Starting phenix.real_space_refine on Tue Dec 31 21:10:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz7_45055/12_2024/9bz7_45055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz7_45055/12_2024/9bz7_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_45055/12_2024/9bz7_45055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz7_45055/12_2024/9bz7_45055.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz7_45055/12_2024/9bz7_45055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz7_45055/12_2024/9bz7_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-5532/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: 5.69, 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: 4.46 Conformation dependent library (CDL) restraints added in 2.2 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: 1.52 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: 5.04 Time building geometry restraints manager: 5.07 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.620 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 32.630 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- 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 : 2.068 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: 1.5124 time to fit residues: 414.1092 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 : 1.978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 2.002 Fit side-chains REVERT: B 303 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6659 (mttt) REVERT: C 48 LEU cc_start: 0.8682 (mt) cc_final: 0.8481 (mm) REVERT: C 154 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8643 (tp) REVERT: D 63 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8228 (tp40) REVERT: D 354 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 355 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: E 339 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8175 (tm-30) REVERT: E 354 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8587 (tm-30) REVERT: F 37 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9085 (mt) REVERT: G 206 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8413 (m-40) REVERT: G 256 ARG cc_start: 0.8796 (mtm110) cc_final: 0.8532 (mtm110) REVERT: G 303 LYS cc_start: 0.7307 (mttt) cc_final: 0.6744 (mppt) outliers start: 98 outliers final: 33 residues processed: 281 average time/residue: 1.5243 time to fit residues: 475.2366 Evaluate side-chains 205 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 2.169 ------------------------------------------------------------------------------- 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 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 C residue 37 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 154 ILE 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 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 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 102 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17395 Z= 0.177 Angle : 0.533 6.398 23660 Z= 0.263 Chirality : 0.039 0.186 2807 Planarity : 0.003 0.037 2842 Dihedral : 3.204 22.088 2256 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.04 % Allowed : 23.06 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.19), residues: 2044 helix: 2.58 (0.14), residues: 1428 sheet: -1.36 (0.52), residues: 84 loop : -1.82 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 74 HIS 0.001 0.000 HIS F 106 PHE 0.008 0.001 PHE B 109 TYR 0.016 0.001 TYR A 111 ARG 0.008 0.001 ARG A 256 *********************** 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 285 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 208 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: B 303 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6660 (mttt) REVERT: D 154 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8302 (tp) REVERT: F 63 GLN cc_start: 0.8445 (mm110) cc_final: 0.8150 (tp-100) REVERT: F 354 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8643 (tm-30) REVERT: G 256 ARG cc_start: 0.8808 (mtm110) cc_final: 0.8585 (mtm110) REVERT: G 303 LYS cc_start: 0.7199 (mttt) cc_final: 0.6678 (mppt) outliers start: 77 outliers final: 31 residues processed: 263 average time/residue: 1.3864 time to fit residues: 405.1839 Evaluate side-chains 202 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 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 C residue 37 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 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 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 182 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN G 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17395 Z= 0.164 Angle : 0.528 5.483 23660 Z= 0.259 Chirality : 0.038 0.172 2807 Planarity : 0.003 0.039 2842 Dihedral : 3.094 12.552 2254 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.36 % Allowed : 23.48 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 2044 helix: 2.59 (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 A 74 HIS 0.001 0.000 HIS C 330 PHE 0.008 0.001 PHE D 109 TYR 0.009 0.001 TYR B 25 ARG 0.008 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 2.003 Fit side-chains REVERT: B 303 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6644 (mttt) REVERT: B 355 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8245 (m-40) REVERT: D 154 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8289 (tp) REVERT: F 63 GLN cc_start: 0.8597 (mm110) cc_final: 0.8364 (tp-100) REVERT: F 339 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8213 (tm-30) REVERT: F 354 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8662 (tm-30) REVERT: G 256 ARG cc_start: 0.8792 (mtm110) cc_final: 0.8472 (mtm110) REVERT: G 303 LYS cc_start: 0.7242 (mttt) cc_final: 0.6719 (mtpt) outliers start: 64 outliers final: 30 residues processed: 251 average time/residue: 1.4877 time to fit residues: 411.6173 Evaluate side-chains 207 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 355 ASN 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 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 E residue 37 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 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 163 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 355 ASN C 63 GLN C 306 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1856 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= 0.294 Angle : 0.589 6.370 23660 Z= 0.289 Chirality : 0.041 0.177 2807 Planarity : 0.004 0.040 2842 Dihedral : 3.188 13.448 2254 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.41 % Allowed : 23.74 % Favored : 71.85 % 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 (0.20), residues: 2044 helix: 2.55 (0.14), residues: 1442 sheet: -1.28 (0.54), residues: 84 loop : -1.99 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.002 0.001 HIS A 134 PHE 0.013 0.001 PHE C 333 TYR 0.013 0.001 TYR B 25 ARG 0.010 0.001 ARG G 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 279 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 195 time to evaluate : 2.054 Fit side-chains REVERT: B 303 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6700 (mttt) REVERT: D 154 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8246 (tp) REVERT: D 355 ASN cc_start: 0.8681 (t0) cc_final: 0.8395 (m-40) REVERT: E 154 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8535 (tp) REVERT: E 354 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 37 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9080 (mt) REVERT: F 339 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8251 (tm-30) REVERT: G 256 ARG cc_start: 0.8785 (mtm110) cc_final: 0.8565 (mtm110) outliers start: 84 outliers final: 42 residues processed: 263 average time/residue: 1.3806 time to fit residues: 403.3390 Evaluate side-chains 212 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ASN 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 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 D residue 30 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain 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 66 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN G 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1795 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= 0.171 Angle : 0.562 6.896 23660 Z= 0.276 Chirality : 0.039 0.182 2807 Planarity : 0.004 0.038 2842 Dihedral : 3.117 12.929 2254 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.41 % Allowed : 24.74 % Favored : 71.85 % 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 (0.19), residues: 2044 helix: 2.64 (0.14), residues: 1442 sheet: -1.21 (0.54), residues: 84 loop : -1.99 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS E 106 PHE 0.008 0.001 PHE E 109 TYR 0.010 0.001 TYR A 25 ARG 0.012 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 273 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 1.949 Fit side-chains REVERT: B 303 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6557 (mttt) REVERT: D 154 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8246 (tp) REVERT: D 355 ASN cc_start: 0.8698 (t0) cc_final: 0.8442 (m-40) REVERT: F 56 GLN cc_start: 0.8209 (pp30) cc_final: 0.7994 (pp30) REVERT: F 339 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8232 (tm-30) REVERT: F 350 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8942 (mm) REVERT: G 144 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8820 (mm-30) REVERT: G 256 ARG cc_start: 0.8834 (mtm110) cc_final: 0.8601 (mtm110) outliers start: 65 outliers final: 31 residues processed: 256 average time/residue: 1.4750 time to fit residues: 417.9141 Evaluate side-chains 215 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain 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 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain D residue 30 LEU 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 F residue 113 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.0770 chunk 143 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17395 Z= 0.171 Angle : 0.578 6.842 23660 Z= 0.285 Chirality : 0.039 0.207 2807 Planarity : 0.004 0.053 2842 Dihedral : 3.088 12.384 2254 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.62 % Allowed : 25.21 % Favored : 71.17 % 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: 2.16 (0.19), residues: 2044 helix: 2.67 (0.14), residues: 1442 sheet: -1.17 (0.54), residues: 84 loop : -1.91 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 74 HIS 0.001 0.000 HIS E 106 PHE 0.009 0.001 PHE E 109 TYR 0.014 0.001 TYR A 25 ARG 0.013 0.001 ARG C 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: 69 poor density : 203 time to evaluate : 1.956 Fit side-chains REVERT: A 151 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: B 152 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7305 (mtm110) REVERT: D 154 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8235 (tp) REVERT: E 354 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8615 (tm-30) REVERT: F 37 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9111 (mt) REVERT: F 339 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8244 (tm-30) REVERT: F 350 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8930 (mm) REVERT: G 144 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8872 (mm-30) REVERT: G 152 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7365 (mtm110) REVERT: G 256 ARG cc_start: 0.8840 (mtm110) cc_final: 0.8603 (mtm110) outliers start: 69 outliers final: 35 residues processed: 256 average time/residue: 1.4237 time to fit residues: 402.6973 Evaluate side-chains 215 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 154 ILE 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 355 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 341 VAL 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 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 254 ILE 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 207 ASN Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.0470 chunk 116 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 133 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- 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 266 GLN C 63 GLN C 306 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17395 Z= 0.188 Angle : 0.602 7.923 23660 Z= 0.295 Chirality : 0.039 0.213 2807 Planarity : 0.004 0.057 2842 Dihedral : 3.090 12.499 2254 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.20 % Allowed : 26.26 % Favored : 70.54 % 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: 2.21 (0.19), residues: 2044 helix: 2.62 (0.14), residues: 1449 sheet: -0.98 (0.45), residues: 126 loop : -1.69 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 134 PHE 0.008 0.001 PHE E 109 TYR 0.016 0.001 TYR A 25 ARG 0.013 0.001 ARG C 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 256 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 2.133 Fit side-chains REVERT: D 151 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: D 154 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8218 (tp) REVERT: F 37 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9096 (mt) REVERT: F 151 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8428 (m-40) REVERT: F 206 ASN cc_start: 0.8904 (t0) cc_final: 0.8700 (t0) REVERT: F 339 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8239 (tm-30) REVERT: F 350 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8934 (mm) REVERT: G 144 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8802 (mm-30) REVERT: G 256 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8562 (mtm110) outliers start: 61 outliers final: 30 residues processed: 240 average time/residue: 1.4318 time to fit residues: 379.8935 Evaluate side-chains 223 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 154 ILE 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 355 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 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 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 F residue 37 LEU Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 182 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 63 GLN C 306 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17395 Z= 0.180 Angle : 0.609 7.507 23660 Z= 0.300 Chirality : 0.039 0.218 2807 Planarity : 0.004 0.057 2842 Dihedral : 3.075 12.070 2254 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.36 % Allowed : 26.94 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 2044 helix: 2.64 (0.14), residues: 1449 sheet: -0.96 (0.45), residues: 126 loop : -1.67 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS E 106 PHE 0.008 0.001 PHE E 109 TYR 0.013 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 251 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 1.997 Fit side-chains REVERT: B 152 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7358 (mtm110) REVERT: D 151 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8530 (m-40) REVERT: D 154 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8230 (tp) REVERT: E 256 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.7916 (mtm-85) REVERT: E 354 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8636 (tm-30) REVERT: F 56 GLN cc_start: 0.8142 (pp30) cc_final: 0.7907 (pp30) REVERT: F 206 ASN cc_start: 0.8858 (t0) cc_final: 0.8644 (t0) REVERT: F 339 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8251 (tm-30) REVERT: F 350 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8928 (mm) REVERT: G 144 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8848 (mm-30) REVERT: G 256 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8607 (mtm110) outliers start: 45 outliers final: 30 residues processed: 239 average time/residue: 1.4990 time to fit residues: 394.4834 Evaluate side-chains 199 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 154 ILE Chi-restraints excluded: chain B residue 207 ASN 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 355 ASN 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 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 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 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 338 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 124 optimal weight: 0.0970 chunk 98 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 355 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 306 ASN C 355 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17395 Z= 0.216 Angle : 0.635 9.110 23660 Z= 0.312 Chirality : 0.040 0.216 2807 Planarity : 0.004 0.065 2842 Dihedral : 3.116 12.545 2254 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.15 % Allowed : 27.05 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 2044 helix: 2.62 (0.14), residues: 1449 sheet: -1.28 (0.54), residues: 84 loop : -1.81 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 134 PHE 0.009 0.001 PHE C 333 TYR 0.014 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 227 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 2.078 Fit side-chains REVERT: B 152 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7360 (mtm110) REVERT: D 151 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: D 154 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8189 (tp) REVERT: E 256 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: F 56 GLN cc_start: 0.8167 (pp30) cc_final: 0.7929 (pp30) REVERT: F 206 ASN cc_start: 0.8890 (t0) cc_final: 0.8672 (t0) REVERT: F 339 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8249 (tm-30) REVERT: F 350 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8942 (mm) REVERT: G 256 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8628 (mtm110) outliers start: 41 outliers final: 31 residues processed: 216 average time/residue: 1.4893 time to fit residues: 354.8147 Evaluate side-chains 227 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 37 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN 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 C residue 113 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 D residue 30 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 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 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 F residue 350 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 29 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN C 306 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** 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 = 0.3671 r_free = 0.3671 target = 0.112922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081568 restraints weight = 28629.220| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.64 r_work: 0.3010 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1874 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= 0.186 Angle : 0.632 11.164 23660 Z= 0.310 Chirality : 0.039 0.220 2807 Planarity : 0.004 0.062 2842 Dihedral : 3.087 12.297 2254 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.05 % Allowed : 27.47 % 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: 2.23 (0.19), residues: 2044 helix: 2.62 (0.14), residues: 1449 sheet: -1.04 (0.45), residues: 126 loop : -1.64 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 PHE 0.008 0.001 PHE F 109 TYR 0.012 0.001 TYR A 25 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: 6014.30 seconds wall clock time: 109 minutes 18.11 seconds (6558.11 seconds total)