1.4615 time to fit residues: 349.2119 Evaluate side-chains 220 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 154 ILE 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 272 VAL 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 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 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 19 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN C 355 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN E 63 GLN F 306 ASN F 355 ASN G 306 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078363 restraints weight = 28581.809| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.67 r_work: 0.2947 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17395 Z= 0.213 Angle : 0.650 8.752 23660 Z= 0.320 Chirality : 0.040 0.215 2807 Planarity : 0.005 0.065 2842 Dihedral : 3.323 20.638 2256 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.36 % Allowed : 28.78 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.19), residues: 2044 helix: 2.58 (0.14), residues: 1442 sheet: -1.07 (0.45), residues: 126 loop : -1.75 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS A 134 PHE 0.008 0.001 PHE C 333 TYR 0.016 0.001 TYR C 111 ARG 0.015 0.001 ARG G 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9522.23 seconds wall clock time: 169 minutes 58.05 seconds (10198.05 seconds total)